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US20190271004A1 - Compositions and methods for the suppression of target polynucleotides from lepidoptera - Google Patents

Compositions and methods for the suppression of target polynucleotides from lepidoptera Download PDF

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Publication number
US20190271004A1
US20190271004A1 US16/411,671 US201916411671A US2019271004A1 US 20190271004 A1 US20190271004 A1 US 20190271004A1 US 201916411671 A US201916411671 A US 201916411671A US 2019271004 A1 US2019271004 A1 US 2019271004A1
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United States
Prior art keywords
plant
sequence
polynucleotide
pest
ise2c
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US16/411,671
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Rafael Herrmann
Michael Lassner
Albert L. Lu
Mark Edward Nelson
James Kevin Presnail
Janet Rice
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Pioneer Hi Bred International Inc
EIDP Inc
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Pioneer Hi Bred International Inc
EI Du Pont de Nemours and Co
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Priority to US16/411,671 priority Critical patent/US20190271004A1/en
Publication of US20190271004A1 publication Critical patent/US20190271004A1/en
Abandoned legal-status Critical Current

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/82—Vectors or expression systems specially adapted for eukaryotic hosts for plant cells, e.g. plant artificial chromosomes (PACs)
    • C12N15/8241—Phenotypically and genetically modified plants via recombinant DNA technology
    • C12N15/8261—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield
    • C12N15/8271—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield for stress resistance, e.g. heavy metal resistance
    • C12N15/8279—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield for stress resistance, e.g. heavy metal resistance for biotic stress resistance, pathogen resistance, disease resistance
    • C12N15/8286—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield for stress resistance, e.g. heavy metal resistance for biotic stress resistance, pathogen resistance, disease resistance for insect resistance
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01N—PRESERVATION OF BODIES OF HUMANS OR ANIMALS OR PLANTS OR PARTS THEREOF; BIOCIDES, e.g. AS DISINFECTANTS, AS PESTICIDES OR AS HERBICIDES; PEST REPELLANTS OR ATTRACTANTS; PLANT GROWTH REGULATORS
    • A01N65/00—Biocides, pest repellants or attractants, or plant growth regulators containing material from algae, lichens, bryophyta, multi-cellular fungi or plants, or extracts thereof
    • A01N65/08—Magnoliopsida [dicotyledons]
    • A01N65/20—Fabaceae or Leguminosae [Pea or Legume family], e.g. pea, lentil, soybean, clover, acacia, honey locust, derris or millettia
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01N—PRESERVATION OF BODIES OF HUMANS OR ANIMALS OR PLANTS OR PARTS THEREOF; BIOCIDES, e.g. AS DISINFECTANTS, AS PESTICIDES OR AS HERBICIDES; PEST REPELLANTS OR ATTRACTANTS; PLANT GROWTH REGULATORS
    • A01N65/00—Biocides, pest repellants or attractants, or plant growth regulators containing material from algae, lichens, bryophyta, multi-cellular fungi or plants, or extracts thereof
    • A01N65/40—Liliopsida [monocotyledons]
    • A01N65/44—Poaceae or Gramineae [Grass family], e.g. bamboo, lemon grass or citronella grass
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/113—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/10—Type of nucleic acid
    • C12N2310/11—Antisense
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/10—Type of nucleic acid
    • C12N2310/14—Type of nucleic acid interfering nucleic acids [NA]
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/50—Physical structure
    • C12N2310/53—Physical structure partially self-complementary or closed
    • C12N2310/531—Stem-loop; Hairpin
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2320/00—Applications; Uses
    • C12N2320/30—Special therapeutic applications
    • C12N2320/32—Special delivery means, e.g. tissue-specific
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
    • Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
    • Y02A40/00—Adaptation technologies in agriculture, forestry, livestock or agroalimentary production
    • Y02A40/10—Adaptation technologies in agriculture, forestry, livestock or agroalimentary production in agriculture
    • Y02A40/146—Genetically Modified [GMO] plants, e.g. transgenic plants
    • Y02A40/162—

Definitions

  • the present invention relates generally to methods of molecular biology and gene silencing to control pests.
  • sequence listing is submitted concurrently with the specification as a text file via EFS-Web, in compliance with the American Standard Code for Information Interchange (ASCII), with a file name of 366590seqlist.txt, a creation date of Jan. 9, 2009, and a size of 102 Kb.
  • ASCII American Standard Code for Information Interchange
  • the sequence listing filed via EFS-Web is part of the specification and is hereby incorporated in its entirety by reference herein.
  • Insect pests are a serious problem in agriculture. They destroy millions of acres of staple crops such as corn, soybeans, peas, and cotton. Yearly, these pests cause over $100 billion dollars in crop damage in the U.S. alone. In an ongoing seasonal battle, farmers must apply billions of gallons of synthetic pesticides to combat these pests.
  • microbial pesticides particularly those obtained from Bacillus strains, have played an important role in agriculture as alternatives to chemical pest control.
  • Agricultural scientists have developed crop plants with enhanced insect resistance by genetically engineering crop plants to produce insecticidal proteins from Bacillus .
  • corn and cotton plants genetically engineered to produce Cry toxins see, e.g., Aronson (2002) Cell Mol. Life Sci. 59(3):417-425; Schnepf et al. (1998) Microbiol. Mol. Biol. Rev. 62(3):775-806
  • Cry toxins see, e.g., Aronson (2002) Cell Mol. Life Sci. 59(3):417-425; Schnepf et al. (1998) Microbiol. Mol. Biol. Rev. 62(3):775-806
  • these Bt insecticidal proteins only protect plants from a relatively narrow range of pests.
  • these modes of insecticidal activity provided varying levels of specificity and, in some cases, caused significant environmental consequences.
  • Methods and compositions which employ a silencing element that, when ingested by a pest, such as a pest from the Lepidoptera order, is capable of decreasing the expression of a target sequence in the pest.
  • a pest such as a pest from the Lepidoptera order
  • the decrease in expression of the target sequence controls the pest and thereby the methods and compositions are capable of limiting damage to a plant.
  • the present invention provides various target polynucleotides encoding polypeptides from specific families as disclosed elsewhere herein and various target polynucleotides set forth in SEQ ID NOS:1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50 or active variants or fragments thereof, wherein a decrease in expression of one or more the sequences in the target pest controls the pest (i.e., has insecticidal activity).
  • silencing elements which when ingested by the pest, decrease the level of expression of one or more of the target polynucleotides.
  • the silencing element comprises at least 15, 20, or 22 consecutive nucleotides of any one of SEQ ID NO:1-50.
  • the pest that is controlled is Spodoptera frugiperda . Plants, plant parts, plant cells, bacteria and other host cells comprising the silencing elements or an active variant or fragment thereof are also provided.
  • a method for controlling a pest such as a pest from the Lepidoptera order.
  • the method comprises feeding to a pest a composition comprising a silencing element, wherein the silencing element, when ingested by the pest, reduces the level of a target sequence in the pest and thereby controls the pest.
  • methods to protect a plant from a pest comprise introducing into the plant or plant part a silencing element of the invention. When the plant expressing the silencing element is ingested by the pest, the level of the target sequence is decreased and the pest is controlled.
  • Methods and compositions which employ a silencing element that, when ingested by a pest, such as a pest from the Lepidoptera order, is capable of decreasing the expression of a target sequence in the pest.
  • a pest such as a pest from the Lepidoptera order
  • the decrease in expression of the target sequence controls the pest and thereby the methods and compositions are capable of limiting damage to a plant or plant part.
  • the present invention provides target polynucleotides which encode polypeptides from a variety of protein classes including, for example, a juvenile hormone polypeptide, a vacuolar polypeptide, a cadherin polypeptide, a cuticle polypeptide, a translation initiation factor, a SARI polypeptide, an elongation factor, a phosphooligosaccharide, a myosin polypeptide, a potassium channel amino acid transporter, a potassium inwardly rectifier polypeptide, an amino acid transporter, a tubulin polypeptide, a ubiquitin polypeptide, and small nuclear ribonucleoprotein.
  • the target polynucleotides are set forth in SEQ ID NOS: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50 or active variants and fragments thereof.
  • Silencing elements designed in view of these target polynucleotides are provided which, when ingested by the pest, decrease the expression of one or more of the target sequences and thereby controls the pest (i.e., has insecticidal activity). See, for example, SEQ ID NOS:51-465.
  • controlling a pest or “controls a pest” is intended any affect on a pest that results in limiting the damage that the pest causes.
  • Controlling a pest includes, but is not limited to, killing the pest, inhibiting development of the pest, altering fertility or growth of the pest in such a manner that the pest provides less damage to the plant, decreasing the number of offspring produced, producing less fit pests, producing pests more susceptible to predator attack, or deterring the pests from eating the plant.
  • disease resistance is intended that the plants avoid the disease symptoms that are the outcome of plant-pathogen interactions. That is, pathogens are prevented from causing plant diseases and the associated disease symptoms, or alternatively, the disease symptoms caused by the pathogen is minimized or lessened.
  • Reducing the level of expression of the target polynucleotide or the polypeptide encoded thereby, in the pest results in the suppression, control, and/or killing the invading pathogenic organism.
  • Reducing the level of expression of the target sequence of the pest will reduce the disease symptoms resulting from pathogen challenge by at least about 2% to at least about 6%, at least about 5% to about 50%, at least about 10% to about 60%, at least about 30% to about 70%, at least about 40% to about 80%, or at least about 50% to about 90% or greater.
  • the methods of the invention can be utilized to protect plants from disease, particularly those diseases that are caused by pests from the Lepidoptera order.
  • Assays that measure the control of a pest are commonly known in the art, as are methods to quantitate disease resistance in plants following pathogen infection. See, for example, U.S. Pat. No. 5,614,395, herein incorporated by reference. Such techniques include, measuring over time, the average lesion diameter, the pathogen biomass, and the overall percentage of decayed plant tissues. See, for example, Thomma et al. (1998) Plant Biology 95:15107-15111, herein incorporated by reference. See, also the examples below.
  • the invention is drawn to compositions and methods for protecting plants from a plant pest, such as pests from the Lepidoptera order or inducing resistance in a plant to a plant pest, such as pests from the Lepidoptera order.
  • Caterpillars and related forms of lepidopteran insects comprise an important group of plant-feeding agricultural pests, especially during the larvae stage of growth. Feeding methods of Lepidoptera larvae typically include chewing plants or plant parts.
  • Lepidoptera is used to refer to any member of the Lepidoptera order.
  • compositions and methods of the invention control Lepidoptera larvae (i.e. caterpillars).
  • compositions and methods are also useful in protecting plants against any Lepidoptera including, for example, Pieris rapae, Pectinophora gossypiella, Synanthedon exitiosa, Melittia cucurbitae, Cydia pomonella, Grapholita molesta, Ostrinia nubilalis, Plodia interpunctella, Galleria mellonella, Manduca sexta, Manduca quinquemaculata, Lymantria dispar, Euproctis chrysorrhoea, Trichoplusia ni, Mamestra brassicae, Agrotis ipsilon, Plutella xylostella, Anticarsia gemmatalis, Psuedoplusia includens, Epinotia aporema, Helicoverpa zea, Heliothis virescens, Heliothis armigera, Spodoptera exigua, Scirpop
  • a “target sequence” or “target polynucleotide” comprises any sequence in the pest that one desires to reduce the level of expression. In specific embodiments, decreasing the level of the target sequence in the pest controls the pest.
  • the target sequence can be essential for growth and development. While the target sequence can be expressed in any tissue of the pest, in specific embodiments of the invention, the sequences targeted for suppression in the pest are expressed in cells of the gut tissue of the pest, cells in the midgut of the pest, and cells lining the gut lumen or the midgut. Such target sequences can be involved in gut cell metabolism, growth or differentiation.
  • the target sequence comprises a polypeptide belonging to one or more classes of enzymes such as a juvenile hormone polypeptide, a vacuolar polypeptide, a cadherin polypeptide, a cuticle polypeptide, a translation initiation factor, a SARI polypeptide, an elongation factor, a phosphooligosaccharide, a myosin polypeptide, a potassium channel amino acid transporter, a potassium inwardly rectifier, an amino acid transporter, a tubulin polypeptide, a ubiquitin polypeptide, and a small nuclear ribonucleoprotein.
  • a juvenile hormone polypeptide such as a juvenile hormone polypeptide, a vacuolar polypeptide, a cadherin polypeptide, a cuticle polypeptide, a translation initiation factor, a SARI polypeptide, an elongation factor, a phosphooligosaccharide, a myosin polypeptide, a potassium channel amino acid transporter,
  • Non-limiting examples of target sequences of the invention include a polynucleotide set forth in SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50.
  • silencing element is intended a polynucleotide which when ingested by a pest, is capable of reducing or eliminating the level or expression of a target polynucleotide or the polypeptide encoded thereby.
  • the silencing element employed can reduce or eliminate the expression level of the target sequence by influencing the level of the target RNA transcript or, alternatively, by influencing translation and thereby affecting the level of the encoded polypeptide.
  • Methods to assay for functional silencing elements that are capable of reducing or eliminating the level of a sequence of interest are disclosed elsewhere herein.
  • a single polynucleotide employed in the methods of the invention can comprises one or more silencing elements to the same or different target polynucleotides.
  • the target sequence is not a plant endogenous gene.
  • the silencing element controls pests, preferably the silencing element has no effect on the normal plant or plant part.
  • silencing elements can include, but are not limited to, a sense suppression element, an antisense suppression element, a double stranded RNA, a miRNA, or a hairpin suppression element.
  • Non-limiting examples of silencing elements that can be employed to decrease expression of these target Lepidoptera sequences comprise fragments and variants of the sense or antisense sequence or consists of the sense or antisense sequence of the sequence set forth in SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 54, 57, 60, 63, 66, 69, 72, 75, 78, 81, 84, 87, 90, 93, 96, 99, 102, 105, 108, 111, 114, 117, 120, 123, 126
  • the silencing element comprises or consists of at least one of the sequences set forth in any one of SEQ ID NOS: 51-465.
  • the silencing elements can comprise at least one thymine residue at the 3′ end. This can aid in stabilization.
  • the silencing elements can have at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more thymine residues at the 3′ end.
  • the silencing element comprises SEQ ID NO: 52 and 53; 55 and 56; 58 and 59; 61 and 62; 64 and 65; 67 and 68; 70 and 71; 73 and 74; 76 and 77; 79 and 80; 82 and 83; 85 and 86; 88 and 89; 91 and 92; 94 and 95; 97 and 98; 100 and 101; 103 and 104; 106 and 107; 109 and 110; 112 and 113; 115 and 116; 118 and 119; 121 and 122; 124 and 125; 127 and 128; 130 and 131; 133 and 134; 136 and 137; 139 and 140; 142 and 143; 145 and 146; 148 and 149; 151 and 152; 154 and 155; 157 and 158; 160 and 161; 163 and 164; 166 and 167; 169 and 170; 172 and 173; 175 and 176; 178 and
  • the polynucleotide or polypeptide level of the target sequence is statistically lower than the polynucleotide level or polypeptide level of the same target sequence in an appropriate control pest which is not exposed to (i.e., has not ingested) the silencing element.
  • reducing the polynucleotide level and/or the polypeptide level of the target sequence in a pest according to the invention results in less than 95%, less than 90%, less than 80%, less than 70%, less than 60%, less than 50%, less than 40%, less than 30%, less than 20%, less than 10%, or less than 5% of the polynucleotide level, or the level of the polypeptide encoded thereby, of the same target sequence in an appropriate control pest.
  • Methods to assay for the level of the RNA transcript, the level of the encoded polypeptide, or the activity of the polynucleotide or polypeptide are discussed elsewhere herein.
  • a “sense suppression element” comprises a polynucleotide designed to express an RNA molecule corresponding to at least a part of a target messenger RNA in the “sense” orientation. Expression of the RNA molecule comprising the sense suppression element reduces or eliminates the level of the target polynucleotide or the polypeptide encoded thereby.
  • the polynucleotide comprising the sense suppression element may correspond to all or part of the sequence of the target polynucleotide, all or part of the 5′ and/or 3 ′ untranslated region of the target polynucleotide, all or part of the coding sequence of the target polynucleotide, or all or part of both the coding sequence and the untranslated regions of the target polynucleotide.
  • a sense suppression element has substantial sequence identity to the target polynucleotide, typically greater than about 65% sequence identity, greater than about 85% sequence identity, about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% sequence identity. See, U.S. Pat. Nos. 5,283,184 and 5,034,323; herein incorporated by reference.
  • the sense suppression element can be any length so long as it allows for the suppression of the targeted sequence.
  • the sense suppression element can be, for example, 15, 20, 22, 25, 30, 50, 100, 150, 200, 250, 300, 350, 400, 450, 500, 600, 700, 900 or longer.
  • an “antisense suppression element” comprises a polynucleotide which is designed to express an RNA molecule complementary to all or part of a target messenger RNA. Expression of the antisense RNA suppression element reduces or eliminates the level of the target polynucleotide.
  • the polynucleotide for use in antisense suppression may correspond to all or part of the complement of the sequence encoding the target polynucleotide, all or part of the complement of the 5′ and/or 3 ′ untranslated region of the target polynucleotide, all or part of the complement of the coding sequence of the target polynucleotide, or all or part of the complement of both the coding sequence and the untranslated regions of the target polynucleotide.
  • the antisense suppression element may be fully complementary (i.e., 100% identical to the complement of the target sequence) or partially complementary (i.e., less than 100% identical to the complement of the target sequence) to the target polynucleotide.
  • the antisense suppression element comprises at least 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence complementarity to the target polynucleotide.
  • Antisense suppression may be used to inhibit the expression of multiple proteins in the same plant. See, for example, U.S. Pat. No. 5,942,657.
  • the antisense suppression element can be complementary to a portion of the target polynucleotide. Generally, sequences of at least 15, 20, 22, 25, 50, 100, 200, 300, 400, 450 nucleotides or greater may be used.
  • a “double stranded RNA silencing element” or “dsRNA” comprises at least one transcript that is capable of forming a dsRNA either before or after ingestion by a pest.
  • a “dsRNA silencing element” includes a dsRNA, a transcript or polyribonucleotide capable of forming a dsRNA or more than one transcript or polyribonucleotide capable of forming a dsRNA.
  • “Double stranded RNA” or “dsRNA” refers to a polyribonucleotide structure formed either by a single self-complementary RNA molecule or a polyribonucleotide structure formed by the expression of least two distinct RNA strands.
  • the dsRNA molecule(s) employed in the methods and compositions of the invention mediate the reduction of expression of a target sequence, for example, by mediating RNA interference “RNAi” or gene silencing in a sequence-specific manner.
  • RNAi RNA interference
  • the dsRNA is capable of reducing or eliminating the level or expression of a target polynucleotide or the polypeptide encoded thereby in a pest.
  • the dsRNA can reduce or eliminate the expression level of the target sequence by influencing the level of the target RNA transcript, by influencing translation and thereby affecting the level of the encoded polypeptide, or by influencing expression at the pre-transcriptional level (i.e., via the modulation of chromatin structure, methylation pattern, etc., to alter gene expression).
  • Verdel et al. (2004) Science 303:672-676; Pal-Bhadra et al. (2004) Science 303:669-672; Allshire (2002) Science 297:1818-1819; Volpe et al. (2002) Science 297:1833-1837; Jenuwein (2002) Science 297:2215-2218; and Hall et al.
  • dsRNA is meant to encompass other terms used to describe nucleic acid molecules that are capable of mediating RNA interference or gene silencing, including, for example, short-interfering RNA (siRNA), double-stranded RNA (dsRNA), micro-RNA (miRNA), hairpin RNA, short hairpin RNA (shRNA), post-transcriptional gene silencing RNA (ptgsRNA), and others.
  • siRNA short-interfering RNA
  • dsRNA double-stranded RNA
  • miRNA micro-RNA
  • shRNA short hairpin RNA
  • ptgsRNA post-transcriptional gene silencing RNA
  • At least one strand of the duplex or double-stranded region of the dsRNA shares sufficient sequence identity or sequence complementarity to the target polynucleotide to allow for the dsRNA to reduce the level of expression of the target sequence.
  • the strand that is complementary to the target polynucleotide is the “antisense strand” and the strand homologous to the target polynucleotide is the “sense strand.”
  • the dsRNA comprises a hairpin RNA.
  • a hairpin RNA comprises an RNA molecule that is capable of folding back onto itself to form a double stranded structure. Multiple structures can be employed as hairpin elements.
  • the dsRNA suppression element comprises a hairpin element which comprises in the following order, a first segment, a second segment, and a third segment, where the first and the third segment share sufficient complementarity to allow the transcribed RNA to form a double-stranded stem-loop structure.
  • the “second segment” of the hairpin comprises a “loop” or a “loop region.”
  • loop region may be substantially single stranded and act as a spacer between the self-complementary regions of the hairpin stem-loop.
  • the loop region can comprise a random or nonsense nucleotide sequence and thus not share sequence identity to a target polynucleotide.
  • the loop region comprises a sense or an antisense RNA sequence or fragment thereof that shares identity to a target polynucleotide. See, for example, International Patent Publication No. WO 02/00904, herein incorporated by reference.
  • the loop region can be optimized to be as short as possible while still providing enough intramolecular flexibility to allow the formation of the base-paired stem region. Accordingly, the loop sequence is generally less than 1000, 900, 800, 700, 600, 500, 400, 300, 200, 100, 50, 25, 20, 15, 10 nucleotides or less.
  • the “first” and the “third” segment of the hairpin RNA molecule comprise the base-paired stem of the hairpin structure.
  • the first and the third segments are inverted repeats of one another and share sufficient complementarity to allow the formation of the base-paired stem region.
  • the first and the third segments are fully complementary to one another.
  • the first and the third segment may be partially complementary to each other so long as they are capable of hybridizing to one another to form a base-paired stem region.
  • the amount of complementarity between the first and the third segment can be calculated as a percentage of the entire segment.
  • the first and the third segment of the hairpin RNA generally share at least 50%, 60%, 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, up to and including 100% complementarity.
  • the first and the third segment are at least about 1000, 500, 400, 300, 200, 100, 50, 40, 30, 25, 22, 20, 15 or 10 nucleotides in length.
  • the length of the first and/or the third segment is about 10-100 nucleotides, about 10 to about 75 nucleotides, about 10 to about 50 nucleotides, about 10 to about 40 nucleotides, about 10 to about 35 nucleotides, about 10 to about 30 nucleotides, about 10 to about 25 nucleotides, about 10 to about 20 nucleotides.
  • the length of the first and/or the third segment comprises at least 10-20 nucleotides, 20-35 nucleotides, 30-45 nucleotides, 40-50 nucleotides, 50-100 nucleotides, or 100-300 nucleotides. See, for example, International Publication No. WO 0200904.
  • the first and the third segment comprise at least 20 nucleotides having at least 85% complementary to the first segment.
  • the first and the third segments which form the stem-loop structure of the hairpin comprises 3′ or 5′ overhang regions having unpaired nucleotide residues.
  • the sequences used in the first, the second, and/or the third segments comprise domains that are designed to have sufficient sequence identity to a target polynucleotide of interest and thereby have the ability to decrease the level of expression of the target polynucleotide.
  • the specificity of the inhibitory RNA transcripts is therefore generally conferred by these domains of the silencing element.
  • the first, second and/or third segment of the silencing element comprise a domain having at least 10, at least 15, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 40, at least 50, at least 100, at least 200, at least 300, at least 500, at least 1000, or more than 1000 nucleotides that share sufficient sequence identity to the target polynucleotide to allow for a decrease in expression levels of the target polynucleotide when expressed in an appropriate cell.
  • the domain is between about 15 to 50 nucleotides, about 20-35 nucleotides, about 25-50 nucleotides, about 20 to 75 nucleotides, about 40-90 nucleotides about 15-100 nucleotides.
  • the domain of the first, the second, and/or the third segment has 100% sequence identity to the target polynucleotide.
  • the domain of the first, the second and/or the third segment having homology to the target polypeptide have at least 50%, 60%, 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or greater sequence identity to a region of the target polynucleotide.
  • the sequence identity of the domains of the first, the second and/or the third segments to the target polynucleotide need only be sufficient to decrease expression of the target polynucleotide of interest. See, for example, Chuang and Meyerowitz (2000) Proc.
  • the amount of complementarity shared between the first, second, and/or third segment and the target polynucleotide or the amount of complementarity shared between the first segment and the third segment may vary depending on the organism in which gene expression is to be controlled. Some organisms or cell types may require exact pairing or 100% identity, while other organisms or cell types may tolerate some mismatching. In some cells, for example, a single nucleotide mismatch in the targeting sequence abrogates the ability to suppress gene expression.
  • the suppression cassettes of the invention can be used to target the suppression of mutant genes, for example, oncogenes whose transcripts comprise point mutations and therefore they can be specifically targeted using the methods and compositions of the invention without altering the expression of the remaining wild-type allele.
  • any region of the target polynucleotide can be used to design the domain of the silencing element that shares sufficient sequence identity to allow expression of the hairpin transcript to decrease the level of the target polynucleotide.
  • the domain can be designed to share sequence identity to the 5′ untranslated region of the target polynucleotide(s), the 3′ untranslated region of the target polynucleotide(s), exonic regions of the target polynucleotide(s), intronic regions of the target polynucleotide(s), and any combination thereof.
  • a domain of the silencing element shares sufficient homology to at least about 15, 20, 22, 25 or 30 consecutive nucleotides from about nucleotides 1-50, 50-100, 100-150, 150-200, 200-250, 250-300, 300-350, 350-400, 400-450, 450-500, 550-600, 600-650, 650-700, 750-800, 850-900, 950-1000, 1000-1050, 1050-1100, 1100-1200, 1200-1300, 1300-1400, 1400-1500, 1500-1600, 1600-1700, 1700-1800, 1800-1900, 1900-2000 of the target sequence.
  • the synthetic oligodeoxyribonucleotide/RNAse H method can be used to determine sites on the target mRNA that are in a conformation that is susceptible to RNA silencing. See, for example, Vickers et al. (2003) J. Biol. Chem 278:7108-7118 and Yang et al. (2002) Proc. Natl. Acad. Sci. USA 99:9442-9447, herein incorporated by reference. These studies indicate that there is a significant correlation between the RNase-H-sensitive sites and sites that promote efficient siRNA-directed mRNA degradation.
  • the hairpin silencing element may also be designed such that the sense sequence or the antisense sequence do not correspond to a target polynucleotide.
  • the sense and antisense sequence flank a loop sequence that comprises a nucleotide sequence corresponding to all or part of the target polynucleotide.
  • it is the loop region that determines the specificity of the RNA interference. See, for example, WO 02/00904, herein incorporated by reference.
  • the silencing element comprising the hairpin comprises sequences selected from the group consisting of SEQ ID NO: 52 and 53; 55 and 56; 58 and 59; 61 and 62; 64 and 65; 67 and 68; 70 and 71; 73 and 74; 76 and 77; 79 and 80; 82 and 83; 85 and 86; 88 and 89; 91 and 92; 94 and 95; 97 and 98; 100 and 101; 103 and 104; 106 and 107; 109 and 110; 112 and 113; 115 and 116; 118 and 119; 121 and 122; 124 and 125; 127 and 128; 130 and 131; 133 and 134; 136 and 137; 139 and 140; 142 and 143; 145 and 146; 148 and 149; 151 and 152; 154 and 155; 157 and 158; 160 and 161; 163 and 164; 166 and 167; 169 and 170;
  • transcriptional gene silencing may be accomplished through use of a hairpin suppression element where the inverted repeat of the hairpin shares sequence identity with the promoter region of a target polynucleotide to be silenced. See, for example, Aufsatz et al. (2002) PNAS 99 (Suppl. 4):16499-16506 and Mette et al. (2000) EMBO J 19(19):5194-5201.
  • the dsRNA can comprise a small RNA (sRNA).
  • sRNAs can comprise both micro RNA (miRNA) and short-interfering RNA (siRNA) (Meister and Tuschl (2004) Nature 431:343-349 and Bonetta et al. (2004) Nature Methods 1:79-86).
  • miRNAs are regulatory agents comprising about 19 ribonucleotides which are highly efficient at inhibiting the expression of target polynucleotides. See, for example Javier et al. (2003) Nature 425: 257-263, herein incorporated by reference.
  • the silencing element can be designed to express a dsRNA molecule that forms a hairpin structure containing a 19-nucleotide sequence that is complementary to the target polynucleotide of interest.
  • the miRNA can be synthetically made, or transcribed as a longer RNA which is subsequently cleaved to produce the active miRNA.
  • the miRNA can comprise 19 nucleotides of the sequence having homology to a target polynucleotide in sense orientation and 19 nucleotides of a corresponding antisense sequence that is complementary to the sense sequence.
  • an miRNA When expressing an miRNA, it is recognized that various forms of an miRNA can be transcribed including, for example, the primary transcript (termed the “pri-miRNA”) which is processed through various nucleolytic steps to a shorter precursor miRNA (termed the “pre-miRNA”); the pre-miRNA; or the final (mature) miRNA is present in a duplex, the two strands being referred to as the miRNA (the strand that will eventually basepair with the target) and miRNA*.
  • the pre-miRNA is a substrate for a form of dicer that removes the miRNA/miRNA* duplex from the precursor, after which, similarly to siRNAs, the duplex can be taken into the RISC complex.
  • miRNAs can be transgenically expressed and be effective through expression of a precursor form, rather than the entire primary form (Parizotto et al. (2004) Genes & Development 18:2237-2242 and Guo et al. (2005) Plant Cell 17:1376-1386).
  • the methods and compositions of the invention employ silencing elements that when transcribed “form” a dsRNA molecule.
  • the heterologous polynucleotide being expressed need not form the dsRNA by itself, but can interact with other sequences in the plant cell or in the pest gut after ingestion to allow the formation of the dsRNA.
  • a chimeric polynucleotide that can selectively silence the target polynucleotide can be generated by expressing a chimeric construct comprising the target sequence for a miRNA or siRNA to a sequence corresponding to all or part of the gene or genes to be silenced.
  • the dsRNA is “formed” when the target for the miRNA or siRNA interacts with the miRNA present in the cell.
  • the resulting dsRNA can then reduce the level of expression of the gene or genes to be silenced. See, for example, U.S. Provisional Application No. 60/691,613, filed Jun. 17, 2005, entitled “Methods and Compositions for Gene Silencing, herein incorporated by reference.
  • the construct can be designed to have a target for an endogenous miRNA or alternatively, a target for a heterologous and/or synthetic miRNA can be employed in the construct.
  • heterologous and/or synthetic miRNA can be introduced into the cell on the same nucleotide construct as the chimeric polynucleotide or on a separate construct. As discussed elsewhere herein, any method can be used to introduce the construct comprising the heterologous miRNA.
  • fragment is intended a portion of the polynucleotide or a portion of the amino acid sequence and hence protein encoded thereby. Fragments of a polynucleotide may encode protein fragments that retain the biological activity of the native protein. Alternatively, fragments of a polynucleotide that are useful as a silencing element do not need to encode fragment proteins that retain biological activity.
  • fragments of a nucleotide sequence may range from at least about 10, about 15, about 20 nucleotides, about 22 nucleotides, about 50 nucleotides, about 75 nucleotides, about 100 nucleotides, 200 nucleotides, 300 nucleotides, 400 nucleotides, 500 nucleotides, 600 nucleotides, 700 nucleotides and up to the full-length polynucleotide employed in the invention.
  • Methods to assay for the activity of a desired silencing element or a suppressor enhancer element are described elsewhere herein.
  • a variant comprises a deletion and/or addition of one or more nucleotides at one or more internal sites within the native polynucleotide and/or a substitution of one or more nucleotides at one or more sites in the native polynucleotide.
  • a “native” polynucleotide or polypeptide comprises a naturally occurring nucleotide sequence or amino acid sequence, respectively.
  • conservative variants include those sequences that, because of the degeneracy of the genetic code, encode the amino acid sequence of one of the polypeptides employed in the invention.
  • Variant polynucleotides also include synthetically derived polynucleotide, such as those generated, for example, by using site-directed mutagenesis, but continue to retain the desired activity.
  • variants of a particular polynucleotide of the invention i.e., a silencing element
  • Variants of a particular polynucleotide of the invention can also be evaluated by comparison of the percent sequence identity between the polypeptide encoded by a variant polynucleotide and the polypeptide encoded by the reference polynucleotide. Percent sequence identity between any two polypeptides can be calculated using sequence alignment programs and parameters described elsewhere herein.
  • the percent sequence identity between the two encoded polypeptides is at least about 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity.
  • Variant protein is intended to mean a protein derived from the native protein by deletion or addition of one or more amino acids at one or more internal sites in the native protein and/or substitution of one or more amino acids at one or more sites in the native protein.
  • Variant proteins encompassed by the present invention are biologically active, that is they continue to possess the desired biological activity of the native protein, as discussed elsewhere herein. Such variants may result from, for example, genetic polymorphism or from human manipulation.
  • Biologically active variants of a native protein will have at least about 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to the amino acid sequence for the native protein as determined by sequence alignment programs and parameters described elsewhere herein.
  • a biologically active variant of a protein of the invention may differ from that protein by as few as 1-15 amino acid residues, as few as 1-10, such as 6-10, as few as 5, as few as 4, 3, 2, or even 1 amino acid residue.
  • sequence relationships between two or more polynucleotides or polypeptides are used to describe the sequence relationships between two or more polynucleotides or polypeptides: (a) “reference sequence”, (b) “comparison window”, (c) “sequence identity”, and, (d) “percentage of sequence identity.”
  • reference sequence is a defined sequence used as a basis for sequence comparison.
  • a reference sequence may be a subset or the entirety of a specified sequence; for example, as a segment of a full-length cDNA or gene sequence, or the complete cDNA or gene sequence.
  • comparison window makes reference to a contiguous and specified segment of a polynucleotide sequence, wherein the polynucleotide sequence in the comparison window may comprise additions or deletions (i.e., gaps) compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two polynucleotides.
  • the comparison window is at least 20 contiguous nucleotides in length, and optionally can be 30, 40, 50, 100, or longer.
  • sequence identity/similarity values provided herein refer to the value obtained using GAP Version 10 using the following parameters: % identity and % similarity for a nucleotide sequence using GAP Weight of 50 and Length Weight of 3, and the nwsgapdna.cmp scoring matrix; % identity and % similarity for an amino acid sequence using GAP Weight of 8 and Length Weight of 2, and the BLOSUM62 scoring matrix; or any equivalent program thereof.
  • equivalent program is intended any sequence comparison program that, for any two sequences in question, generates an alignment having identical nucleotide or amino acid residue matches and an identical percent sequence identity when compared to the corresponding alignment generated by GAP Version 10.
  • sequence identity or “identity” in the context of two polynucleotides or polypeptide sequences makes reference to the residues in the two sequences that are the same when aligned for maximum correspondence over a specified comparison window.
  • sequence identity or “identity” in the context of two polynucleotides or polypeptide sequences makes reference to the residues in the two sequences that are the same when aligned for maximum correspondence over a specified comparison window.
  • percentage of sequence identity is used in reference to proteins it is recognized that residue positions which are not identical often differ by conservative amino acid substitutions, where amino acid residues are substituted for other amino acid residues with similar chemical properties (e.g., charge or hydrophobicity) and therefore do not change the functional properties of the molecule.
  • sequences differ in conservative substitutions the percent sequence identity may be adjusted upwards to correct for the conservative nature of the substitution.
  • Sequences that differ by such conservative substitutions are said to have “sequence similarity” or “similarity”. Means for making this adjustment are well known to those of skill in the art. Typically this involves scoring a conservative substitution as a partial rather than a full mismatch, thereby increasing the percentage sequence identity. Thus, for example, where an identical amino acid is given a score of 1 and a non-conservative substitution is given a score of zero, a conservative substitution is given a score between zero and 1. The scoring of conservative substitutions is calculated, e.g., as implemented in the program PC/GENE (Intelligenetics, Mountain View, Calif.).
  • percentage of sequence identity means the value determined by comparing two optimally aligned sequences over a comparison window, wherein the portion of the polynucleotide sequence in the comparison window may comprise additions or deletions (i.e., gaps) as compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences. The percentage is calculated by determining the number of positions at which the identical nucleic acid base or amino acid residue occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison, and multiplying the result by 100 to yield the percentage of sequence identity.
  • polynucleotide is not intended to limit the present invention to polynucleotides comprising DNA.
  • polynucleotides can comprise ribonucleotides and combinations of ribonucleotides and deoxyribonucleotides. Such deoxyribonucleotides and ribonucleotides include both naturally occurring molecules and synthetic analogues.
  • the polynucleotides of the invention also encompass all forms of sequences including, but not limited to, single-stranded forms, double-stranded forms, hairpins, stem-and-loop structures, and the like.
  • the polynucleotide encoding the silencing element or in specific embodiments employed in the methods and compositions of the invention can be provided in expression cassettes for expression in a plant or organism of interest. It is recognized that multiple silencing elements including multiple identical silencing elements, multiple silencing elements targeting different regions of the target sequence, or multiple silencing elements from different target sequences can be used. In this embodiment, it is recognized that each silencing element can be contained in a single or separate cassette, DNA construct, or vector. As discussed, any means of providing the silencing element is contemplated.
  • a plant or plant cell can be transformed with a single cassette comprising DNA encoding one or more silencing elements or separate cassettes comprising each silencing element can be used to transform a plant or plant cell or host cell.
  • a plant transformed with one component can be subsequently transformed with the second component.
  • One or more silencing elements can also be brought together by sexual crossing. That is, a first plant comprising one component is crossed with a second plant comprising the second component. Progeny plants from the cross will comprise both components.
  • the expression cassette can include 5′ and 3′ regulatory sequences operably linked to the polynucleotide of the invention.
  • “Operably linked” is intended to mean a functional linkage between two or more elements.
  • an operable linkage between a polynucleotide of the invention and a regulatory sequence i.e., a promoter
  • Operably linked elements may be contiguous or non-contiguous. When used to refer to the joining of two protein coding regions, by operably linked is intended that the coding regions are in the same reading frame.
  • the cassette may additionally contain at least one additional polynucleotide to be cotransformed into the organism.
  • the additional polypeptide(s) can be provided on multiple expression cassettes.
  • Expression cassettes can be provided with a plurality of restriction sites and/or recombination sites for insertion of the polynucleotide to be under the transcriptional regulation of the regulatory regions.
  • the expression cassette may additionally contain selectable marker genes.
  • the expression cassette will include in the 5′-3′ direction of transcription, a transcriptional and translational initiation region (i.e., a promoter), a polynucleotide comprising the silencing element employed in the methods and compositions of the invention, and a transcriptional and translational termination region (i.e., termination region) functional in plants.
  • the regulatory regions (i.e., promoters, transcriptional regulatory regions, and translational termination regions) and/or the polynucleotides employed in the invention may be native/analogous to the host cell or to each other. Alternatively, the regulatory regions and/or the polynucleotide employed in the invention may be heterologous to the host cell or to each other.
  • heterologous in reference to a sequence is a sequence that originates from a foreign species, or, if from the same species, is substantially modified from its native form in composition and/or genomic locus by deliberate human intervention.
  • a promoter operably linked to a heterologous polynucleotide is from a species different from the species from which the polynucleotide was derived, or, if from the same/analogous species, one or both are substantially modified from their original form and/or genomic locus, or the promoter is not the native promoter for the operably linked polynucleotide.
  • a chimeric gene comprises a coding sequence operably linked to a transcription initiation region that is heterologous to the coding sequence.
  • the termination region may be native with the transcriptional initiation region, may be native with the operably linked polynucleotide encoding the silencing element, may be native with the plant host, or may be derived from another source (i.e., foreign or heterologous) to the promoter, the polynucleotide comprising silencing element, the plant host, or any combination thereof.
  • Convenient termination regions are available from the Ti-plasmid of A. tumefaciens , such as the octopine synthase and nopaline synthase termination regions. See also Guerineau et al. (1991) Mol. Gen. Genet.
  • Additional sequence modifications are known to enhance gene expression in a cellular host. These include elimination of sequences encoding spurious polyadenylation signals, exon-intron splice site signals, transposon-like repeats, and other such well-characterized sequences that may be deleterious to gene expression.
  • the G-C content of the sequence may be adjusted to levels average for a given cellular host, as calculated by reference to known genes expressed in the host cell. When possible, the sequence is modified to avoid predicted hairpin secondary mRNA structures.
  • the various DNA fragments may be manipulated, so as to provide for the DNA sequences in the proper orientation and, as appropriate, in the proper reading frame.
  • adapters or linkers may be employed to join the DNA fragments or other manipulations may be involved to provide for convenient restriction sites, removal of superfluous DNA, removal of restriction sites, or the like.
  • in vitro mutagenesis, primer repair, restriction, annealing, resubstitutions, e.g., transitions and transversions may be involved.
  • a number of promoters can be used in the practice of the invention.
  • the polynucleotide encoding the silencing element can be combined with constitutive, tissue-preferred, or other promoters for expression in plants.
  • Such constitutive promoters include, for example, the core promoter of the Rsyn7 promoter and other constitutive promoters disclosed in WO 99/43838 and U.S. Pat. No. 6,072,050; the core CaMV 35S promoter (Odell et al. (1985) Nature 313:810-812); rice actin (McElroy et al. (1990) Plant Cell 2:163-171); ubiquitin (Christensen et al. (1989) Plant Mol. Biol. 12:619-632 and Christensen et al. (1992) Plant Mol. Biol. 18:675-689); pEMU (Last et al. (1991) Theor. Appl. Genet.
  • an inducible promoter for instance, a pathogen-inducible promoter could also be employed.
  • Such promoters include those from pathogenesis-related proteins (PR proteins), which are induced following infection by a pathogen; e.g., PR proteins, SAR proteins, beta-1,3-glucanase, chitinase, etc. See, for example, Redolfi et al. (1983) Neth. J. Plant Pathol. 89:245-254; Uknes et al. (1992) Plant Cell 4:645-656; and Van Loon (1985) Plant Mol. Virol. 4:111-116. See also WO 99/43819, herein incorporated by reference.
  • promoters that are expressed locally at or near the site of pathogen infection. See, for example, Marineau et al. (1987) Plant Mol. Biol. 9:335-342; Matton et al. (1989) Molecular Plant - Microbe Interactions 2:325-331; Somsisch et al. (1986) Proc. Natl. Acad. Sci. USA 83:2427-2430; Somsisch et al. (1988) Mol. Gen. Genet. 2:93-98; and Yang (1996) Proc. Natl. Acad. Sci. USA 93:14972-14977. See also, Chen et al. (1996) Plant J. 10:955-966; Zhang et al. (1994) Proc.
  • a wound-inducible promoter may be used in the constructions of the invention.
  • Such wound-inducible promoters include potato proteinase inhibitor (pin II) gene (Ryan (1990) Ann. Rev. Phytopath. 28:425-449; Duan et al. (1996) Nature Biotechnology 14:494-498); wun1 and wun2, U.S. Pat. No. 5,428,148; win1 and win2 (Stanford et al. (1989) Mol. Gen. Genet. 215:200-208); systemin (McGurl et al. (1992) Science 225:1570-1573); WIP1 (Rohmeier et al.
  • Chemical-regulated promoters can be used to modulate the expression of a gene in a plant through the application of an exogenous chemical regulator.
  • the promoter may be a chemical-inducible promoter, where application of the chemical induces gene expression, or a chemical-repressible promoter, where application of the chemical represses gene expression.
  • Chemical-inducible promoters are known in the art and include, but are not limited to, the maize In2-2 promoter, which is activated by benzenesulfonamide herbicide safeners, the maize GST promoter, which is activated by hydrophobic electrophilic compounds that are used as pre-emergent herbicides, and the tobacco PR-la promoter, which is activated by salicylic acid.
  • promoters of interest include steroid-responsive promoters (see, for example, the glucocorticoid-inducible promoter in Schena et al. (1991) Proc. Natl. Acad. Sci. USA 88:10421-10425 and McNellis et al. (1998) Plant J. 14(2):247-257) and tetracycline-inducible and tetracycline-repressible promoters (see, for example, Gatz et al. (1991) Mol. Gen. Genet. 227:229-237, and U.S. Pat. Nos. 5,814,618 and 5,789,156), herein incorporated by reference.
  • Tissue-preferred promoters can be utilized to target enhanced expression within a particular plant tissue.
  • Tissue-preferred promoters include Yamamoto et al. (1997) Plant J. 12(2):255-265; Kawamata et al. (1997) Plant Cell Physiol. 38(7):792-803; Hansen et al. (1997) Mol. Gen Genet. 254(3):337-343; Russell et al. (1997) Transgenic Res. 6(2):157-168; Rinehart et al. (1996) Plant Physiol. 112(3):1331-1341; Van Camp et al. (1996) Plant Physiol. 112(2):525-535; Canevascini et al. (1996) Plant Physiol.
  • Leaf-preferred promoters are known in the art. See, for example, Yamamoto et al. (1997) Plant J. 12(2):255-265; Kwon et al. (1994) Plant Physiol. 105:357-67; Yamamoto et al. (1994) Plant Cell Physiol. 35(5):773-778; Gotor et al. (1993) Plant J. 3:509-18; Orozco et al. (1993) Plant Mol. Biol. 23(6):1129-1138; and Matsuoka et al. (1993) Proc. Natl. Acad. Sci. USA 90(20):9586-9590.
  • Root-preferred promoters are known and can be selected from the many available from the literature or isolated de novo from various compatible species. See, for example, Hire et al. (1992) Plant Mol. Biol. 20(2):207-218 (soybean root-specific glutamine synthetase gene); Keller and Baumgartner (1991) Plant Cell 3(10):1051-1061 (root-specific control element in the GRP 1.8 gene of French bean); Sanger et al. (1990) Plant Mol. Biol. 14(3):433-443 (root-specific promoter of the mannopine synthase (MAS) gene of Agrobacterium tumefaciens ); and Miao et al.
  • MAS mannopine synthase
  • the plant-expressed promoter is a vascular-specific promoter such as a phloem-specific promoter.
  • a “vascular-specific” promoter as used herein, is a promoter which is at least expressed in vascular cells, or a promoter which is preferentially expressed in vascular cells. Expression of a vascular-specific promoter need not be exclusively in vascular cells, expression in other cell types or tissues is possible.
  • a “phloem-specific promoter” as used herein, is a plant-expressible promoter which is at least expressed in phloem cells, or a promoter which is preferentially expressed in phloem cells.
  • a phloem-specific promoter need not be exclusively in phloem cells, expression in other cell types or tissues, e.g., xylem tissue, is possible.
  • a phloem-specific promoter is a plant-expressible promoter at least expressed in phloem cells, wherein the expression in non-phloem cells is more limited (or absent) compared to the expression in phloem cells.
  • vascular-specific or phloem-specific promoters include but are not limited to the promoters selected from the group consisting of: the SCSV3, SCSV4, SCSV5, and SCSV7 promoters (Schunmann et al. (2003) Plant Functional Biology 30:453-60; the rolC gene promoter of Agrobacterium rhizogenes (Kiyokawa et al. (1994) Plant Physiology 104:801-02; Pandolfini et al. (2003) BioMedCentral ( BMC ) Biotechnology 3:7, (www.biomedcentral.com/1472-6750/3/7); Graham et al. (1997) Plant Mol. Biol.
  • VAHOX1 promoter region (Tornero et al. (1996) Plant J. 9:639-48); the pea cell wall invertase gene promoter (Zhang et al. (1996) Plant Physiol. 112:1111-17); the promoter of the endogenous cotton protein related to chitinase of US published patent application 20030106097, an acid invertase gene promoter from carrot (Ramloch-Lorenz et al. (1993) The Plant J. 4:545-54); the promoter of the sulfate transporter geneSultrl; 3 (Yoshimoto et al. (2003) Plant Physiol.
  • Possible promoters also include the Black Cherry promoter for Prunasin Hydrolase (PH DL1.4 PRO) (U.S. Pat. No. 6,797,859), Thioredoxin H promoter from cucumber and rice (Fukuda A et al. (2005). Plant Cell Physiol. 46(11):1779-86), Rice (RSs1) (Shi, T. Wang et al. (1994). J. Exp. Bot. 45(274): 623-631) and maize sucrose synthese-1 promoters (Yang., N-S. et al. (1990) PNAS 87:4144-4148), PP2 promoter from pumpkin Guo, H. et al.
  • PH DL1.4 PRO Black Cherry promoter for Prunasin Hydrolase
  • the expression cassette can also comprise a selectable marker gene for the selection of transformed cells.
  • Selectable marker genes are utilized for the selection of transformed cells or tissues.
  • Marker genes include genes encoding antibiotic resistance, such as those encoding neomycin phosphotransferase II (NEO) and hygromycin phosphotransferase (HPT), as well as genes conferring resistance to herbicidal compounds, such as glufosinate ammonium, bromoxynil, imidazolinones, and 2,4-dichlorophenoxyacetate (2,4-D).
  • Additional selectable markers include phenotypic markers such as ⁇ -galactosidase and fluorescent proteins such as green fluorescent protein (GFP) (Su et al.
  • selectable marker genes are not meant to be limiting. Any selectable marker gene can be used in the present invention.
  • One or more of the polynucleotides comprising the silencing element can be provided as an external composition such as a spray or powder to the plant, plant part, seed, a pest, or an area of cultivation.
  • a plant is transformed with a DNA construct or expression cassette for expression of at least one silencing element.
  • the silencing element when ingested by an insect, can reduce the level of a target pest sequence and thereby control the pest (i.e., any pest from the Lepidoptera order, such as, Spodoptera frugiperda ).
  • compositions can comprise a cell (such as plant cell or a bacterial cell), in which a polynucleotide encoding the silencing element is stably incorporated into the genome and operably linked to promoters active in the cell.
  • Compositions comprising a mixture of cells, some cells expressing at least one silencing element are also encompassed.
  • compositions comprising the silencing elements are not contained in a cell.
  • the composition can be applied to an area inhabited by a pest.
  • the composition is applied externally to a plant (i.e., by spraying a field or area of cultivation) to protect the plant from the pest.
  • the composition comprising the silencing element that controls a pest from the Lepidoptera order does not comprise a heterologous cationic oligopeptide to facilitate uptake of the RNAi into the insect cells.
  • insecticidal activity occurs in the compositions of the invention (i.e., the plant, plant part, plant cell, or microbe) in the absence of a cationic oligopeptide that is heterologous to the plant, plant part or microbe.
  • the cationic oligopeptide is target non-specific and interacts non-specifically with RNA via electrostatic interactions and neutralization of charge to penetrate membranes and lacks a specific activity that promotes a specific interaction with a cell membrane.
  • composition of the invention can further be formulated as bait.
  • the compositions comprise a food substance or an attractant which enhances the attractiveness of the composition to the pest.
  • the composition comprising the silencing element can be formulated in an agriculturally suitable and/or environmentally acceptable carrier.
  • Such carriers can be any material that the animal, plant or environment to be treated can tolerate. Furthermore, the carrier must be such that the composition remains effective at controlling a pest. Examples of such carriers include water, saline, Ringer's solution, dextrose or other sugar solutions, Hank's solution, and other aqueous physiologically balanced salt solutions, phosphate buffer, bicarbonate buffer and Tris buffer.
  • the composition may include compounds that increase the half-life of a composition.
  • polynucleotides comprising sequences encoding the silencing element can be used to transform organisms to provide for host organism production of these components, and subsequent application of the host organism to the environment of the target pest(s).
  • host organisms include baculoviruses, bacteria, and the like.
  • the combination of polynucleotides encoding the silencing element may be introduced via a suitable vector into a microbial host, and said host applied to the environment, or to plants or animals.
  • the term “introduced” in the context of inserting a nucleic acid into a cell means “transfection” or “transformation” or “transduction” and includes reference to the incorporation of a nucleic acid into a eukaryotic or prokaryotic cell where the nucleic acid may be stably incorporated into the genome of the cell (e.g., chromosome, plasmid, plastid, or mitochondrial DNA), converted into an autonomous replicon, or transiently expressed (e.g., transfected mRNA).
  • Microbial hosts that are known to occupy the “phytosphere” (phylloplane, phyllosphere, rhizosphere, and/or rhizoplana) of one or more crops of interest may be selected.
  • These microorganisms are selected so as to be capable of successfully competing in the particular environment with the wild-type microorganisms, provide for stable maintenance and expression of the sequences encoding the silencing element, and desirably, provide for improved protection of the components from environmental degradation and inactivation.
  • microorganisms include bacteria, algae, and fungi.
  • microorganisms such as bacteria, e.g., Pseudomonas, Erwinia, Serratia, Klebsiella, Xanthomonas, Streptomyces, Rhizobium, Rhodopseudomonas, Methylius, Agrobacterium, Acetobacter, Lactobacillus, Arthrobacter, Azotobacter, Leuconostoc , and Alcaligenes , fungi, particularly yeast, e.g., Saccharomyces, Cryptococcus, Kluyveromyces, Sporobolomyces, Rhodotorula , and Aureobasidium .
  • phytosphere bacterial species as Pseudomonas syringae, Pseudomonas fluorescens, Serratia marcescens, Acetobacter xylinum, Agrobacteria, Rhodopseudomonas spheroides, Xanthomonas campestris, Rhizobium melioti, Alcaligenes entrophus, Clavibacter xyli and Azotobacter vinlandir , and phytosphere yeast species such as Rhodotorula rubra, R. glutinis, R. marina, R. aurantiaca, Cryptococcus albidus, C. diffluens, C.
  • expression cassettes can be constructed which include the nucleotide constructs of interest operably linked with the transcriptional and translational regulatory signals for expression of the nucleotide constructs, and a nucleotide sequence homologous with a sequence in the host organism, whereby integration will occur, and/or a replication system that is functional in the host, whereby integration or stable maintenance will occur.
  • Transcriptional and translational regulatory signals include, but are not limited to, promoters, transcriptional initiation start sites, operators, activators, enhancers, other regulatory elements, ribosomal binding sites, an initiation codon, termination signals, and the like. See, for example, U.S. Pat. Nos. 5,039,523 and 4,853,331; EPO 0480762A2; Sambrook et al. (2000); Molecular Cloning: A Laboratory Manual (3 rd ed.; Cold Spring Harbor Laboratory Press, Plainview, N.Y.); Davis et al. (1980) Advanced Bacterial Genetics (Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.); and the references cited therein.
  • Suitable host cells include the prokaryotes and the lower eukaryotes, such as fungi.
  • Illustrative prokaryotes both Gram-negative and Gram-positive, include Enterobacteriaceae, such as Escherichia, Erwinia, Shigella, Salmonella , and Proteus ; Bacillaceae; Rhizobiceae, such as Rhizobium ; Spirillaceae, such as photobacterium, Zymomonas, Serratia, Aeromonas, Vibrio, Desulfovibrio , Spirillum; Lactobacillaceae; Pseudomonadaceae, such as Pseudomonas and Acetobacter ; Azotobacteraceae and Nitrobacteraceae.
  • fungi such as Phycomycetes and Ascomycetes, which includes yeast, such as Saccharomyces and Schizosaccharomyces ; and Basidiomycetes yeast, such as Rhodotorula, Aureobasidium, Sporobolomyces , and the like.
  • Characteristics of particular interest in selecting a host cell for purposes of the invention include ease of introducing the coding sequence into the host, availability of expression systems, efficiency of expression, stability in the host, and the presence of auxiliary genetic capabilities.
  • Characteristics of interest for use as a pesticide microcapsule include protective qualities, such as thick cell walls, pigmentation, and intracellular packaging or formation of inclusion bodies; leaf affinity; lack of mammalian toxicity; attractiveness to pests for ingestion; and the like. Other considerations include ease of formulation and handling, economics, storage stability, and the like.
  • Host organisms of particular interest include yeast, such as Rhodotorula spp., Aureobasidium spp., Saccharomyces spp., and Sporobolomyces spp., phylloplane organisms such as Pseudomonas spp., Erwinia spp., and Flavobacterium spp., and other such organisms, including Pseudomonas aeruginosa, Pseudomonas fluorescens, Saccharomyces cerevisiae, Bacillus thuringiensis, Escherichia coli, Bacillus subtilis , and the like.
  • yeast such as Rhodotorula spp., Aureobasidium spp., Saccharomyces spp., and Sporobolomyces spp.
  • phylloplane organisms such as Pseudomonas spp., Erwinia spp
  • sequences encoding the silencing elements encompassed by the invention can be introduced into microorganisms that multiply on plants (epiphytes) to deliver these components to potential target pests.
  • Epiphytes for example, can be gram-positive or gram-negative bacteria.
  • the silencing element can be fermented in a bacterial host and the resulting bacteria processed and used as a microbial spray in the same manner that Bacillus thuringiensis strains have been used as insecticidal sprays. Any suitable microorganism can be used for this purpose.
  • Pseudomonas has been used to express Bacillus thuringiensis endotoxins as encapsulated proteins and the resulting cells processed and sprayed as an insecticide Gaertner et al. (1993), in Advanced Engineered Pesticides , ed. L. Kim (Marcel Decker, Inc.).
  • the components of the invention are produced by introducing heterologous genes into a cellular host. Expression of the heterologous sequences results, directly or indirectly, in the intracellular production of the silencing element.
  • These compositions may then be formulated in accordance with conventional techniques for application to the environment hosting a target pest, e.g., soil, water, and foliage of plants. See, for example, EPA 0192319, and the references cited therein.
  • a transformed microorganism can be formulated with an acceptable carrier into separate or combined compositions that are, for example, a suspension, a solution, an emulsion, a dusting powder, a dispersible granule, a wettable powder, and an emulsifiable concentrate, an aerosol, an impregnated granule, an adjuvant, a coatable paste, and also encapsulations in, for example, polymer substances.
  • compositions disclosed above may be obtained by the addition of a surface-active agent, an inert carrier, a preservative, a humectant, a feeding stimulant, an attractant, an encapsulating agent, a binder, an emulsifier, a dye, a UV protectant, a buffer, a flow agent or fertilizers, micronutrient donors, or other preparations that influence plant growth.
  • One or more agrochemicals including, but not limited to, herbicides, insecticides, fungicides, bactericides, nematicides, molluscicides, acaracides, plant growth regulators, harvest aids, and fertilizers, can be combined with carriers, surfactants or adjuvants customarily employed in the art of formulation or other components to facilitate product handling and application for particular target pests.
  • Suitable carriers and adjuvants can be solid or liquid and correspond to the substances ordinarily employed in formulation technology, e.g., natural or regenerated mineral substances, solvents, dispersants, wetting agents, tackifiers, binders, or fertilizers.
  • the active ingredients of the present invention are normally applied in the form of compositions and can be applied to the crop area, plant, or seed to be treated.
  • the compositions may be applied to grain in preparation for or during storage in a grain bin or silo, etc.
  • the compositions may be applied simultaneously or in succession with other compounds.
  • Methods of applying an active ingredient or a composition that contains at least one silencing element include, but are not limited to, foliar application, seed coating, and soil application. The number of applications and the rate of application depend on the intensity of infestation by the corresponding pest.
  • Suitable surface-active agents include, but are not limited to, anionic compounds such as a carboxylate of, for example, a metal; carboxylate of a long chain fatty acid; an N-acylsarcosinate; mono- or di-esters of phosphoric acid with fatty alcohol ethoxylates or salts of such esters; fatty alcohol sulfates such as sodium dodecyl sulfate, sodium octadecyl sulfate, or sodium cetyl sulfate; ethoxylated fatty alcohol sulfates; ethoxylated alkylphenol sulfates; lignin sulfonates; petroleum sulfonates; alkyl aryl sulfonates such as alkyl-benzene sulfonates or lower alkylnaphtalene sulfonates, e.g., butyl-naphthalene sulfonate; salt
  • Non-ionic agents include condensation products of fatty acid esters, fatty alcohols, fatty acid amides or fatty-alkyl- or alkenyl-substituted phenols with ethylene oxide, fatty esters of polyhydric alcohol ethers, e.g., sorbitan fatty acid esters, condensation products of such esters with ethylene oxide, e.g., polyoxyethylene sorbitan fatty acid esters, block copolymers of ethylene oxide and propylene oxide, acetylenic glycols such as 2,4,7,9-tetraethyl-5-decyn-4,7-diol, or ethoxylated acetylenic glycols.
  • a cationic surface-active agent examples include, for instance, an aliphatic mono-, di-, or polyamine such as an acetate, naphthenate or oleate; or oxygen-containing amine such as an amine oxide of polyoxyethylene alkylamine; an amide-linked amine prepared by the condensation of a carboxylic acid with a di- or polyamine; or a quaternary ammonium salt.
  • inert materials include, but are not limited to, inorganic minerals such as kaolin, phyllosilicates, carbonates, sulfates, phosphates, or botanical materials such as cork, powdered corncobs, peanut hulls, rice hulls, and walnut shells.
  • inorganic minerals such as kaolin, phyllosilicates, carbonates, sulfates, phosphates, or botanical materials such as cork, powdered corncobs, peanut hulls, rice hulls, and walnut shells.
  • compositions comprising the silencing element can be in a suitable form for direct application or as a concentrate of primary composition that requires dilution with a suitable quantity of water or other dilutant before application.
  • compositions can be applied to the environment of an insect pest (such as a pest from the Lepidoptera order) by, for example, spraying, atomizing, dusting, scattering, coating or pouring, introducing into or on the soil, introducing into irrigation water, by seed treatment or general application or dusting at the time when the pest has begun to appear or before the appearance of pests as a protective measure.
  • insect pest such as a pest from the Lepidoptera order
  • the composition(s) and/or transformed microorganism(s) may be mixed with grain to protect the grain during storage. It is generally important to obtain good control of pests in the early stages of plant growth, as this is the time when the plant can be most severely damaged.
  • the compositions can conveniently contain another insecticide if this is thought necessary.
  • the composition(s) is applied directly to the soil, at a time of planting, in granular form of a composition of a carrier and dead cells of a Bacillus strain or transformed microorganism of the invention.
  • Another embodiment is a granular form of a composition comprising an agrochemical such as, for example, a herbicide, an insecticide, a fertilizer, in an inert carrier, and dead cells of a Bacillus strain or transformed microorganism of the invention.
  • the methods of the invention involve introducing a polypeptide or polynucleotide into a plant.
  • “Introducing” is intended to mean presenting to the plant the polynucleotide or polypeptide in such a manner that the sequence gains access to the interior of a cell of the plant.
  • the methods of the invention do not depend on a particular method for introducing a sequence into a plant, only that the polynucleotide or polypeptides gains access to the interior of at least one cell of the plant.
  • Methods for introducing polynucleotide or polypeptides into plants are known in the art including, but not limited to, stable transformation methods, transient transformation methods, and vim s-mediated methods.
  • “Stable transformation” is intended to mean that the nucleotide construct introduced into a plant integrates into the genome of the plant and is capable of being inherited by the progeny thereof. “Transient transformation” is intended to mean that a polynucleotide is introduced into the plant and does not integrate into the genome of the plant or a polypeptide is introduced into a plant.
  • Transformation protocols as well as protocols for introducing polypeptides or polynucleotide sequences into plants may vary depending on the type of plant or plant cell, i.e., monocot or dicot, targeted for transformation. Suitable methods of introducing polypeptides and polynucleotides into plant cells include microinjection (Crossway et al. (1986) Biotechniques 4:320-334), electroporation (Riggs et al. (1986) Proc. Natl. Acad. Sci. USA 83:5602-5606, Agrobacterium -mediated transformation (U.S. Pat. Nos. 5,563,055 and 5,981,840), direct gene transfer (Paszkowski et al. (1984) EMBO J.
  • the silencing element sequences of the invention can be provided to a plant using a variety of transient transformation methods.
  • transient transformation methods include, but are not limited to, the introduction of the protein or variants and fragments thereof directly into the plant or the introduction of the transcript into the plant.
  • Such methods include, for example, microinjection or particle bombardment. See, for example, Crossway et al. (1986) Mol Gen. Genet. 202:179-185; Nomura et al. (1986) Plant Sci. 44:53-58; Hepler et al. (1994) Proc. Natl. Acad. Sci. 91: 2176-2180 and Hush et al.
  • polynucleotides can be transiently transformed into the plant using techniques known in the art. Such techniques include viral vector system and the precipitation of the polynucleotide in a manner that precludes subsequent release of the DNA. Thus, the transcription from the particle-bound DNA can occur, but the frequency with which it is released to become integrated into the genome is greatly reduced. Such methods include the use of particles coated with polyethylimine (PEI; Sigma #P3143).
  • the polynucleotide of the invention may be introduced into plants by contacting plants with a virus or viral nucleic acids.
  • such methods involve incorporating a nucleotide construct of the invention within a viral DNA or RNA molecule.
  • promoters of the invention also encompass promoters utilized for transcription by viral RNA polymerases. Methods for introducing polynucleotides into plants and expressing a protein encoded therein, involving viral DNA or RNA molecules, are known in the art. See, for example, U.S. Pat. Nos. 5,889,191, 5,889,190, 5,866,785, 5,589,367, 5,316,931, and Porta et al. (1996) Molecular Biotechnology 5:209-221; herein incorporated by reference.
  • the insertion of the polynucleotide at a desired genomic location is achieved using a site-specific recombination system.
  • a site-specific recombination system See, for example, WO99/25821, WO99/25854, WO99/25840, WO99/25855, and WO99/25853, all of which are herein incorporated by reference.
  • the polynucleotide of the invention can be contained in transfer cassette flanked by two non-recombinogenic recombination sites.
  • the transfer cassette is introduced into a plant having stably incorporated into its genome a target site which is flanked by two non-recombinogenic recombination sites that correspond to the sites of the transfer cassette.
  • An appropriate recombinase is provided and the transfer cassette is integrated at the target site.
  • the polynucleotide of interest is thereby integrated at a specific chromosomal position in the plant genome.
  • the cells that have been transformed may be grown into plants in accordance with conventional ways. See, for example, McCormick et al. (1986) Plant Cell Reports 5:81-84. These plants may then be grown, and either pollinated with the same transformed strain or different strains, and the resulting progeny having constitutive expression of the desired phenotypic characteristic identified. Two or more generations may be grown to ensure that expression of the desired phenotypic characteristic is stably maintained and inherited and then seeds harvested to ensure expression of the desired phenotypic characteristic has been achieved. In this manner, the present invention provides transformed seed (also referred to as “transgenic seed”) having a polynucleotide of the invention, for example, an expression cassette of the invention, stably incorporated into their genome.
  • the term plant includes plant cells, plant protoplasts, plant cell tissue cultures from which plants can be regenerated, plant calli, plant clumps, and plant cells that are intact in plants or parts of plants such as embryos, pollen, ovules, seeds, leaves, flowers, branches, fruit, kernels, ears, cobs, husks, stalks, roots, root tips, anthers, and the like.
  • Grain is intended to mean the mature seed produced by commercial growers for purposes other than growing or reproducing the species.
  • Progeny, variants, and mutants of the regenerated plants are also included within the scope of the invention, provided that these parts comprise the introduced polynucleotides.
  • the present invention may be used for transformation of any plant species, including, but not limited to, monocots and dicots.
  • plant species of interest include, but are not limited to, corn ( Zea mays ), Brassica sp. (e.g., B. napus, B. rapa, B.
  • juncea particularly those Brassica species useful as sources of seed oil, alfalfa ( Medicago sativa ), rice ( Oryza sativa ), rye ( Secale cereale ), sorghum ( Sorghum bicolor, Sorghum vulgare ), millet (e.g., pearl millet ( Pennisetum glaucum ), proso millet ( Panicum miliaceum ), foxtail millet ( Setaria italica ), finger millet ( Eleusine coracana )), sunflower ( Helianthus annuus ), safflower (Carthamus tinctorius), wheat ( Triticum aestivum ), soybean ( Glycine max ), tobacco ( Nicotiana tabacum ), potato ( Solanum tuberosum ), peanuts ( Arachis hypogaea ), cotton ( Gossypium barbadense, Gossypium hirsutum ), sweet potato ( Ipomoea batat
  • Vegetables include tomatoes ( Lycopersicon esculentum ), lettuce (e.g., Lactuca sativa ), green beans ( Phaseolus vulgaris ), lima beans ( Phaseolus limensis), peas ( Lathyrus spp.), and members of the genus Cucumis such as cucumber ( C. sativus ), cantaloupe (C. cantalupensis), and musk melon ( C. melo ).
  • tomatoes Lycopersicon esculentum
  • lettuce e.g., Lactuca sativa
  • green beans Phaseolus vulgaris
  • lima beans Phaseolus limensis
  • peas Lathyrus spp.
  • members of the genus Cucumis such as cucumber ( C. sativus ), cantaloupe (C. cantalupensis), and musk melon ( C. melo ).
  • Ornamentals include azalea ( Rhododendron spp.), hydrangea ( Macrophylla hydrangea ), hibiscus (Hibiscus rosasanensis), roses (Rosa spp.), tulips (Tulipa spp.), daffodils ( Narcissus spp.), petunias ( Petunia hybrida ), carnation ( Dianthus caryophyllus ), poinsettia ( Euphorbia pulcherrima ), and chrysanthemum.
  • Conifers that may be employed in practicing the present invention include, for example, pines such as loblolly pine ( Pinus taeda ), slash pine ( Pinus elliotii ), ponderosa pine ( Pinus ponderosa ), lodgepole pine ( Pinus contorta ), and Monterey pine ( Pinus radiata ); Douglas-fir ( Pseudotsuga menziesii ); Western hemlock ( Tsuga canadensis ); Sitka spruce ( Picea glauca ); redwood ( Sequoia sempervirens ); true firs such as silver fir ( Abies amabilis ) and balsam fir ( Abies balsamea ); and cedars such as Western red cedar ( Thuja plicata ) and Alaska yellow-cedar ( Chamaecyparis nootkatensis ).
  • pines such as loblolly pine ( Pinus taeda ),
  • plants of the present invention are crop plants (for example, corn, alfalfa, sunflower, Brassica , soybean, cotton, safflower, peanut, sorghum, wheat, millet, tobacco, etc.).
  • corn and soybean plants are optimal, and in yet other embodiments corn plants are optimal.
  • plants of interest include grain plants that provide seeds of interest, oil-seed plants, and leguminous plants.
  • Seeds of interest include grain seeds, such as corn, wheat, barley, rice, sorghum, rye, etc.
  • Oil-seed plants include cotton, soybean, safflower, sunflower, Brassica , maize, alfalfa, palm, coconut, etc.
  • Leguminous plants include beans and peas. Beans include guar, locust bean, fenugreek, soybean, garden beans, cowpea, mungbean, lima bean, fava bean, lentils, chickpea, etc.
  • the methods of the invention comprise methods for controlling a pest (i.e., pest from the Lepidoptera order, such as, Spodoptera frugiperda ).
  • the method comprises feeding to a pest a composition comprising a silencing element of the invention, wherein said silencing element, when ingested by a pest (i.e., pests from the Lepidoptera order, such as, Spodoptera frugiperda ), reduces the level of a target polynucleotide of the pest and thereby controls the pest.
  • the pest can be fed the silencing element in a variety of ways.
  • the polynucleotide comprising the silencing element is introduced into a plant.
  • the silencing element is delivered to the pest.
  • the silencing element can be expressed constitutively or alternatively, it may be produced in a stage-specific manner by employing the various inducible or tissue-preferred or developmentally regulated promoters that are discussed elsewhere herein.
  • the silencing element expressed in the roots, stalk or stem, leaf including pedicel, xylem and phloem, fruit or reproductive tissue, silk, flowers and all parts therein or any combination thereof.
  • a composition comprising at least one silencing element of the invention is applied to a plant.
  • the silencing element can be formulated in an agronomically suitable and/or environmentally acceptable carrier, which is preferably, suitable for dispersal in fields.
  • the carrier can also include compounds that increase the half life of the composition.
  • the composition comprising the silencing element is formulated in such a manner such that it persists in the environment for a length of time sufficient to allow it to be delivered to a pest.
  • the composition can be applied to an area inhabited by a pest.
  • the composition is applied externally to a plant (i.e., by spraying a field) to protect the plant from pests.
  • the constructs of the present invention can be stacked with any combination of polynucleotide sequences of interest in order to create plants with a desired trait.
  • a trait refers to the phenotype derived from a particular sequence or groups of sequences.
  • the polynucleotides of the present invention may be stacked with any other polynucleotides encoding polypeptides having pesticidal and/or insecticidal activity, such as other Bacillus thuringiensis toxic proteins (described in U.S. Pat. Nos. 5,366,892; 5,747,450; 5,737,514; 5,723,756; 5,593,881; and Geiser et al.
  • the combinations generated can also include multiple copies of any one of the polynucleotides of interest.
  • the polynucleotides of the present invention can also be stacked with any other gene or combination of genes to produce plants with a variety of desired trait combinations including, but not limited to, traits desirable for animal feed such as high oil genes (e.g., U.S. Pat. No. 6,232,529); balanced amino acids (e.g., hordothionins (U.S. Pat. Nos.
  • polynucleotides of the present invention can also be stacked with traits desirable for disease or herbicide resistance (e.g., fumonisin detoxification genes (U.S. Pat. No. 5,792,931); avirulence and disease resistance genes (Jones et al. (1994) Science 266:789; Martin et al. (1993) Science 262:1432; Mindrinos et al.
  • diseases or herbicide resistance e.g., fumonisin detoxification genes (U.S. Pat. No. 5,792,931)
  • avirulence and disease resistance genes Jones et al. (1994) Science 266:789; Martin et al. (1993) Science 262:1432; Mindrinos et al.
  • acetolactate synthase (ALS) mutants that lead to herbicide resistance such as the S4 and/or Hra mutations
  • inhibitors of glutamine synthase such as phosphinothricin or basta (e.g., bar gene); and glyphosate resistance (EPSPS gene)
  • traits desirable for processing or process products such as high oil (e.g., U.S. Pat. No. 6,232,529); modified oils (e.g., fatty acid desaturase genes (U.S. Pat. No.
  • modified starches e.g., ADPG pyrophosphorylases (AGPase), starch synthases (SS), starch branching enzymes (SBE), and starch debranching enzymes (SDBE)
  • polymers or bioplastics e.g., U.S. Pat. No. 5,602,321; beta-ketothiolase, polyhydroxybutyrate synthase, and acetoacetyl-CoA reductase (Schubert et al. (1988) J. Bacteriol. 170:5837-5847) facilitate expression of polyhydroxyalkanoates (PHAs)); the disclosures of which are herein incorporated by reference.
  • polynucleotides of the present invention could also combine with polynucleotides providing agronomic traits such as male sterility (e.g., see U.S. Pat. No. 5,583,210), stalk strength, flowering time, or transformation technology traits such as cell cycle regulation or gene targeting (e.g., WO 99/61619, WO 00/17364, and WO 99/25821); the disclosures of which are herein incorporated by reference.
  • agronomic traits such as male sterility (e.g., see U.S. Pat. No. 5,583,210), stalk strength, flowering time, or transformation technology traits such as cell cycle regulation or gene targeting (e.g., WO 99/61619, WO 00/17364, and WO 99/25821); the disclosures of which are herein incorporated by reference.
  • stacked combinations can be created by any method including, but not limited to, cross-breeding plants by any conventional or TopCross methodology, or genetic transformation. If the sequences are stacked by genetically transforming the plants, the polynucleotide sequences of interest can be combined at any time and in any order. For example, a transgenic plant comprising one or more desired traits can be used as the target to introduce further traits by subsequent transformation. The traits can be introduced simultaneously in a co-transformation protocol with the polynucleotides of interest provided by any combination of transformation cassettes. For example, if two sequences will be introduced, the two sequences can be contained in separate transformation cassettes (trans) or contained on the same transformation cassette (cis).
  • sequences can be driven by the same promoter or by different promoters. In certain cases, it may be desirable to introduce a transformation cassette that will suppress the expression of the polynucleotide of interest. This may be combined with any combination of other suppression cassettes or overexpression cassettes to generate the desired combination of traits in the plant. It is further recognized that polynucleotide sequences can be stacked at a desired genomic location using a site-specific recombination system. See, for example, WO99/25821, WO99/25854, WO99/25840, WO99/25855, and WO99/25853, all of which are herein incorporated by reference.
  • Methods and compositions are further provided which allow for an increase in RNAi produced from the silencing element.
  • the methods and compositions employ a first polynucleotide comprising a silencing element for a target pest sequence operably linked to a promoter active in the plant cell; and, a second polynucleotide comprising a suppressor enhancer element comprising the target pest sequence or an active variant or fragment thereof operably linked to a promoter active in the plant cell.
  • the combined expression of the silencing element with suppressor enhancer element leads to an increased amplification of the inhibitory RNA produced from the silencing element over that achievable with only the expression of the silencing element alone.
  • the methods and compositions further allow for the production of a diverse population of RNAi species that can enhance the effectiveness of disrupting target gene expression.
  • the methods and composition can allow for the systemic production of RNAi throughout the plant; the production of greater amounts of RNAi than would be observed with just the silencing element construct alone; and, the improved loading of RNAi into the phloem of the plant, thus providing better control of phloem feeding insects by an RNAi approach.
  • the various methods and compositions provide improved methods for the delivery of inhibitory RNA to the target organism. See, for example, U.S. Provisional Application No. 61/021,676, entitled “Compositions and Methods for the Suppression of Target Polynucleotides”, filed Jan. 17, 2008 and herein incorporated by reference in its entirety.
  • a “suppressor enhancer element” comprises a polynucleotide comprising the target sequence to be suppressed or an active fragment or variant thereof. It is recognize that the suppressor enhancer element need not be identical to the target sequence, but rather, the suppressor enhancer element can comprise a variant of the target sequence, so long as the suppressor enhancer element has sufficient sequence identity to the target sequence to allow for an increased level of the RNAi produced by the silencing element over that achievable with only the expression of the silencing element. Similarly, the suppressor enhancer element can comprise a fragment of the target sequence, wherein the fragment is of sufficient length to allow for an increased level of the RNAi produced by the silencing element over that achievable with only the expression of the silencing element.
  • the suppressor enhancer element comprises a fragment or a variant of a polynucleotide encoding a juvenile hormone polypeptide, a vacuolar polypeptide, a cadherin polypeptide, a cuticle polypeptide, a translation initiation factor, a SARI polypeptide, an elongation factor, a phosphooligosaccharide, a myosin polypeptide, a potassium channel amino acid transporter, a potassium inwardly rectifier polypeptide, an amino acid transporter, a tubulin polypeptide, a ubiquitin polypeptide, small nuclear ribonucleoprotein, or any other polynucleotide fo interest disclosed herein.
  • the suppressor enhancer element comprises a polynucleotide set forth in SEQ ID NO: 1-50 or an active variant or fragment thereof.
  • the suppressor enhancer elements employed can comprise fragments of the target sequence derived from different region of the target sequence (i.e., from the 3′UTR, coding sequence, intron, and/or 5′UTR).
  • the suppressor enhancer element can be contained in an expression cassette, as described elsewhere herein, and in specific embodiments, the suppressor enhancer element is on the same or on a different DNA vector or construct as the silencing element.
  • the suppressor enhancer element can be operably linked to a promoter as disclosed herein. It is recognized that the suppressor enhancer element can be expressed constitutively or alternatively, it may be produced in a stage-specific manner employing the various inducible or tissue-preferred or developmentally regulated promoters that are discussed elsewhere herein.
  • RNAi RNAi-derived RNAi
  • the plant or plant parts of the invention have an improved loading of RNAi into the phloem of the plant than would be observed with the expression of the silencing element construct alone and, thus provide better control of phloem feeding insects by an RNAi approach.
  • the plants, plant parts, and plant cells of the invention can further be characterized as allowing for the production of a diversity of RNAi species that can enhance the effectiveness of disrupting target gene expression.
  • the combined expression of the silencing element and the suppressor enhancer element increases the concentration of the inhibitory RNA in the plant cell, plant, plant part, plant tissue or phloem over the level that is achieved when the silencing element is expressed alone.
  • an “increased level of inhibitory RNA” comprises any statistically significant increase in the level of RNAi produced in a plant having the combined expression when compared to an appropriate control plant.
  • an increase in the level of RNAi in the plant, plant part or the plant cell can comprise at least about a 1%, about a 1%-5%, about a 5%-10%, about a 10%-20%, about a 20%-30%, about a 30%-40%, about a 40%-50%, about a 50%-60%, about 60-70%, about 70%-80%, about a 80%-90%, about a 90%-100% or greater increase in the level of RNAi in the plant, plant part, plant cell, or phloem when compared to an appropriate control.
  • the increase in the level of RNAi in the plant, plant part, plant cell, or phloem can comprise at least about a 1 fold, about a 1 fold-5 fold, about a 5 fold-10 fold, about a 10 fold-20 fold, about a 20 fold-30 fold, about a 30 fold-40 fold, about a 40 fold-50 fold, about a 50 fold-60 fold, about 60 fold-70 fold, about 70 fold-80 fold, about a 80 fold-90 fold, about a 90 fold-100 fold or greater increase in the level of RNAi in the plant, plant part, plant cell or phloem when compared to an appropriate control.
  • Methods to assay for an increase in the level of RNAi are discussed elsewhere herein.
  • RNAi Disruption of insect gene function via RNAi can produce specific activity against target insects. This specificity is enhanced by delivery of the dsRNAs via transgenic plants. Identification of gene function in insects via RNAi has been largely limited to injection of dsRNAs. In fact, past experiments have indicated that insects are not capable of systemic RNAi response based on exposure to dsRNAs.
  • dsRNAs As described below, we have demonstrated acute activity of numerous dsRNA pairs through injection experiments and additionally have demonstrated insect antagonism through ingestion of dsRNAs. This evidence identifies several gene/primer pair combinations with clear insecticidal properties.
  • the use of dsRNAs in transgenic plants also addresses the potential complication of heterologous protein expression and the possible risks of allergic reaction, non-target activity, and environmental- or bioaccumulation.
  • the data presented below represents the first test of disruption of these particular genes resulting in insecticidal activity in whole organisms and the first report of insecticidal activity of dsRNAs against Spodoptera frugiperda.
  • the invention describes specific target genes and the dsRNA sequences causing insecticidal activity against the Lepidopteran Spodoptera frugiperda through RNA interference of the target gene's expression. Disruption of the genes targeted by the dsRNA sequences may be broadly insecticidal in numerous species.
  • the specific dsRNA sequences display insecticidal activity upon ingestion and can be utilized with a transgenic plant mode of delivery.
  • Table 1 provides the polynucleotide of non-limiting examples of target sequence from Spodoptera frugiperda , a brief description of the function of the protein encoded by the target sequence, and a SEQ ID NO.
  • Table 2 provides a summary of primers used to suppress the target polynucleotides.
  • Serial dilution assays starting with a high dose of 20 uM and including 10, 5, 2.5, 1.25, 0.6, and 0 uMolar concentrations were also performed in this manner.
  • Neonate larvae were fed 25 uMolar dsRNAs. Treated insects were weighed en masse at 72 hours and compared to sucrose controls. 2 replicates of the experiment were averaged.
  • Second instar fall armyworm were injected using a micromanipulator and microinjection needles pulled on a Sutter Instrument (Novato, Calif.) P-2000 horizontal needle puller. The needle was back loaded with dsRNA solution. Initial injection experiments employed a concentration of 2 ug/ul (see Table X). This rate produced high mortality across all primers tested. Subsequent assays were performed with lower concentrations. Blue McCormick food coloring was included in the dsRNA solution to better visualize the injection process. Prior to injection, the insects were affixed to a microscope slide using a glue stick (Office Depot, Delray Beach, Fla.). The injection needle was connected to a 20 ml hypodermic syringe via Teflon tubing.
  • the injection needle was then mounted on a Leitz micromanipulator.
  • the dsRNA solution was dispensed from the microinjection needle by pressing on the plunger of the 20 ml syringe.
  • Injection volumes were variable but averaged approximately 250 nL (based on injection of approximately 20 insects injected from a 5 ul volume loaded into the needle). Following injection, insects were removed from the microscope slide with the aid of a moistened fine camelhair brush. The insects were then placed on multispecies diet and were evaluated for mortality at 24 and 48 hours. Water injections were used as controls. Silencer® Negative Control #1, 2, and 3 siRNA control primers from Ambion (Austin, Tex.) were also included as negative controls.
  • the term “topical diet assay” refers to assays where artificial diets are pipetted into microtiter plates and the dsRNA solution is dispensed on the surface of the diet.
  • 100 ul of diet was dispensed per well.
  • the surface of the well was then treated with 10 ul of a dsRNA solution of varying concentrations.
  • the plates were then infested with 1 neonate fall armyworm per well and sealed with mylar. The mylar seal was punctured with a small insect pin to allow for air exchange. Plates were then stored in a growth chamber at 28 C and the assay was scored for stunting or mortality at 4 days.
  • Table 6-12 represents several experiments using this method.
  • Table 13 provides a summary of the data.
  • topical assay #1 the primers that previously showed activity in injection assays were tested in a FAW topical diet assay. These results are shown in Table 6.
  • a 50 uMolar solution (0.66 ug/ul) was used as the test concentration. 5 ul of this sample was loaded onto the top of 100 ul of diet producing a final concentration of 2.5 uMolar or 30 ppm.
  • A1-A11 A12 is a negative control
  • the other samples are those with no known human orthologs.
  • the plate was infested with aprox. 5 neonates/well. The scoring period was 72 hours.
  • topical assay #2 primers were tested in a FAW topical diet assay, and the results are shown in table 7.
  • the 2.7 ug/ul stock was diluted to a starting concentration of 0.67 ug/ul. 2 fold serial dilution was carried out to produce stocks of 0.32 ug/ul and 0.16 ug/ul. 5 ul of these stocks were added to the 100 ul of diet producing final concentrations of 30, 15, and 8 ppm in diet.
  • the scoring period was 72 hours.
  • topical assay #4 primers were tested in a FAW topical diet assay, and the results are shown in table 9.
  • the 2.7 ug/ul stock was diluted to a starting concentration of 0.67 ug/ul. 2 fold serial dilution was carried out to produce stocks of 0.32 ug/ul and 0.16 ug/ul. 5 ul of these stocks were added to the 100 ul of diet producing final concentrations of 30, 15, and 8 ppm in diet.
  • the scoring period was 72 hours.
  • Immature maize embryos from greenhouse donor plants are bombarded with a plasmid containing the silencing element of the invention operably linked to either a tissue specific, tissue selective, or constitutive promoter and the selectable marker gene PAT (Wohlleben et al. (1988) Gene 70:25-37), which confers resistance to the herbicide Bialaphos.
  • the constructs will have 2 identical 2-300 bp segments of the target gene in opposite orientations with an “intron” segment between them acting as a hairpin loop.
  • Such a construct can be linked to the dMMB promoter.
  • the selectable marker gene is provided on a separate plasmid. Transformation is performed as follows. Media recipes follow below.
  • the ears are husked and surface sterilized in 30% Clorox bleach plus 0.5% Micro detergent for 20 minutes, and rinsed two times with sterile water.
  • the immature embryos are excised and placed embryo axis side down (scutellum side up), 25 embryos per plate, on 560Y medium for 4 hours and then aligned within the 2.5 cm target zone in preparation for bombardment.
  • a plasmid vector comprising the silencing element of interest operably linked to either the tissue specific, tissue selective, or constitutive promoter is made.
  • This plasmid DNA plus plasmid DNA containing a PAT selectable marker is precipitated onto 1.1 ⁇ m (average diameter) tungsten pellets using a CaCl 2 precipitation procedure as follows: 100 ⁇ l prepared tungsten particles in water; 10 ⁇ l (1 ⁇ g) DNA in Tris EDTA buffer (1 ⁇ g total DNA); 100 ⁇ l 2.5 M CaCl 2 ; and, 10 ⁇ l 0.1 M spermidine.
  • Each reagent is added sequentially to the tungsten particle suspension, while maintained on the multitube vortexer.
  • the final mixture is sonicated briefly and allowed to incubate under constant vortexing for 10 minutes.
  • the tubes are centrifuged briefly, liquid removed, washed with 500 ml 100% ethanol, and centrifuged for 30 seconds. Again the liquid is removed, and 105 ⁇ l 100% ethanol is added to the final tungsten particle pellet.
  • the tungsten/DNA particles are briefly sonicated and 10 ⁇ l spotted onto the center of each macrocarrier and allowed to dry about 2 minutes before bombardment.
  • sample plates are bombarded at level #4 in a particle gun. All samples receive a single shot at 650 PSI, with a total of ten aliquots taken from each tube of prepared particles/DNA.
  • the embryos are kept on 560Y medium for 2 days, then transferred to 560R selection medium containing 3 mg/liter Bialaphos, and subcultured every 2 weeks. After approximately 10 weeks of selection, selection-resistant callus clones are transferred to 288 J medium to initiate plant regeneration. Following somatic embryo maturation (2-4 weeks), well-developed somatic embryos are transferred to medium for germination and transferred to the lighted culture room. Approximately 7-10 days later, developing plantlets are transferred to 272V hormone-free medium in tubes for 7-10 days until plantlets are well established.
  • Plants are then transferred to inserts in flats (equivalent to 2.5′′ pot) containing potting soil and grown for 1 week in a growth chamber, subsequently grown an additional 1-2 weeks in the greenhouse, then transferred to classic 600 pots (1.6 gallon) and grown to maturity.
  • Plants are monitored and scored for the appropriate marker, such as the control of Lepidoptera and have insecticidal activity.
  • a FAW feeding assay could be preformed.
  • leaf discs from the transgenic plant are excised using a 1 cm cork borer or leaf punch.
  • Six leaf discs are prepared for each plant. The leaves are placed in a 24 well microtiter plate on top of 500 ul of 0.8% agar. Each leaf disc is infested with 2 neonate Fall armyworm and the plate is then sealed with mylar. A small ventilation hole is made for each well and the plates are then stored in a 28 C growth chamber.
  • the assay is scored for mortality, stunting, and leaf consumption at 96 hours.
  • Bombardment medium comprises 4.0 g/l N6 basal salts (SIGMA C-1416), 1.0 ml/l Eriksson's Vitamin Mix (1000 ⁇ SIGMA-1511), 0.5 mg/l thiamine HCl, 120.0 g/l sucrose, 1.0 mg/l 2,4-D, and 2.88 g/l L-proline (brought to volume with D-I H 2 O following adjustment to pH 5.8 with KOH); 2.0 g/l Gelrite (added after bringing to volume with D-I H 2 O); and 8.5 mg/l silver nitrate (added after sterilizing the medium and cooling to room temperature).
  • Selection medium comprises 4.0 g/l N6 basal salts (SIGMA C-1416), 1.0 ml/l Eriksson's Vitamin Mix (1000 ⁇ SIGMA-1511), 0.5 mg/l thiamine HCl, 30.0 g/l sucrose, and 2.0 mg/l 2,4-D (brought to volume with D-I H 2 O following adjustment to pH 5.8 with KOH); 3.0 g/l Gelrite (added after bringing to volume with D-I H 2 O); and 0.85 mg/l silver nitrate and 3.0 mg/l bialaphos (both added after sterilizing the medium and cooling to room temperature).
  • Plant regeneration medium (288 J) comprises 4.3 g/l MS salts (GIBCO 11117-074), 5.0 ml/l MS vitamins stock solution (0.100 g nicotinic acid, 0.02 g/l thiamine HCl, 0.10 g/l pyridoxine HCl, and 0.40 g/l glycine brought to volume with polished D-I H 2 O) (Murashige and Skoog (1962) Physiol. Plant.
  • Hormone-free medium comprises 4.3 g/l MS salts (GIBCO 11117-074), 5.0 ml/l MS vitamins stock solution (0.100 g/l nicotinic acid, 0.02 g/l thiamine HCl, 0.10 g/l pyridoxine HCl, and 0.40 g/l glycine brought to volume with polished D-I H 2 O), 0.1 g/l myo-inositol, and 40.0 g/l sucrose (brought to volume with polished D-I H 2 O after adjusting pH to 5.6); and 6 g/l bacto-agar (added after bringing to volume with polished D-I H 2 O), sterilized and cooled to 60° C.
  • Such as a construct can comprise 2 identical 2-300 bp segments of the target gene in opposite orientations with an “intron” segment between them acting as a hairpin loop.
  • Such a construct can be linked to the dMMB promoter.
  • immature embryos are isolated from maize and the embryos contacted with a suspension of Agrobacterium , where the bacteria are capable of transferring the polynucleotide comprising the silencing element to at least one cell of at least one of the immature embryos (step 1: the infection step).
  • the immature embryos are immersed in an Agrobacterium suspension for the initiation of inoculation.
  • the embryos are co-cultured for a time with the Agrobacterium (step 2: the co-cultivation step).
  • the immature embryos are cultured on solid medium following the infection step. Following this co-cultivation period an optional “resting” step is contemplated.
  • step 3 resting step
  • the immature embryos are cultured on solid medium with antibiotic, but without a selecting agent, for elimination of Agrobacterium and for a resting phase for the infected cells.
  • step 4 inoculated embryos are cultured on medium containing a selective agent and growing transformed callus is recovered (step 4: the selection step).
  • the immature embryos are cultured on solid medium with a selective agent resulting in the selective growth of transformed cells.
  • the callus is then regenerated into plants (step 5: the regeneration step), and calli grown on selective medium are cultured on solid medium to regenerate the plants.
  • Soybean embryogenic suspension cultures (cv. Jack) are maintained in 35 ml liquid medium SB196 (see recipes below) on rotary shaker, 150 rpm, 26° C. with cool white fluorescent lights on 16:8 hr day/night photoperiod at light intensity of 60-85 ⁇ E/m2/s. Cultures are subcultured every 7 days to two weeks by inoculating approximately 35 mg of tissue into 35 ml of fresh liquid SB196 (the preferred subculture interval is every 7 days).
  • Soybean embryogenic suspension cultures are transformed with the plasmids and DNA fragments described in the examples above by the method of particle gun bombardment (Klein et al. (1987) Nature, 327:70).
  • Soybean cultures are initiated twice each month with 5-7 days between each initiation.
  • soybeans with immature seeds from available soybean plants 45-55 days after planting are picked, removed from their shells and placed into a sterilized magenta box.
  • the soybean seeds are sterilized by shaking them for 15 minutes in a 5% Clorox solution with 1 drop of ivory soap (95 ml of autoclaved distilled water plus 5 ml Clorox and 1 drop of soap). Mix well.
  • Seeds are rinsed using 2 1-liter bottles of sterile distilled water and those less than 4 mm are placed on individual microscope slides. The small end of the seed are cut and the cotyledons pressed out of the seed coat. Cotyledons are transferred to plates containing SB1 medium (25-30 cotyledons per plate). Plates are wrapped with fiber tape and stored for 8 weeks. After this time secondary embryos are cut and placed into SB196 liquid media for 7 days.
  • Plasmid DNA for bombardment are routinely prepared and purified using the method described in the PromegaTM Protocols and Applications Guide, Second Edition (page 106). Fragments of the plasmids carrying the silencing element of interest are obtained by gel isolation of double digested plasmids. In each case, 100 ug of plasmid DNA is digested in 0.5 ml of the specific enzyme mix that is appropriate for the plasmid of interest.
  • the resulting DNA fragments are separated by gel electrophoresis on 1% SeaPlaque GTG agarose (BioWhitaker Molecular Applications) and the DNA fragments containing silencing element of interest are cut from the agarose gel.
  • DNA is purified from the agarose using the GELase digesting enzyme following the manufacturer's protocol.
  • a 50 ⁇ l aliquot of sterile distilled water containing 3 mg of gold particles (3 mg gold) is added to 5 ⁇ l of a 1 ⁇ g/ ⁇ l DNA solution (either intact plasmid or DNA fragment prepared as described above), 50 ⁇ l 2.5M CaCl 2 and 20 ⁇ l of 0.1 M spermidine.
  • the mixture is shaken 3 min on level 3 of a vortex shaker and spun for 10 sec in a bench microfuge. After a wash with 400 ⁇ l 100% ethanol the pellet is suspended by sonication in 40 ⁇ l of 100% ethanol.
  • Five ⁇ l of DNA suspension is dispensed to each flying disk of the Biolistic PDS1000/HE instrument disk. Each 5 ⁇ l aliquot contains approximately 0.375 mg gold per bombardment (i.e. per disk).
  • Tissue is bombarded 1 or 2 shots per plate with membrane rupture pressure set at 1100 PSI and the chamber evacuated to a vacuum of 27-28 inches of mercury. Tissue is placed approximately 3.5 inches from the retaining/stopping screen.
  • Transformed embryos were selected either using hygromycin (when the hygromycin phosphotransferase, HPT, gene was used as the selectable marker) or chlorsulfuron (when the acetolactate synthase, ALS, gene was used as the selectable marker).
  • the tissue is placed into fresh SB196 media and cultured as described above.
  • the SB196 is exchanged with fresh SB196 containing a selection agent of 30 mg/L hygromycin.
  • the selection media is refreshed weekly.
  • green, transformed tissue may be observed growing from untransformed, necrotic embryogenic clusters. Isolated, green tissue is removed and inoculated into multiwell plates to generate new, clonally propagated, transformed embryogenic suspension cultures.
  • the tissue is divided between 2 flasks with fresh SB196 media and cultured as described above.
  • the SB196 is exchanged with fresh SB196 containing selection agent of 100 ng/ml Chlorsulfuron.
  • the selection media is refreshed weekly.
  • green, transformed tissue may be observed growing from untransformed, necrotic embryogenic clusters. Isolated, green tissue is removed and inoculated into multiwell plates containing SB196 to generate new, clonally propagated, transformed embryogenic suspension cultures.
  • the tissue In order to obtain whole plants from embryogenic suspension cultures, the tissue must be regenerated.
  • Embryos are cultured for 4-6 weeks at 26° C. in SB196 under cool white fluorescent (Phillips cool white Econowatt F40/CW/RS/EW) and Agro (Phillips F40 Agro) bulbs (40 watt) on a 16:8 hr photoperiod with light intensity of 90-120 uE/m2s. After this time embryo clusters are removed to a solid agar media, SB166, for 1-2 weeks. Clusters are then subcultured to medium SB103 for 3 weeks. During this period, individual embryos can be removed from the clusters and screened for the appropriate marker or the ability of the plant, when injected with the silencing elements, to contol the Lepidoptera.
  • white fluorescent Phillips cool white Econowatt F40/CW/RS/EW
  • Agro Phillips F40 Agro bulbs
  • Matured individual embryos are desiccated by placing them into an empty, small petri dish (35 ⁇ 10 mm) for approximately 4-7 days. The plates are sealed with fiber tape (creating a small humidity chamber). Desiccated embryos are planted into SB71-4 medium where they were left to germinate under the same culture conditions described above. Germinated plantlets are removed from germination medium and rinsed thoroughly with water and then planted in Redi-Earth in 24-cell pack tray, covered with clear plastic dome. After 2 weeks the dome is removed and plants hardened off for a further week. If plantlets looked hardy they are transplanted to 10′′ pot of Redi-Earth with up to 3 plantlets per pot.
  • SB1 solid medium (per liter) comprises: 1 pkg. MS salts (Gibco/BRL—Cat#11117-066); 1 ml B5 vitamins 1000 ⁇ stock; 31.5 g sucrose; 2 ml 2,4-D (20 mg/L final concentration); pH 5.7; and, 8 g TC agar.
  • SB 166 solid medium (per liter) comprises: 1 pkg. MS salts (Gibco/BRL—Cat#11117-066); 1 ml B5 vitamins 1000 ⁇ stock; 60 g maltose; 750 mg MgCl2 hexahydrate; 5 g activated charcoal; pH 5.7; and, 2 g gelrite.
  • SB 103 solid medium (per liter) comprises: 1 pkg. MS salts (Gibco/BRL—Cat#11117-066); 1 ml B5 vitamins 1000 ⁇ stock; 60 g maltose; 750 mg MgCl2 hexahydrate; pH 5.7; and, 2 g gelrite.
  • SB 71-4 solid medium (per liter) comprises: 1 bottle Gamborg's B5 salts w/sucrose (Gibco/BRL—Cat#21153-036); pH 5.7; and, 5 g TC agar.
  • 2,4-D stock is obtained premade from Phytotech cat# D 295—concentration is 1 mg/ml.
  • B5 Vitamins Stock (per 100 ml) which is stored in aliquots at ⁇ 20 C comprises: 10 g myo-inositol; 100 mg nicotinic acid; 100 mg pyridoxine HCl; and, 1 g thiamine. If the solution does not dissolve quickly enough, apply a low level of heat via the hot stir plate.
  • Chlorsulfuron Stock comprises 1 mg/ml in 0.01 N Ammonium Hydroxide

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Abstract

Methods and compositions are provided which employ a silencing element that, when ingested by a pest, such as a pest from the Lepidoptera order, they are capable of decreasing the expression of a target sequence in the pest. In specific embodiments, the decrease in expression of the target sequence controls the pest and thereby the methods and compositions are capable of limiting damage to a plant. The present invention provides target polynucleotides encoding polypeptides from specific protein families and various target polynucleotides set forth in SEQ ID NOS: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50 or active variants and fragments thereof, wherein a decrease in expression of one or more the sequences in the target pest controls the pest (i.e., has insecticidal activity). Further provided are silencing elements which when ingested by the pest decrease the level of the target polypeptide and thereby control the pest. In specific embodiment, the pest is Spodoptera frugiperda. Plants, plant part, bacteria and other host cells comprising the silencing elements or an active variant or fragment thereof of the invention are also provided.

Description

    CROSS-REFERENCE TO RELATED APPLICATIONS
  • This application claims priority to, U.S. Provisional Application No. 61/021,699, filed Jan. 17, 2008, and U.S. Provisional Application No. 61/021,676, filed Jan. 17, 2008; and of U.S. Non Provisional application Ser. No. 12/351,267 filed Jan. 9, 2009, now granted as U.S. Pat. No. 8,847,013, and is a divisional of U.S. Non Provisional application Ser. No. 14/501,240 Sep. 30, 2014, which are herein incorporated by reference in their entirety.
    • FIELD OF THE INVENTION
  • The present invention relates generally to methods of molecular biology and gene silencing to control pests.
    • REFERENCE TO A SEQUENCE LISTING SUBMITTED AS A TEXT FILE VIA EFS-WEB
  • The official copy of the sequence listing is submitted concurrently with the specification as a text file via EFS-Web, in compliance with the American Standard Code for Information Interchange (ASCII), with a file name of 366590seqlist.txt, a creation date of Jan. 9, 2009, and a size of 102 Kb. The sequence listing filed via EFS-Web is part of the specification and is hereby incorporated in its entirety by reference herein.
    • BACKGROUND OF THE INVENTION
  • Insect pests are a serious problem in agriculture. They destroy millions of acres of staple crops such as corn, soybeans, peas, and cotton. Yearly, these pests cause over $100 billion dollars in crop damage in the U.S. alone. In an ongoing seasonal battle, farmers must apply billions of gallons of synthetic pesticides to combat these pests. Other methods employed in the past delivered insecticidal activity by microorganisms or genes derived from microorganisms expressed in transgenic plants. For example, certain species of microorganisms of the genus Bacillus are known to possess pesticidal activity against a broad range of insect pests including Lepidoptera, Diptera, Coleoptera, Hemiptera, and others. In fact, microbial pesticides, particularly those obtained from Bacillus strains, have played an important role in agriculture as alternatives to chemical pest control. Agricultural scientists have developed crop plants with enhanced insect resistance by genetically engineering crop plants to produce insecticidal proteins from Bacillus. For example, corn and cotton plants genetically engineered to produce Cry toxins (see, e.g., Aronson (2002) Cell Mol. Life Sci. 59(3):417-425; Schnepf et al. (1998) Microbiol. Mol. Biol. Rev. 62(3):775-806) are now widely used in American agriculture and have provided the farmer with an alternative to traditional insect-control methods. However, these Bt insecticidal proteins only protect plants from a relatively narrow range of pests. Moreover, these modes of insecticidal activity provided varying levels of specificity and, in some cases, caused significant environmental consequences. Thus, there is an immediate need for alternative methods to control pests.
    • BRIEF SUMMARY OF THE INVENTION
  • Methods and compositions are provided which employ a silencing element that, when ingested by a pest, such as a pest from the Lepidoptera order, is capable of decreasing the expression of a target sequence in the pest. In specific embodiments, the decrease in expression of the target sequence controls the pest and thereby the methods and compositions are capable of limiting damage to a plant. The present invention provides various target polynucleotides encoding polypeptides from specific families as disclosed elsewhere herein and various target polynucleotides set forth in SEQ ID NOS:1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50 or active variants or fragments thereof, wherein a decrease in expression of one or more the sequences in the target pest controls the pest (i.e., has insecticidal activity). Further provided are silencing elements, which when ingested by the pest, decrease the level of expression of one or more of the target polynucleotides. In specific embodiments, the silencing element comprises at least 15, 20, or 22 consecutive nucleotides of any one of SEQ ID NO:1-50. In specific embodiments, the pest that is controlled is Spodoptera frugiperda. Plants, plant parts, plant cells, bacteria and other host cells comprising the silencing elements or an active variant or fragment thereof are also provided.
  • In another embodiment, a method for controlling a pest, such as a pest from the Lepidoptera order, is provided. The method comprises feeding to a pest a composition comprising a silencing element, wherein the silencing element, when ingested by the pest, reduces the level of a target sequence in the pest and thereby controls the pest. Further provided are methods to protect a plant from a pest. Such methods comprise introducing into the plant or plant part a silencing element of the invention. When the plant expressing the silencing element is ingested by the pest, the level of the target sequence is decreased and the pest is controlled.
    • DETAILED DESCRIPTION OF THE INVENTION
  • The present inventions now will be described more fully hereinafter with reference to the accompanying drawings, in which some, but not all embodiments of the inventions are shown. Indeed, these inventions may be embodied in many different forms and should not be construed as limited to the embodiments set forth herein; rather, these embodiments are provided so that this disclosure will satisfy applicable legal requirements Like numbers refer to like elements throughout.
  • Many modifications and other embodiments of the inventions set forth herein will come to mind to one skilled in the art to which these inventions pertain having the benefit of the teachings presented in the foregoing descriptions and the associated drawings. Therefore, it is to be understood that the inventions are not to be limited to the specific embodiments disclosed and that modifications and other embodiments are intended to be included within the scope of the appended claims. Although specific terms are employed herein, they are used in a generic and descriptive sense only and not for purposes of limitation.
    • I. Overview
  • Methods and compositions are provided which employ a silencing element that, when ingested by a pest, such as a pest from the Lepidoptera order, is capable of decreasing the expression of a target sequence in the pest. In specific embodiments, the decrease in expression of the target sequence controls the pest and thereby the methods and compositions are capable of limiting damage to a plant or plant part. The present invention provides target polynucleotides which encode polypeptides from a variety of protein classes including, for example, a juvenile hormone polypeptide, a vacuolar polypeptide, a cadherin polypeptide, a cuticle polypeptide, a translation initiation factor, a SARI polypeptide, an elongation factor, a phosphooligosaccharide, a myosin polypeptide, a potassium channel amino acid transporter, a potassium inwardly rectifier polypeptide, an amino acid transporter, a tubulin polypeptide, a ubiquitin polypeptide, and small nuclear ribonucleoprotein. In other embodiments the target polynucleotides are set forth in SEQ ID NOS: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50 or active variants and fragments thereof. Silencing elements designed in view of these target polynucleotides are provided which, when ingested by the pest, decrease the expression of one or more of the target sequences and thereby controls the pest (i.e., has insecticidal activity). See, for example, SEQ ID NOS:51-465.
  • As used herein, by “controlling a pest” or “controls a pest” is intended any affect on a pest that results in limiting the damage that the pest causes. Controlling a pest includes, but is not limited to, killing the pest, inhibiting development of the pest, altering fertility or growth of the pest in such a manner that the pest provides less damage to the plant, decreasing the number of offspring produced, producing less fit pests, producing pests more susceptible to predator attack, or deterring the pests from eating the plant.
  • By “disease resistance” is intended that the plants avoid the disease symptoms that are the outcome of plant-pathogen interactions. That is, pathogens are prevented from causing plant diseases and the associated disease symptoms, or alternatively, the disease symptoms caused by the pathogen is minimized or lessened.
  • Reducing the level of expression of the target polynucleotide or the polypeptide encoded thereby, in the pest results in the suppression, control, and/or killing the invading pathogenic organism. Reducing the level of expression of the target sequence of the pest will reduce the disease symptoms resulting from pathogen challenge by at least about 2% to at least about 6%, at least about 5% to about 50%, at least about 10% to about 60%, at least about 30% to about 70%, at least about 40% to about 80%, or at least about 50% to about 90% or greater. Hence, the methods of the invention can be utilized to protect plants from disease, particularly those diseases that are caused by pests from the Lepidoptera order.
  • Assays that measure the control of a pest are commonly known in the art, as are methods to quantitate disease resistance in plants following pathogen infection. See, for example, U.S. Pat. No. 5,614,395, herein incorporated by reference. Such techniques include, measuring over time, the average lesion diameter, the pathogen biomass, and the overall percentage of decayed plant tissues. See, for example, Thomma et al. (1998) Plant Biology 95:15107-15111, herein incorporated by reference. See, also the examples below.
  • The invention is drawn to compositions and methods for protecting plants from a plant pest, such as pests from the Lepidoptera order or inducing resistance in a plant to a plant pest, such as pests from the Lepidoptera order. Caterpillars and related forms of lepidopteran insects comprise an important group of plant-feeding agricultural pests, especially during the larvae stage of growth. Feeding methods of Lepidoptera larvae typically include chewing plants or plant parts. As used herein, the term “Lepidoptera” is used to refer to any member of the Lepidoptera order. In particular embodiments, compositions and methods of the invention control Lepidoptera larvae (i.e. caterpillars). Accordingly, the compositions and methods are also useful in protecting plants against any Lepidoptera including, for example, Pieris rapae, Pectinophora gossypiella, Synanthedon exitiosa, Melittia cucurbitae, Cydia pomonella, Grapholita molesta, Ostrinia nubilalis, Plodia interpunctella, Galleria mellonella, Manduca sexta, Manduca quinquemaculata, Lymantria dispar, Euproctis chrysorrhoea, Trichoplusia ni, Mamestra brassicae, Agrotis ipsilon, Plutella xylostella, Anticarsia gemmatalis, Psuedoplusia includens, Epinotia aporema, Helicoverpa zea, Heliothis virescens, Heliothis armigera, Spodoptera exigua, Scirpophaga incertulus, Sesamia spp., Buseola fusca, Cnaphalocrocis medinalis, Chilo suppressalis, or Spodoptera littoralis. In particular embodiments, methods control Spodoptera frugiperda.
    • II. Target Sequences
  • As used herein, a “target sequence” or “target polynucleotide” comprises any sequence in the pest that one desires to reduce the level of expression. In specific embodiments, decreasing the level of the target sequence in the pest controls the pest. For instance, the target sequence can be essential for growth and development. While the target sequence can be expressed in any tissue of the pest, in specific embodiments of the invention, the sequences targeted for suppression in the pest are expressed in cells of the gut tissue of the pest, cells in the midgut of the pest, and cells lining the gut lumen or the midgut. Such target sequences can be involved in gut cell metabolism, growth or differentiation.
  • In one embodiment of the invention the target sequence comprises a polypeptide belonging to one or more classes of enzymes such as a juvenile hormone polypeptide, a vacuolar polypeptide, a cadherin polypeptide, a cuticle polypeptide, a translation initiation factor, a SARI polypeptide, an elongation factor, a phosphooligosaccharide, a myosin polypeptide, a potassium channel amino acid transporter, a potassium inwardly rectifier, an amino acid transporter, a tubulin polypeptide, a ubiquitin polypeptide, and a small nuclear ribonucleoprotein. Non-limiting examples of target sequences of the invention include a polynucleotide set forth in SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50. As exemplified elsewhere herein, decreasing the level of expression of these target sequence or members of the recited enzyme classes in Lepidoptera controls the pest.
    • III. Silencing Elements
  • By “silencing element” is intended a polynucleotide which when ingested by a pest, is capable of reducing or eliminating the level or expression of a target polynucleotide or the polypeptide encoded thereby. The silencing element employed can reduce or eliminate the expression level of the target sequence by influencing the level of the target RNA transcript or, alternatively, by influencing translation and thereby affecting the level of the encoded polypeptide. Methods to assay for functional silencing elements that are capable of reducing or eliminating the level of a sequence of interest are disclosed elsewhere herein. A single polynucleotide employed in the methods of the invention can comprises one or more silencing elements to the same or different target polynucleotides.
  • In specific embodiments, the target sequence is not a plant endogenous gene. In other embodiments, while the silencing element controls pests, preferably the silencing element has no effect on the normal plant or plant part.
  • As discussed in further detail below, silencing elements can include, but are not limited to, a sense suppression element, an antisense suppression element, a double stranded RNA, a miRNA, or a hairpin suppression element. Non-limiting examples of silencing elements that can be employed to decrease expression of these target Lepidoptera sequences comprise fragments and variants of the sense or antisense sequence or consists of the sense or antisense sequence of the sequence set forth in SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 54, 57, 60, 63, 66, 69, 72, 75, 78, 81, 84, 87, 90, 93, 96, 99, 102, 105, 108, 111, 114, 117, 120, 123, 126, 129, 132, 135, 138, 141, 144, 147, 150, 153, 156, 159, 162, 165, 168, 171, 174, 177, 180, 183, 186, 189, 192, 195, 198, 201, 204, 207, 210, 213, 216, 219, 222, 225, 228, 231, 234, 237, 240, 243, 246, 249, 252, 255, 258, 261, 264, 267, 270, 273, 276, 279, 282, 285, 288, 291, 294, 297, 300, 303, 306, 309, 312, 315, 318, 321, 324, 327, 330, 333, 336, 339, 342, 345, 348, 351, 354, 357, 360, 363, 366, 369, 372, 375, 378, 381, 384, 387, 390, 393, 396, 399, 402, 405, 408, 411, 415, 418, 421, 424, 427, 430, 433, 436, 439, 442, 457, 460, and/or 463 or a biologically active variant or fragment thereof. In specific embodiments, the silencing element comprises or consists of at least one of the sequences set forth in any one of SEQ ID NOS: 51-465. In further embodiments, the silencing elements can comprise at least one thymine residue at the 3′ end. This can aid in stabilization. Thus, the silencing elements can have at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more thymine residues at the 3′ end.
  • In further embodiments, the silencing element comprises SEQ ID NO: 52 and 53; 55 and 56; 58 and 59; 61 and 62; 64 and 65; 67 and 68; 70 and 71; 73 and 74; 76 and 77; 79 and 80; 82 and 83; 85 and 86; 88 and 89; 91 and 92; 94 and 95; 97 and 98; 100 and 101; 103 and 104; 106 and 107; 109 and 110; 112 and 113; 115 and 116; 118 and 119; 121 and 122; 124 and 125; 127 and 128; 130 and 131; 133 and 134; 136 and 137; 139 and 140; 142 and 143; 145 and 146; 148 and 149; 151 and 152; 154 and 155; 157 and 158; 160 and 161; 163 and 164; 166 and 167; 169 and 170; 172 and 173; 175 and 176; 178 and 179; 181 and 182; 184 and 185; 187 and 188; 190 and 191; 193 and 194; 196 and 197; 199 and 200; 202 and 203; 205 and 206; 208 and 209; 211 and 212; 214 and 215; 217 and 218; 220 and 221; 223 and 224; 226 and 227; 229 and 230; 232 and 233; 235 and 236; 238 and 239; 241 and 242; 244 and 245; 247 and 248; 250 and 251; 253 and 254; 256 and 257; 259 and 260; 262 and 263; 265 and 266; 268 and 269; 271 and 272; 274 and 275; 277 and 278; 280 and 281; 283 and 284; 286 and 287; 289 and 290; 292 and 293; 295 and 296; 298 and 299; 301 and 302; 304 and 305; 307 and 308; 310 and 311; 313 and 314; 316 and 317; 139 and 320; 322 and 323; 325 and 326; 328 and 329; 331 and 332; 334 and 335; 337 and 338; 340 and 341; 343 and 344; 346 and 347; 349 and 350; 352 and 353; 355 and 356; 358 and 359; 361 and 362; 364 and 365; 367 and 368; 370 and 371; 373 and 374; 376 and 377; 379 and 380; 382 and 383; 385 and 386; 388 and 389; 391 and 392; 394 and 395; 397 and 398; 400 and 401; 403 and 404; 406 and 407; 409 and 410; 412 and 413; 416 and 417; 419 and 420; 422 and 423; 425 and 426; 428 and 429; 431 and 432; 434 and 435; 437 and 438; 440 and 441; 443 and 444; 458 and 459; 461 and 462; and/or 464 and 465.
  • By “reduces” or “reducing” the expression level of a polynucleotide or a polypeptide encoded thereby is intended to mean, the polynucleotide or polypeptide level of the target sequence is statistically lower than the polynucleotide level or polypeptide level of the same target sequence in an appropriate control pest which is not exposed to (i.e., has not ingested) the silencing element. In particular embodiments of the invention, reducing the polynucleotide level and/or the polypeptide level of the target sequence in a pest according to the invention results in less than 95%, less than 90%, less than 80%, less than 70%, less than 60%, less than 50%, less than 40%, less than 30%, less than 20%, less than 10%, or less than 5% of the polynucleotide level, or the level of the polypeptide encoded thereby, of the same target sequence in an appropriate control pest. Methods to assay for the level of the RNA transcript, the level of the encoded polypeptide, or the activity of the polynucleotide or polypeptide are discussed elsewhere herein.
  • i. Sense Suppression Elements
  • As used herein, a “sense suppression element” comprises a polynucleotide designed to express an RNA molecule corresponding to at least a part of a target messenger RNA in the “sense” orientation. Expression of the RNA molecule comprising the sense suppression element reduces or eliminates the level of the target polynucleotide or the polypeptide encoded thereby. The polynucleotide comprising the sense suppression element may correspond to all or part of the sequence of the target polynucleotide, all or part of the 5′ and/or 3′ untranslated region of the target polynucleotide, all or part of the coding sequence of the target polynucleotide, or all or part of both the coding sequence and the untranslated regions of the target polynucleotide.
  • Typically, a sense suppression element has substantial sequence identity to the target polynucleotide, typically greater than about 65% sequence identity, greater than about 85% sequence identity, about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% sequence identity. See, U.S. Pat. Nos. 5,283,184 and 5,034,323; herein incorporated by reference. The sense suppression element can be any length so long as it allows for the suppression of the targeted sequence. The sense suppression element can be, for example, 15, 20, 22, 25, 30, 50, 100, 150, 200, 250, 300, 350, 400, 450, 500, 600, 700, 900 or longer.
  • ii. Antisense Suppression Elements
  • As used herein, an “antisense suppression element” comprises a polynucleotide which is designed to express an RNA molecule complementary to all or part of a target messenger RNA. Expression of the antisense RNA suppression element reduces or eliminates the level of the target polynucleotide. The polynucleotide for use in antisense suppression may correspond to all or part of the complement of the sequence encoding the target polynucleotide, all or part of the complement of the 5′ and/or 3′ untranslated region of the target polynucleotide, all or part of the complement of the coding sequence of the target polynucleotide, or all or part of the complement of both the coding sequence and the untranslated regions of the target polynucleotide. In addition, the antisense suppression element may be fully complementary (i.e., 100% identical to the complement of the target sequence) or partially complementary (i.e., less than 100% identical to the complement of the target sequence) to the target polynucleotide. In specific embodiments, the antisense suppression element comprises at least 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence complementarity to the target polynucleotide. Antisense suppression may be used to inhibit the expression of multiple proteins in the same plant. See, for example, U.S. Pat. No. 5,942,657. Furthermore, the antisense suppression element can be complementary to a portion of the target polynucleotide. Generally, sequences of at least 15, 20, 22, 25, 50, 100, 200, 300, 400, 450 nucleotides or greater may be used. Methods for using antisense suppression to inhibit the expression of endogenous genes in plants are described, for example, in Liu et al (2002) Plant Physiol. 129:1732-1743 and U.S. Pat. Nos. 5,759,829 and 5,942,657, each of which is herein incorporated by reference.
  • iii. Double Stranded RNA Suppression Element
  • A “double stranded RNA silencing element” or “dsRNA” comprises at least one transcript that is capable of forming a dsRNA either before or after ingestion by a pest. Thus, a “dsRNA silencing element” includes a dsRNA, a transcript or polyribonucleotide capable of forming a dsRNA or more than one transcript or polyribonucleotide capable of forming a dsRNA. “Double stranded RNA” or “dsRNA” refers to a polyribonucleotide structure formed either by a single self-complementary RNA molecule or a polyribonucleotide structure formed by the expression of least two distinct RNA strands. The dsRNA molecule(s) employed in the methods and compositions of the invention mediate the reduction of expression of a target sequence, for example, by mediating RNA interference “RNAi” or gene silencing in a sequence-specific manner. In the context of the present invention, the dsRNA is capable of reducing or eliminating the level or expression of a target polynucleotide or the polypeptide encoded thereby in a pest.
  • The dsRNA can reduce or eliminate the expression level of the target sequence by influencing the level of the target RNA transcript, by influencing translation and thereby affecting the level of the encoded polypeptide, or by influencing expression at the pre-transcriptional level (i.e., via the modulation of chromatin structure, methylation pattern, etc., to alter gene expression). See, for example, Verdel et al. (2004) Science 303:672-676; Pal-Bhadra et al. (2004) Science 303:669-672; Allshire (2002) Science 297:1818-1819; Volpe et al. (2002) Science 297:1833-1837; Jenuwein (2002) Science 297:2215-2218; and Hall et al. (2002) Science 297:2232-2237. Methods to assay for functional iRNA that are capable of reducing or eliminating the level of a sequence of interest are disclosed elsewhere herein. Accordingly, as used herein, the term “dsRNA” is meant to encompass other terms used to describe nucleic acid molecules that are capable of mediating RNA interference or gene silencing, including, for example, short-interfering RNA (siRNA), double-stranded RNA (dsRNA), micro-RNA (miRNA), hairpin RNA, short hairpin RNA (shRNA), post-transcriptional gene silencing RNA (ptgsRNA), and others.
  • In specific embodiments, at least one strand of the duplex or double-stranded region of the dsRNA shares sufficient sequence identity or sequence complementarity to the target polynucleotide to allow for the dsRNA to reduce the level of expression of the target sequence. As used herein, the strand that is complementary to the target polynucleotide is the “antisense strand” and the strand homologous to the target polynucleotide is the “sense strand.”
  • In one embodiment, the dsRNA comprises a hairpin RNA. A hairpin RNA comprises an RNA molecule that is capable of folding back onto itself to form a double stranded structure. Multiple structures can be employed as hairpin elements. In specific embodiments, the dsRNA suppression element comprises a hairpin element which comprises in the following order, a first segment, a second segment, and a third segment, where the first and the third segment share sufficient complementarity to allow the transcribed RNA to form a double-stranded stem-loop structure.
  • The “second segment” of the hairpin comprises a “loop” or a “loop region.” These terms are used synonymously herein and are to be construed broadly to comprise any nucleotide sequence that confers enough flexibility to allow self-pairing to occur between complementary regions of a polynucleotide (i.e., segments 1 and 3 which form the stem of the hairpin). For example, in some embodiments, the loop region may be substantially single stranded and act as a spacer between the self-complementary regions of the hairpin stem-loop. In some embodiments, the loop region can comprise a random or nonsense nucleotide sequence and thus not share sequence identity to a target polynucleotide. In other embodiments, the loop region comprises a sense or an antisense RNA sequence or fragment thereof that shares identity to a target polynucleotide. See, for example, International Patent Publication No. WO 02/00904, herein incorporated by reference. In specific embodiments, the loop region can be optimized to be as short as possible while still providing enough intramolecular flexibility to allow the formation of the base-paired stem region. Accordingly, the loop sequence is generally less than 1000, 900, 800, 700, 600, 500, 400, 300, 200, 100, 50, 25, 20, 15, 10 nucleotides or less.
  • The “first” and the “third” segment of the hairpin RNA molecule comprise the base-paired stem of the hairpin structure. The first and the third segments are inverted repeats of one another and share sufficient complementarity to allow the formation of the base-paired stem region. In specific embodiments, the first and the third segments are fully complementary to one another. Alternatively, the first and the third segment may be partially complementary to each other so long as they are capable of hybridizing to one another to form a base-paired stem region. The amount of complementarity between the first and the third segment can be calculated as a percentage of the entire segment. Thus, the first and the third segment of the hairpin RNA generally share at least 50%, 60%, 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, up to and including 100% complementarity.
  • The first and the third segment are at least about 1000, 500, 400, 300, 200, 100, 50, 40, 30, 25, 22, 20, 15 or 10 nucleotides in length. In specific embodiments, the length of the first and/or the third segment is about 10-100 nucleotides, about 10 to about 75 nucleotides, about 10 to about 50 nucleotides, about 10 to about 40 nucleotides, about 10 to about 35 nucleotides, about 10 to about 30 nucleotides, about 10 to about 25 nucleotides, about 10 to about 20 nucleotides. In other embodiments, the length of the first and/or the third segment comprises at least 10-20 nucleotides, 20-35 nucleotides, 30-45 nucleotides, 40-50 nucleotides, 50-100 nucleotides, or 100-300 nucleotides. See, for example, International Publication No. WO 0200904. In specific embodiments, the first and the third segment comprise at least 20 nucleotides having at least 85% complementary to the first segment. In still other embodiments, the first and the third segments which form the stem-loop structure of the hairpin comprises 3′ or 5′ overhang regions having unpaired nucleotide residues.
  • In specific embodiments, the sequences used in the first, the second, and/or the third segments comprise domains that are designed to have sufficient sequence identity to a target polynucleotide of interest and thereby have the ability to decrease the level of expression of the target polynucleotide. The specificity of the inhibitory RNA transcripts is therefore generally conferred by these domains of the silencing element. Thus, in some embodiments of the invention, the first, second and/or third segment of the silencing element comprise a domain having at least 10, at least 15, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 40, at least 50, at least 100, at least 200, at least 300, at least 500, at least 1000, or more than 1000 nucleotides that share sufficient sequence identity to the target polynucleotide to allow for a decrease in expression levels of the target polynucleotide when expressed in an appropriate cell. In other embodiments, the domain is between about 15 to 50 nucleotides, about 20-35 nucleotides, about 25-50 nucleotides, about 20 to 75 nucleotides, about 40-90 nucleotides about 15-100 nucleotides.
  • In specific embodiments, the domain of the first, the second, and/or the third segment has 100% sequence identity to the target polynucleotide. In other embodiments, the domain of the first, the second and/or the third segment having homology to the target polypeptide have at least 50%, 60%, 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or greater sequence identity to a region of the target polynucleotide. The sequence identity of the domains of the first, the second and/or the third segments to the target polynucleotide need only be sufficient to decrease expression of the target polynucleotide of interest. See, for example, Chuang and Meyerowitz (2000) Proc. Natl. Acad. Sci. USA 97:4985-4990; Stoutjesdijk et al. (2002) Plant Physiol. 129:1723-1731; Waterhouse and Helliwell (2003) Nat. Rev. Genet. 4:29-38; Pandolfini et al. BMC Biotechnology 3:7, and U.S. Patent Publication No. 20030175965; each of which is herein incorporated by reference. A transient assay for the efficiency of hpRNA constructs to silence gene expression in vivo has been described by Panstruga et al. (2003) Mol. Biol. Rep. 30:135-140, herein incorporated by reference.
  • The amount of complementarity shared between the first, second, and/or third segment and the target polynucleotide or the amount of complementarity shared between the first segment and the third segment (i.e., the stem of the hairpin structure) may vary depending on the organism in which gene expression is to be controlled. Some organisms or cell types may require exact pairing or 100% identity, while other organisms or cell types may tolerate some mismatching. In some cells, for example, a single nucleotide mismatch in the targeting sequence abrogates the ability to suppress gene expression. In these cells, the suppression cassettes of the invention can be used to target the suppression of mutant genes, for example, oncogenes whose transcripts comprise point mutations and therefore they can be specifically targeted using the methods and compositions of the invention without altering the expression of the remaining wild-type allele.
  • Any region of the target polynucleotide can be used to design the domain of the silencing element that shares sufficient sequence identity to allow expression of the hairpin transcript to decrease the level of the target polynucleotide. For instance, the domain can be designed to share sequence identity to the 5′ untranslated region of the target polynucleotide(s), the 3′ untranslated region of the target polynucleotide(s), exonic regions of the target polynucleotide(s), intronic regions of the target polynucleotide(s), and any combination thereof. In specific embodiments a domain of the silencing element shares sufficient homology to at least about 15, 20, 22, 25 or 30 consecutive nucleotides from about nucleotides 1-50, 50-100, 100-150, 150-200, 200-250, 250-300, 300-350, 350-400, 400-450, 450-500, 550-600, 600-650, 650-700, 750-800, 850-900, 950-1000, 1000-1050, 1050-1100, 1100-1200, 1200-1300, 1300-1400, 1400-1500, 1500-1600, 1600-1700, 1700-1800, 1800-1900, 1900-2000 of the target sequence. In some instances to optimize the siRNA sequences employed in the hairpin, the synthetic oligodeoxyribonucleotide/RNAse H method can be used to determine sites on the target mRNA that are in a conformation that is susceptible to RNA silencing. See, for example, Vickers et al. (2003) J. Biol. Chem 278:7108-7118 and Yang et al. (2002) Proc. Natl. Acad. Sci. USA 99:9442-9447, herein incorporated by reference. These studies indicate that there is a significant correlation between the RNase-H-sensitive sites and sites that promote efficient siRNA-directed mRNA degradation.
  • The hairpin silencing element may also be designed such that the sense sequence or the antisense sequence do not correspond to a target polynucleotide. In this embodiment, the sense and antisense sequence flank a loop sequence that comprises a nucleotide sequence corresponding to all or part of the target polynucleotide. Thus, it is the loop region that determines the specificity of the RNA interference. See, for example, WO 02/00904, herein incorporated by reference.
  • In specific embodiments, the silencing element comprising the hairpin comprises sequences selected from the group consisting of SEQ ID NO: 52 and 53; 55 and 56; 58 and 59; 61 and 62; 64 and 65; 67 and 68; 70 and 71; 73 and 74; 76 and 77; 79 and 80; 82 and 83; 85 and 86; 88 and 89; 91 and 92; 94 and 95; 97 and 98; 100 and 101; 103 and 104; 106 and 107; 109 and 110; 112 and 113; 115 and 116; 118 and 119; 121 and 122; 124 and 125; 127 and 128; 130 and 131; 133 and 134; 136 and 137; 139 and 140; 142 and 143; 145 and 146; 148 and 149; 151 and 152; 154 and 155; 157 and 158; 160 and 161; 163 and 164; 166 and 167; 169 and 170; 172 and 173; 175 and 176; 178 and 179; 181 and 182; 184 and 185; 187 and 188; 190 and 191; 193 and 194; 196 and 197; 199 and 200; 202 and 203; 205 and 206; 208 and 209; 211 and 212; 214 and 215; 217 and 218; 220 and 221; 223 and 224; 226 and 227; 229 and 230; 232 and 233; 235 and 236; 238 and 239; 241 and 242; 244 and 245; 247 and 248; 250 and 251; 253 and 254; 256 and 257; 259 and 260; 262 and 263; 265 and 266; 268 and 269; 271 and 272; 274 and 275; 277 and 278; 280 and 281; 283 and 284; 286 and 287; 289 and 290; 292 and 293; 295 and 296; 298 and 299; 301 and 302; 304 and 305; 307 and 308; 310 and 311; 313 and 314; 316 and 317; 139 and 320; 322 and 323; 325 and 326; 328 and 329; 331 and 332; 334 and 335; 337 and 338; 340 and 341; 343 and 344; 346 and 347; 349 and 350; 352 and 353; 355 and 356; 358 and 359; 361 and 362; 364 and 365; 367 and 368; 370 and 371; 373 and 374; 376 and 377; 379 and 380; 382 and 383; 385 and 386; 388 and 389; 391 and 392; 394 and 395; 397 and 398; 400 and 401; 403 and 404; 406 and 407; 409 and 410; 412 and 413; 416 and 417; 419 and 420; 422 and 423; 425 and 426; 428 and 429; 431 and 432; 434 and 435; 437 and 438; 440 and 441; 443 and 444; 458 and 459; 461 and 462; and/or 464 and 465.
  • In addition, transcriptional gene silencing (TGS) may be accomplished through use of a hairpin suppression element where the inverted repeat of the hairpin shares sequence identity with the promoter region of a target polynucleotide to be silenced. See, for example, Aufsatz et al. (2002) PNAS 99 (Suppl. 4):16499-16506 and Mette et al. (2000) EMBO J 19(19):5194-5201.
  • In other embodiments, the dsRNA can comprise a small RNA (sRNA). sRNAs can comprise both micro RNA (miRNA) and short-interfering RNA (siRNA) (Meister and Tuschl (2004) Nature 431:343-349 and Bonetta et al. (2004) Nature Methods 1:79-86). miRNAs are regulatory agents comprising about 19 ribonucleotides which are highly efficient at inhibiting the expression of target polynucleotides. See, for example Javier et al. (2003) Nature 425: 257-263, herein incorporated by reference. For miRNA interference, the silencing element can be designed to express a dsRNA molecule that forms a hairpin structure containing a 19-nucleotide sequence that is complementary to the target polynucleotide of interest. The miRNA can be synthetically made, or transcribed as a longer RNA which is subsequently cleaved to produce the active miRNA. Specifically, the miRNA can comprise 19 nucleotides of the sequence having homology to a target polynucleotide in sense orientation and 19 nucleotides of a corresponding antisense sequence that is complementary to the sense sequence.
  • When expressing an miRNA, it is recognized that various forms of an miRNA can be transcribed including, for example, the primary transcript (termed the “pri-miRNA”) which is processed through various nucleolytic steps to a shorter precursor miRNA (termed the “pre-miRNA”); the pre-miRNA; or the final (mature) miRNA is present in a duplex, the two strands being referred to as the miRNA (the strand that will eventually basepair with the target) and miRNA*. The pre-miRNA is a substrate for a form of dicer that removes the miRNA/miRNA* duplex from the precursor, after which, similarly to siRNAs, the duplex can be taken into the RISC complex. It has been demonstrated that miRNAs can be transgenically expressed and be effective through expression of a precursor form, rather than the entire primary form (Parizotto et al. (2004) Genes & Development 18:2237-2242 and Guo et al. (2005) Plant Cell 17:1376-1386).
  • The methods and compositions of the invention employ silencing elements that when transcribed “form” a dsRNA molecule. Accordingly, the heterologous polynucleotide being expressed need not form the dsRNA by itself, but can interact with other sequences in the plant cell or in the pest gut after ingestion to allow the formation of the dsRNA. For example, a chimeric polynucleotide that can selectively silence the target polynucleotide can be generated by expressing a chimeric construct comprising the target sequence for a miRNA or siRNA to a sequence corresponding to all or part of the gene or genes to be silenced. In this embodiment, the dsRNA is “formed” when the target for the miRNA or siRNA interacts with the miRNA present in the cell. The resulting dsRNA can then reduce the level of expression of the gene or genes to be silenced. See, for example, U.S. Provisional Application No. 60/691,613, filed Jun. 17, 2005, entitled “Methods and Compositions for Gene Silencing, herein incorporated by reference. The construct can be designed to have a target for an endogenous miRNA or alternatively, a target for a heterologous and/or synthetic miRNA can be employed in the construct. If a heterologous and/or synthetic miRNA is employed, it can be introduced into the cell on the same nucleotide construct as the chimeric polynucleotide or on a separate construct. As discussed elsewhere herein, any method can be used to introduce the construct comprising the heterologous miRNA.
    • IV. Variants and Fragments
  • By “fragment” is intended a portion of the polynucleotide or a portion of the amino acid sequence and hence protein encoded thereby. Fragments of a polynucleotide may encode protein fragments that retain the biological activity of the native protein. Alternatively, fragments of a polynucleotide that are useful as a silencing element do not need to encode fragment proteins that retain biological activity. Thus, fragments of a nucleotide sequence may range from at least about 10, about 15, about 20 nucleotides, about 22 nucleotides, about 50 nucleotides, about 75 nucleotides, about 100 nucleotides, 200 nucleotides, 300 nucleotides, 400 nucleotides, 500 nucleotides, 600 nucleotides, 700 nucleotides and up to the full-length polynucleotide employed in the invention. Methods to assay for the activity of a desired silencing element or a suppressor enhancer element are described elsewhere herein.
  • “Variants” is intended to mean substantially similar sequences. For polynucleotides, a variant comprises a deletion and/or addition of one or more nucleotides at one or more internal sites within the native polynucleotide and/or a substitution of one or more nucleotides at one or more sites in the native polynucleotide. As used herein, a “native” polynucleotide or polypeptide comprises a naturally occurring nucleotide sequence or amino acid sequence, respectively. For polynucleotides, conservative variants include those sequences that, because of the degeneracy of the genetic code, encode the amino acid sequence of one of the polypeptides employed in the invention. Variant polynucleotides also include synthetically derived polynucleotide, such as those generated, for example, by using site-directed mutagenesis, but continue to retain the desired activity. Generally, variants of a particular polynucleotide of the invention (i.e., a silencing element) will have at least about 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to that particular polynucleotide as determined by sequence alignment programs and parameters described elsewhere herein.
  • Variants of a particular polynucleotide of the invention (i.e., the reference polynucleotide) can also be evaluated by comparison of the percent sequence identity between the polypeptide encoded by a variant polynucleotide and the polypeptide encoded by the reference polynucleotide. Percent sequence identity between any two polypeptides can be calculated using sequence alignment programs and parameters described elsewhere herein. Where any given pair of polynucleotides employed in the invention is evaluated by comparison of the percent sequence identity shared by the two polypeptides they encode, the percent sequence identity between the two encoded polypeptides is at least about 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity.
  • “Variant” protein is intended to mean a protein derived from the native protein by deletion or addition of one or more amino acids at one or more internal sites in the native protein and/or substitution of one or more amino acids at one or more sites in the native protein. Variant proteins encompassed by the present invention are biologically active, that is they continue to possess the desired biological activity of the native protein, as discussed elsewhere herein. Such variants may result from, for example, genetic polymorphism or from human manipulation. Biologically active variants of a native protein will have at least about 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to the amino acid sequence for the native protein as determined by sequence alignment programs and parameters described elsewhere herein. A biologically active variant of a protein of the invention may differ from that protein by as few as 1-15 amino acid residues, as few as 1-10, such as 6-10, as few as 5, as few as 4, 3, 2, or even 1 amino acid residue.
  • The following terms are used to describe the sequence relationships between two or more polynucleotides or polypeptides: (a) “reference sequence”, (b) “comparison window”, (c) “sequence identity”, and, (d) “percentage of sequence identity.”
  • (a) As used herein, “reference sequence” is a defined sequence used as a basis for sequence comparison. A reference sequence may be a subset or the entirety of a specified sequence; for example, as a segment of a full-length cDNA or gene sequence, or the complete cDNA or gene sequence.
  • (b) As used herein, “comparison window” makes reference to a contiguous and specified segment of a polynucleotide sequence, wherein the polynucleotide sequence in the comparison window may comprise additions or deletions (i.e., gaps) compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two polynucleotides. Generally, the comparison window is at least 20 contiguous nucleotides in length, and optionally can be 30, 40, 50, 100, or longer. Those of skill in the art understand that to avoid a high similarity to a reference sequence due to inclusion of gaps in the polynucleotide sequence a gap penalty is typically introduced and is subtracted from the number of matches.
  • Unless otherwise stated, sequence identity/similarity values provided herein refer to the value obtained using GAP Version 10 using the following parameters: % identity and % similarity for a nucleotide sequence using GAP Weight of 50 and Length Weight of 3, and the nwsgapdna.cmp scoring matrix; % identity and % similarity for an amino acid sequence using GAP Weight of 8 and Length Weight of 2, and the BLOSUM62 scoring matrix; or any equivalent program thereof. By “equivalent program” is intended any sequence comparison program that, for any two sequences in question, generates an alignment having identical nucleotide or amino acid residue matches and an identical percent sequence identity when compared to the corresponding alignment generated by GAP Version 10.
  • (c) As used herein, “sequence identity” or “identity” in the context of two polynucleotides or polypeptide sequences makes reference to the residues in the two sequences that are the same when aligned for maximum correspondence over a specified comparison window. When percentage of sequence identity is used in reference to proteins it is recognized that residue positions which are not identical often differ by conservative amino acid substitutions, where amino acid residues are substituted for other amino acid residues with similar chemical properties (e.g., charge or hydrophobicity) and therefore do not change the functional properties of the molecule. When sequences differ in conservative substitutions, the percent sequence identity may be adjusted upwards to correct for the conservative nature of the substitution. Sequences that differ by such conservative substitutions are said to have “sequence similarity” or “similarity”. Means for making this adjustment are well known to those of skill in the art. Typically this involves scoring a conservative substitution as a partial rather than a full mismatch, thereby increasing the percentage sequence identity. Thus, for example, where an identical amino acid is given a score of 1 and a non-conservative substitution is given a score of zero, a conservative substitution is given a score between zero and 1. The scoring of conservative substitutions is calculated, e.g., as implemented in the program PC/GENE (Intelligenetics, Mountain View, Calif.).
  • (d) As used herein, “percentage of sequence identity” means the value determined by comparing two optimally aligned sequences over a comparison window, wherein the portion of the polynucleotide sequence in the comparison window may comprise additions or deletions (i.e., gaps) as compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences. The percentage is calculated by determining the number of positions at which the identical nucleic acid base or amino acid residue occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison, and multiplying the result by 100 to yield the percentage of sequence identity.
    • V. DNA Constructs
  • The use of the term “polynucleotide” is not intended to limit the present invention to polynucleotides comprising DNA. Those of ordinary skill in the art will recognize that polynucleotides can comprise ribonucleotides and combinations of ribonucleotides and deoxyribonucleotides. Such deoxyribonucleotides and ribonucleotides include both naturally occurring molecules and synthetic analogues. The polynucleotides of the invention also encompass all forms of sequences including, but not limited to, single-stranded forms, double-stranded forms, hairpins, stem-and-loop structures, and the like.
  • The polynucleotide encoding the silencing element or in specific embodiments employed in the methods and compositions of the invention can be provided in expression cassettes for expression in a plant or organism of interest. It is recognized that multiple silencing elements including multiple identical silencing elements, multiple silencing elements targeting different regions of the target sequence, or multiple silencing elements from different target sequences can be used. In this embodiment, it is recognized that each silencing element can be contained in a single or separate cassette, DNA construct, or vector. As discussed, any means of providing the silencing element is contemplated. A plant or plant cell can be transformed with a single cassette comprising DNA encoding one or more silencing elements or separate cassettes comprising each silencing element can be used to transform a plant or plant cell or host cell. Likewise, a plant transformed with one component can be subsequently transformed with the second component. One or more silencing elements can also be brought together by sexual crossing. That is, a first plant comprising one component is crossed with a second plant comprising the second component. Progeny plants from the cross will comprise both components.
  • The expression cassette can include 5′ and 3′ regulatory sequences operably linked to the polynucleotide of the invention. “Operably linked” is intended to mean a functional linkage between two or more elements. For example, an operable linkage between a polynucleotide of the invention and a regulatory sequence (i.e., a promoter) is a functional link that allows for expression of the polynucleotide of the invention. Operably linked elements may be contiguous or non-contiguous. When used to refer to the joining of two protein coding regions, by operably linked is intended that the coding regions are in the same reading frame. The cassette may additionally contain at least one additional polynucleotide to be cotransformed into the organism. Alternatively, the additional polypeptide(s) can be provided on multiple expression cassettes. Expression cassettes can be provided with a plurality of restriction sites and/or recombination sites for insertion of the polynucleotide to be under the transcriptional regulation of the regulatory regions. The expression cassette may additionally contain selectable marker genes.
  • The expression cassette will include in the 5′-3′ direction of transcription, a transcriptional and translational initiation region (i.e., a promoter), a polynucleotide comprising the silencing element employed in the methods and compositions of the invention, and a transcriptional and translational termination region (i.e., termination region) functional in plants. The regulatory regions (i.e., promoters, transcriptional regulatory regions, and translational termination regions) and/or the polynucleotides employed in the invention may be native/analogous to the host cell or to each other. Alternatively, the regulatory regions and/or the polynucleotide employed in the invention may be heterologous to the host cell or to each other. As used herein, “heterologous” in reference to a sequence is a sequence that originates from a foreign species, or, if from the same species, is substantially modified from its native form in composition and/or genomic locus by deliberate human intervention. For example, a promoter operably linked to a heterologous polynucleotide is from a species different from the species from which the polynucleotide was derived, or, if from the same/analogous species, one or both are substantially modified from their original form and/or genomic locus, or the promoter is not the native promoter for the operably linked polynucleotide. As used herein, a chimeric gene comprises a coding sequence operably linked to a transcription initiation region that is heterologous to the coding sequence.
  • The termination region may be native with the transcriptional initiation region, may be native with the operably linked polynucleotide encoding the silencing element, may be native with the plant host, or may be derived from another source (i.e., foreign or heterologous) to the promoter, the polynucleotide comprising silencing element, the plant host, or any combination thereof. Convenient termination regions are available from the Ti-plasmid of A. tumefaciens, such as the octopine synthase and nopaline synthase termination regions. See also Guerineau et al. (1991) Mol. Gen. Genet. 262:141-144; Proudfoot (1991) Cell 64:671-674; Sanfacon et al. (1991) Genes Dev. 5:141-149; Mogen et al. (1990) Plant Cell 2:1261-1272; Munroe et al. (1990) Gene 91:151-158; Ballas et al. (1989) Nucleic Acids Res. 17:7891-7903; and Joshi et al. (1987) Nucleic Acids Res. 15:9627-9639.
  • Additional sequence modifications are known to enhance gene expression in a cellular host. These include elimination of sequences encoding spurious polyadenylation signals, exon-intron splice site signals, transposon-like repeats, and other such well-characterized sequences that may be deleterious to gene expression. The G-C content of the sequence may be adjusted to levels average for a given cellular host, as calculated by reference to known genes expressed in the host cell. When possible, the sequence is modified to avoid predicted hairpin secondary mRNA structures.
  • In preparing the expression cassette, the various DNA fragments may be manipulated, so as to provide for the DNA sequences in the proper orientation and, as appropriate, in the proper reading frame. Toward this end, adapters or linkers may be employed to join the DNA fragments or other manipulations may be involved to provide for convenient restriction sites, removal of superfluous DNA, removal of restriction sites, or the like. For this purpose, in vitro mutagenesis, primer repair, restriction, annealing, resubstitutions, e.g., transitions and transversions, may be involved.
  • A number of promoters can be used in the practice of the invention. The polynucleotide encoding the silencing element can be combined with constitutive, tissue-preferred, or other promoters for expression in plants.
  • Such constitutive promoters include, for example, the core promoter of the Rsyn7 promoter and other constitutive promoters disclosed in WO 99/43838 and U.S. Pat. No. 6,072,050; the core CaMV 35S promoter (Odell et al. (1985) Nature 313:810-812); rice actin (McElroy et al. (1990) Plant Cell 2:163-171); ubiquitin (Christensen et al. (1989) Plant Mol. Biol. 12:619-632 and Christensen et al. (1992) Plant Mol. Biol. 18:675-689); pEMU (Last et al. (1991) Theor. Appl. Genet. 81:581-588); MAS (Velten et al. (1984) EMBO J. 3:2723-2730); ALS promoter (U.S. Pat. No. 5,659,026), and the like. Other constitutive promoters include, for example, U.S. Pat. Nos. 5,608,149; 5,608,144; 5,604,121; 5,569,597; 5,466,785; 5,399,680; 5,268,463; 5,608,142; and 6,177,611.
  • An inducible promoter, for instance, a pathogen-inducible promoter could also be employed. Such promoters include those from pathogenesis-related proteins (PR proteins), which are induced following infection by a pathogen; e.g., PR proteins, SAR proteins, beta-1,3-glucanase, chitinase, etc. See, for example, Redolfi et al. (1983) Neth. J. Plant Pathol. 89:245-254; Uknes et al. (1992) Plant Cell 4:645-656; and Van Loon (1985) Plant Mol. Virol. 4:111-116. See also WO 99/43819, herein incorporated by reference.
  • Of interest are promoters that are expressed locally at or near the site of pathogen infection. See, for example, Marineau et al. (1987) Plant Mol. Biol. 9:335-342; Matton et al. (1989) Molecular Plant-Microbe Interactions 2:325-331; Somsisch et al. (1986) Proc. Natl. Acad. Sci. USA 83:2427-2430; Somsisch et al. (1988) Mol. Gen. Genet. 2:93-98; and Yang (1996) Proc. Natl. Acad. Sci. USA 93:14972-14977. See also, Chen et al. (1996) Plant J. 10:955-966; Zhang et al. (1994) Proc. Natl. Acad. Sci. USA 91:2507-2511; Warner et al. (1993) Plant J. 3:191-201; Siebertz et al. (1989) Plant Cell 1:961-968; U.S. Pat. No. 5,750,386 (nematode-inducible); and the references cited therein. Of particular interest is the inducible promoter for the maize PRms gene, whose expression is induced by the pathogen Fusarium moniliforme (see, for example, Cordero et al. (1992) Physiol. Mol. Plant Path. 41:189-200).
  • Additionally, as pathogens find entry into plants through wounds or insect damage, a wound-inducible promoter may be used in the constructions of the invention. Such wound-inducible promoters include potato proteinase inhibitor (pin II) gene (Ryan (1990) Ann. Rev. Phytopath. 28:425-449; Duan et al. (1996) Nature Biotechnology 14:494-498); wun1 and wun2, U.S. Pat. No. 5,428,148; win1 and win2 (Stanford et al. (1989) Mol. Gen. Genet. 215:200-208); systemin (McGurl et al. (1992) Science 225:1570-1573); WIP1 (Rohmeier et al. (1993) Plant Mol. Biol. 22:783-792; Eckelkamp et al. (1993) FEBS Letters 323:73-76); MPI gene (Corderok et al. (1994) Plant J. 6(2):141-150); and the like, herein incorporated by reference.
  • Chemical-regulated promoters can be used to modulate the expression of a gene in a plant through the application of an exogenous chemical regulator. Depending upon the objective, the promoter may be a chemical-inducible promoter, where application of the chemical induces gene expression, or a chemical-repressible promoter, where application of the chemical represses gene expression. Chemical-inducible promoters are known in the art and include, but are not limited to, the maize In2-2 promoter, which is activated by benzenesulfonamide herbicide safeners, the maize GST promoter, which is activated by hydrophobic electrophilic compounds that are used as pre-emergent herbicides, and the tobacco PR-la promoter, which is activated by salicylic acid. Other chemical-regulated promoters of interest include steroid-responsive promoters (see, for example, the glucocorticoid-inducible promoter in Schena et al. (1991) Proc. Natl. Acad. Sci. USA 88:10421-10425 and McNellis et al. (1998) Plant J. 14(2):247-257) and tetracycline-inducible and tetracycline-repressible promoters (see, for example, Gatz et al. (1991) Mol. Gen. Genet. 227:229-237, and U.S. Pat. Nos. 5,814,618 and 5,789,156), herein incorporated by reference.
  • Tissue-preferred promoters can be utilized to target enhanced expression within a particular plant tissue. Tissue-preferred promoters include Yamamoto et al. (1997) Plant J. 12(2):255-265; Kawamata et al. (1997) Plant Cell Physiol. 38(7):792-803; Hansen et al. (1997) Mol. Gen Genet. 254(3):337-343; Russell et al. (1997) Transgenic Res. 6(2):157-168; Rinehart et al. (1996) Plant Physiol. 112(3):1331-1341; Van Camp et al. (1996) Plant Physiol. 112(2):525-535; Canevascini et al. (1996) Plant Physiol. 112(2):513-524; Yamamoto et al. (1994) Plant Cell Physiol. 35(5):773-778; Lam (1994) Results Probl. Cell Differ. 20:181-196; Orozco et al. (1993) Plant Mol Biol. 23(6):1129-1138; Matsuoka et al. (1993) Proc Natl. Acad. Sci. USA 90(20):9586-9590; and Guevara-Garcia et al. (1993) Plant J. 4(3):495-505. Such promoters can be modified, if necessary, for weak expression.
  • Leaf-preferred promoters are known in the art. See, for example, Yamamoto et al. (1997) Plant J. 12(2):255-265; Kwon et al. (1994) Plant Physiol. 105:357-67; Yamamoto et al. (1994) Plant Cell Physiol. 35(5):773-778; Gotor et al. (1993) Plant J. 3:509-18; Orozco et al. (1993) Plant Mol. Biol. 23(6):1129-1138; and Matsuoka et al. (1993) Proc. Natl. Acad. Sci. USA 90(20):9586-9590.
  • Root-preferred promoters are known and can be selected from the many available from the literature or isolated de novo from various compatible species. See, for example, Hire et al. (1992) Plant Mol. Biol. 20(2):207-218 (soybean root-specific glutamine synthetase gene); Keller and Baumgartner (1991) Plant Cell 3(10):1051-1061 (root-specific control element in the GRP 1.8 gene of French bean); Sanger et al. (1990) Plant Mol. Biol. 14(3):433-443 (root-specific promoter of the mannopine synthase (MAS) gene of Agrobacterium tumefaciens); and Miao et al. (1991) Plant Cell 3(1):11-22 (full-length cDNA clone encoding cytosolic glutamine synthetase (GS), which is expressed in roots and root nodules of soybean). See also Bogusz et al. (1990) Plant Cell 2(7):633-641, where two root-specific promoters isolated from hemoglobin genes from the nitrogen-fixing nonlegume Parasponia andersonii and the related non-nitrogen-fixing nonlegume Trema tomentosa are described. The promoters of these genes were linked to a β-glucuronidase reporter gene and introduced into both the nonlegume Nicotiana tabacum and the legume Lotus corniculatus, and in both instances root-specific promoter activity was preserved. Leach and Aoyagi (1991) describe their analysis of the promoters of the highly expressed rolC and rolD root-inducing genes of Agrobacterium rhizogenes (see Plant Science (Limerick) 79(1):69-76). They concluded that enhancer and tissue-preferred DNA determinants are dissociated in those promoters. Teeri et al. (1989) used gene fusion to lacZ to show that the Agrobacterium T-DNA gene encoding octopine synthase is especially active in the epidermis of the root tip and that the TR2′ gene is root specific in the intact plant and stimulated by wounding in leaf tissue, an especially desirable combination of characteristics for use with an insecticidal or larvicidal gene (see EMBO J. 8(2):343-350). The TR1′ gene, fused to nptll (neomycin phosphotransferase II) showed similar characteristics. Additional root-preferred promoters include the VfENOD-GRP3 gene promoter (Kuster et al. (1995) Plant Mol. Biol. 29(4):759-772); and rolB promoter (Capana et al. (1994) Plant Mol. Biol. 25(4):681-691. See also U.S. Pat. Nos. 5,837,876; 5,750,386; 5,633,363; 5,459,252; 5,401,836; 5,110,732; and 5,023,179.
  • In one embodiment of this invention the plant-expressed promoter is a vascular-specific promoter such as a phloem-specific promoter. A “vascular-specific” promoter, as used herein, is a promoter which is at least expressed in vascular cells, or a promoter which is preferentially expressed in vascular cells. Expression of a vascular-specific promoter need not be exclusively in vascular cells, expression in other cell types or tissues is possible. A “phloem-specific promoter” as used herein, is a plant-expressible promoter which is at least expressed in phloem cells, or a promoter which is preferentially expressed in phloem cells.
  • Expression of a phloem-specific promoter need not be exclusively in phloem cells, expression in other cell types or tissues, e.g., xylem tissue, is possible. In one embodiment of this invention, a phloem-specific promoter is a plant-expressible promoter at least expressed in phloem cells, wherein the expression in non-phloem cells is more limited (or absent) compared to the expression in phloem cells. Examples of suitable vascular-specific or phloem-specific promoters in accordance with this invention include but are not limited to the promoters selected from the group consisting of: the SCSV3, SCSV4, SCSV5, and SCSV7 promoters (Schunmann et al. (2003) Plant Functional Biology 30:453-60; the rolC gene promoter of Agrobacterium rhizogenes(Kiyokawa et al. (1994) Plant Physiology 104:801-02; Pandolfini et al. (2003) BioMedCentral (BMC) Biotechnology 3:7, (www.biomedcentral.com/1472-6750/3/7); Graham et al. (1997) Plant Mol. Biol. 33:729-35; Guivarc'h et al. (1996); Almon et al. (1997) Plant Physiol. 115:1599-607; the rolA gene promoter of Agrobacterium rhizogenes (Dehio et al. (1993) Plant Mol. Biol. 23:1199-210); the promoter of the Agrobacterium tumefaciens T-DNA gene 5 (Korber et al. (1991) EMBO J. 10:3983-91); the rice sucrose synthase RSs1 gene promoter (Shi et al. (1994) J. Exp. Bot. 45:623-31); the CoYMV or Commelina yellow mottle badnavirus promoter (Medberry et al. (1992) Plant Cell 4:185-92; Zhou et al. (1998) Chin. J. Biotechnol. 14:9-16); the CFDV or coconut foliar decay virus promoter (Rohde et al. (1994) Plant Mol. Biol. 27:623-28; Hehn and Rhode (1998) J. Gen. Virol. 79:1495-99); the RTBV or rice tungro bacilliform virus promoter (Yin and Beachy (1995) Plant J. 7:969-80; Yin et al. (1997) Plant J. 12:1179-80); the pea glutamin synthase GS3A gene (Edwards et al. (1990) Proc. Natl. Acad. Sci. USA 87:3459-63; Brears et al. (1991) Plant J. 1:235-44); the inv CD111 and inv CD141 promoters of the potato invertase genes (Hedley et al. (2000) J. Exp. Botany 51:817-21); the promoter isolated from Arabidopsis shown to have phloem-specific expression in tobacco by Kertbundit et al. (1991) Proc. Natl. Acad. Sci. USA 88:5212-16); the VAHOX1 promoter region (Tornero et al. (1996) Plant J. 9:639-48); the pea cell wall invertase gene promoter (Zhang et al. (1996) Plant Physiol. 112:1111-17); the promoter of the endogenous cotton protein related to chitinase of US published patent application 20030106097, an acid invertase gene promoter from carrot (Ramloch-Lorenz et al. (1993) The Plant J. 4:545-54); the promoter of the sulfate transporter geneSultrl; 3 (Yoshimoto et al. (2003) Plant Physiol. 131:1511-17); a promoter of a sucrose synthase gene (Nolte and Koch (1993) Plant Physiol. 101:899-905); and the promoter of a tobacco sucrose transporter gene (Kuhn et al. (1997) Science 275-1298-1300).
  • Possible promoters also include the Black Cherry promoter for Prunasin Hydrolase (PH DL1.4 PRO) (U.S. Pat. No. 6,797,859), Thioredoxin H promoter from cucumber and rice (Fukuda A et al. (2005). Plant Cell Physiol. 46(11):1779-86), Rice (RSs1) (Shi, T. Wang et al. (1994). J. Exp. Bot. 45(274): 623-631) and maize sucrose synthese-1 promoters (Yang., N-S. et al. (1990) PNAS 87:4144-4148), PP2 promoter from pumpkin Guo, H. et al. (2004) Transgenic Research 13:559-566), At SUC2 promoter (Truernit, E. et al. (1995) Planta 196(3):564-70. At SAM-1 (S-adenosylmethionine synthetase) (Mijnsbrugge KV. et al. (1996) Planr. Cell. Physiol. 37(8): 1108-1115), and the Rice tungro bacilliform virus (RTBV) promoter (Bhattacharyya-Pakrasi et al. (1993) Plant J. 4(1):71-79).
  • The expression cassette can also comprise a selectable marker gene for the selection of transformed cells. Selectable marker genes are utilized for the selection of transformed cells or tissues. Marker genes include genes encoding antibiotic resistance, such as those encoding neomycin phosphotransferase II (NEO) and hygromycin phosphotransferase (HPT), as well as genes conferring resistance to herbicidal compounds, such as glufosinate ammonium, bromoxynil, imidazolinones, and 2,4-dichlorophenoxyacetate (2,4-D). Additional selectable markers include phenotypic markers such as β-galactosidase and fluorescent proteins such as green fluorescent protein (GFP) (Su et al. (2004) Biotechnol Bioeng 85:610-9 and Fetter et al. (2004) Plant Cell/6:215-28), cyan florescent protein (CYP) (Bolte et al. (2004) J. Cell Science 117:943-54 and Kato et al. (2002) Plant Physiol 129:913-42), and yellow florescent protein (PhiYFP™ from Evrogen, see, Bolte et al. (2004) J. Cell Science 117:943-54). For additional selectable markers, see generally, Yarranton (1992) Curr. Opin. Biotech. 3:506-511; Christopherson et al. (1992) Proc. Natl. Acad. Sci. USA 89:6314-6318; Yao et al. (1992) Cell 71:63-72; Reznikoff (1992) Mol. Microbiol. 6:2419-2422; Barkley et al. (1980) in The Operon, pp. 177-220; Hu et al. (1987) Cell 48:555-566; Brown et al. (1987) Cell 49:603-612; Figge et al. (1988) Cell 52:713-722; Deuschle et al. (1989) Proc. Natl. Acad. Sci. USA 86:5400-5404; Fuerst et al. (1989) Proc. Natl. Acad. Sci. USA 86:2549-2553; Deuschle et al. (1990) Science 248:480-483; Gossen (1993) Ph.D. Thesis, University of Heidelberg; Reines et al. (1993) Proc. Natl. Acad. Sci. USA 90:1917-1921; Labow et al. (1990) Mol. Cell. Biol. 10:3343-3356; Zambretti et al. (1992) Proc. Natl. Acad. Sci. USA 89:3952-3956; Bairn et al. (1991) Proc. Natl. Acad. Sci. USA 88:5072-5076; Wyborski et al. (1991) Nucleic Acids Res. 19:4647-4653; Hillenand-Wissman (1989) Topics Mol. Struc. Biol. 10:143-162; Degenkolb et al. (1991) Antimicrob. Agents Chemother. 35:1591-1595; Kleinschnidt et al. (1988) Biochemistry 27:1094-1104; Bonin (1993) Ph.D. Thesis, University of Heidelberg; Gossen et al. (1992) Proc. Natl. Acad. Sci. USA 89:5547-5551; Oliva et al. (1992) Antimicrob. Agents Chemother. 36:913-919; Hlavka et al. (1985) Handbook of Experimental Pharmacology, Vol. 78 (Springer-Verlag, Berlin); Gill et al. (1988) Nature 334:721-724. Such disclosures are herein incorporated by reference. The above list of selectable marker genes is not meant to be limiting. Any selectable marker gene can be used in the present invention.
    • VI. Compositions Comprising Silencing Elements
  • One or more of the polynucleotides comprising the silencing element can be provided as an external composition such as a spray or powder to the plant, plant part, seed, a pest, or an area of cultivation. In another example, a plant is transformed with a DNA construct or expression cassette for expression of at least one silencing element. In either compositions, the silencing element, when ingested by an insect, can reduce the level of a target pest sequence and thereby control the pest (i.e., any pest from the Lepidoptera order, such as, Spodoptera frugiperda). It is recognized that the composition can comprise a cell (such as plant cell or a bacterial cell), in which a polynucleotide encoding the silencing element is stably incorporated into the genome and operably linked to promoters active in the cell. Compositions comprising a mixture of cells, some cells expressing at least one silencing element are also encompassed. In other embodiments, compositions comprising the silencing elements are not contained in a cell. In such embodiments, the composition can be applied to an area inhabited by a pest. In one embodiment, the composition is applied externally to a plant (i.e., by spraying a field or area of cultivation) to protect the plant from the pest.
  • In one embodiment, the composition comprising the silencing element that controls a pest from the Lepidoptera order does not comprise a heterologous cationic oligopeptide to facilitate uptake of the RNAi into the insect cells. Accordingly, in such embodiments, insecticidal activity occurs in the compositions of the invention (i.e., the plant, plant part, plant cell, or microbe) in the absence of a cationic oligopeptide that is heterologous to the plant, plant part or microbe. The cationic oligopeptide is target non-specific and interacts non-specifically with RNA via electrostatic interactions and neutralization of charge to penetrate membranes and lacks a specific activity that promotes a specific interaction with a cell membrane.
  • The composition of the invention can further be formulated as bait. In this embodiment, the compositions comprise a food substance or an attractant which enhances the attractiveness of the composition to the pest.
  • The composition comprising the silencing element can be formulated in an agriculturally suitable and/or environmentally acceptable carrier. Such carriers can be any material that the animal, plant or environment to be treated can tolerate. Furthermore, the carrier must be such that the composition remains effective at controlling a pest. Examples of such carriers include water, saline, Ringer's solution, dextrose or other sugar solutions, Hank's solution, and other aqueous physiologically balanced salt solutions, phosphate buffer, bicarbonate buffer and Tris buffer. In addition, the composition may include compounds that increase the half-life of a composition.
  • It is recognized that the polynucleotides comprising sequences encoding the silencing element can be used to transform organisms to provide for host organism production of these components, and subsequent application of the host organism to the environment of the target pest(s). Such host organisms include baculoviruses, bacteria, and the like. In this manner, the combination of polynucleotides encoding the silencing element may be introduced via a suitable vector into a microbial host, and said host applied to the environment, or to plants or animals.
  • The term “introduced” in the context of inserting a nucleic acid into a cell, means “transfection” or “transformation” or “transduction” and includes reference to the incorporation of a nucleic acid into a eukaryotic or prokaryotic cell where the nucleic acid may be stably incorporated into the genome of the cell (e.g., chromosome, plasmid, plastid, or mitochondrial DNA), converted into an autonomous replicon, or transiently expressed (e.g., transfected mRNA).
  • Microbial hosts that are known to occupy the “phytosphere” (phylloplane, phyllosphere, rhizosphere, and/or rhizoplana) of one or more crops of interest may be selected. These microorganisms are selected so as to be capable of successfully competing in the particular environment with the wild-type microorganisms, provide for stable maintenance and expression of the sequences encoding the silencing element, and desirably, provide for improved protection of the components from environmental degradation and inactivation.
  • Such microorganisms include bacteria, algae, and fungi. Of particular interest are microorganisms such as bacteria, e.g., Pseudomonas, Erwinia, Serratia, Klebsiella, Xanthomonas, Streptomyces, Rhizobium, Rhodopseudomonas, Methylius, Agrobacterium, Acetobacter, Lactobacillus, Arthrobacter, Azotobacter, Leuconostoc, and Alcaligenes, fungi, particularly yeast, e.g., Saccharomyces, Cryptococcus, Kluyveromyces, Sporobolomyces, Rhodotorula, and Aureobasidium. Of particular interest are such phytosphere bacterial species as Pseudomonas syringae, Pseudomonas fluorescens, Serratia marcescens, Acetobacter xylinum, Agrobacteria, Rhodopseudomonas spheroides, Xanthomonas campestris, Rhizobium melioti, Alcaligenes entrophus, Clavibacter xyli and Azotobacter vinlandir, and phytosphere yeast species such as Rhodotorula rubra, R. glutinis, R. marina, R. aurantiaca, Cryptococcus albidus, C. diffluens, C. laurentii, Saccharomyces rosei, S. pretoriensis, S. cerevisiae, Sporobolomyces rosues, S. odorus, Kluyveromyces veronae, and Aureobasidium pollulans. Of particular interest are the pigmented microorganisms.
  • A number of ways are available for introducing the polynucleotide comprising the silencing element into the microbial host under conditions that allow for stable maintenance and expression of such nucleotide encoding sequences. For example, expression cassettes can be constructed which include the nucleotide constructs of interest operably linked with the transcriptional and translational regulatory signals for expression of the nucleotide constructs, and a nucleotide sequence homologous with a sequence in the host organism, whereby integration will occur, and/or a replication system that is functional in the host, whereby integration or stable maintenance will occur.
  • Transcriptional and translational regulatory signals include, but are not limited to, promoters, transcriptional initiation start sites, operators, activators, enhancers, other regulatory elements, ribosomal binding sites, an initiation codon, termination signals, and the like. See, for example, U.S. Pat. Nos. 5,039,523 and 4,853,331; EPO 0480762A2; Sambrook et al. (2000); Molecular Cloning: A Laboratory Manual (3rd ed.; Cold Spring Harbor Laboratory Press, Plainview, N.Y.); Davis et al. (1980) Advanced Bacterial Genetics (Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.); and the references cited therein.
  • Suitable host cells include the prokaryotes and the lower eukaryotes, such as fungi. Illustrative prokaryotes, both Gram-negative and Gram-positive, include Enterobacteriaceae, such as Escherichia, Erwinia, Shigella, Salmonella, and Proteus; Bacillaceae; Rhizobiceae, such as Rhizobium; Spirillaceae, such as photobacterium, Zymomonas, Serratia, Aeromonas, Vibrio, Desulfovibrio, Spirillum; Lactobacillaceae; Pseudomonadaceae, such as Pseudomonas and Acetobacter; Azotobacteraceae and Nitrobacteraceae. Among eukaryotes are fungi, such as Phycomycetes and Ascomycetes, which includes yeast, such as Saccharomyces and Schizosaccharomyces; and Basidiomycetes yeast, such as Rhodotorula, Aureobasidium, Sporobolomyces, and the like.
  • Characteristics of particular interest in selecting a host cell for purposes of the invention include ease of introducing the coding sequence into the host, availability of expression systems, efficiency of expression, stability in the host, and the presence of auxiliary genetic capabilities. Characteristics of interest for use as a pesticide microcapsule include protective qualities, such as thick cell walls, pigmentation, and intracellular packaging or formation of inclusion bodies; leaf affinity; lack of mammalian toxicity; attractiveness to pests for ingestion; and the like. Other considerations include ease of formulation and handling, economics, storage stability, and the like.
  • Host organisms of particular interest include yeast, such as Rhodotorula spp., Aureobasidium spp., Saccharomyces spp., and Sporobolomyces spp., phylloplane organisms such as Pseudomonas spp., Erwinia spp., and Flavobacterium spp., and other such organisms, including Pseudomonas aeruginosa, Pseudomonas fluorescens, Saccharomyces cerevisiae, Bacillus thuringiensis, Escherichia coli, Bacillus subtilis, and the like.
  • The sequences encoding the silencing elements encompassed by the invention can be introduced into microorganisms that multiply on plants (epiphytes) to deliver these components to potential target pests. Epiphytes, for example, can be gram-positive or gram-negative bacteria.
  • The silencing element can be fermented in a bacterial host and the resulting bacteria processed and used as a microbial spray in the same manner that Bacillus thuringiensis strains have been used as insecticidal sprays. Any suitable microorganism can be used for this purpose. Pseudomonas has been used to express Bacillus thuringiensis endotoxins as encapsulated proteins and the resulting cells processed and sprayed as an insecticide Gaertner et al. (1993), in Advanced Engineered Pesticides, ed. L. Kim (Marcel Decker, Inc.).
  • Alternatively, the components of the invention are produced by introducing heterologous genes into a cellular host. Expression of the heterologous sequences results, directly or indirectly, in the intracellular production of the silencing element. These compositions may then be formulated in accordance with conventional techniques for application to the environment hosting a target pest, e.g., soil, water, and foliage of plants. See, for example, EPA 0192319, and the references cited therein.
  • In the present invention, a transformed microorganism can be formulated with an acceptable carrier into separate or combined compositions that are, for example, a suspension, a solution, an emulsion, a dusting powder, a dispersible granule, a wettable powder, and an emulsifiable concentrate, an aerosol, an impregnated granule, an adjuvant, a coatable paste, and also encapsulations in, for example, polymer substances.
  • Such compositions disclosed above may be obtained by the addition of a surface-active agent, an inert carrier, a preservative, a humectant, a feeding stimulant, an attractant, an encapsulating agent, a binder, an emulsifier, a dye, a UV protectant, a buffer, a flow agent or fertilizers, micronutrient donors, or other preparations that influence plant growth. One or more agrochemicals including, but not limited to, herbicides, insecticides, fungicides, bactericides, nematicides, molluscicides, acaracides, plant growth regulators, harvest aids, and fertilizers, can be combined with carriers, surfactants or adjuvants customarily employed in the art of formulation or other components to facilitate product handling and application for particular target pests. Suitable carriers and adjuvants can be solid or liquid and correspond to the substances ordinarily employed in formulation technology, e.g., natural or regenerated mineral substances, solvents, dispersants, wetting agents, tackifiers, binders, or fertilizers. The active ingredients of the present invention (i.e., at least one silencing element) are normally applied in the form of compositions and can be applied to the crop area, plant, or seed to be treated. For example, the compositions may be applied to grain in preparation for or during storage in a grain bin or silo, etc. The compositions may be applied simultaneously or in succession with other compounds. Methods of applying an active ingredient or a composition that contains at least one silencing element include, but are not limited to, foliar application, seed coating, and soil application. The number of applications and the rate of application depend on the intensity of infestation by the corresponding pest.
  • Suitable surface-active agents include, but are not limited to, anionic compounds such as a carboxylate of, for example, a metal; carboxylate of a long chain fatty acid; an N-acylsarcosinate; mono- or di-esters of phosphoric acid with fatty alcohol ethoxylates or salts of such esters; fatty alcohol sulfates such as sodium dodecyl sulfate, sodium octadecyl sulfate, or sodium cetyl sulfate; ethoxylated fatty alcohol sulfates; ethoxylated alkylphenol sulfates; lignin sulfonates; petroleum sulfonates; alkyl aryl sulfonates such as alkyl-benzene sulfonates or lower alkylnaphtalene sulfonates, e.g., butyl-naphthalene sulfonate; salts of sulfonated naphthalene-formaldehyde condensates; salts of sulfonated phenol-formaldehyde condensates; more complex sulfonates such as the amide sulfonates, e.g., the sulfonated condensation product of oleic acid and N-methyl taurine; or the dialkyl sulfosuccinates, e.g., the sodium sulfonate or dioctyl succinate. Non-ionic agents include condensation products of fatty acid esters, fatty alcohols, fatty acid amides or fatty-alkyl- or alkenyl-substituted phenols with ethylene oxide, fatty esters of polyhydric alcohol ethers, e.g., sorbitan fatty acid esters, condensation products of such esters with ethylene oxide, e.g., polyoxyethylene sorbitan fatty acid esters, block copolymers of ethylene oxide and propylene oxide, acetylenic glycols such as 2,4,7,9-tetraethyl-5-decyn-4,7-diol, or ethoxylated acetylenic glycols. Examples of a cationic surface-active agent include, for instance, an aliphatic mono-, di-, or polyamine such as an acetate, naphthenate or oleate; or oxygen-containing amine such as an amine oxide of polyoxyethylene alkylamine; an amide-linked amine prepared by the condensation of a carboxylic acid with a di- or polyamine; or a quaternary ammonium salt.
  • Examples of inert materials include, but are not limited to, inorganic minerals such as kaolin, phyllosilicates, carbonates, sulfates, phosphates, or botanical materials such as cork, powdered corncobs, peanut hulls, rice hulls, and walnut shells.
  • The compositions comprising the silencing element can be in a suitable form for direct application or as a concentrate of primary composition that requires dilution with a suitable quantity of water or other dilutant before application.
  • The compositions (including the transformed microorganisms) can be applied to the environment of an insect pest (such as a pest from the Lepidoptera order) by, for example, spraying, atomizing, dusting, scattering, coating or pouring, introducing into or on the soil, introducing into irrigation water, by seed treatment or general application or dusting at the time when the pest has begun to appear or before the appearance of pests as a protective measure. For example, the composition(s) and/or transformed microorganism(s) may be mixed with grain to protect the grain during storage. It is generally important to obtain good control of pests in the early stages of plant growth, as this is the time when the plant can be most severely damaged. The compositions can conveniently contain another insecticide if this is thought necessary. In an embodiment of the invention, the composition(s) is applied directly to the soil, at a time of planting, in granular form of a composition of a carrier and dead cells of a Bacillus strain or transformed microorganism of the invention. Another embodiment is a granular form of a composition comprising an agrochemical such as, for example, a herbicide, an insecticide, a fertilizer, in an inert carrier, and dead cells of a Bacillus strain or transformed microorganism of the invention.
  • VII. Plants, Plant Parts, and Methods of Introducing Sequences into Plants
  • In one embodiment, the methods of the invention involve introducing a polypeptide or polynucleotide into a plant. “Introducing” is intended to mean presenting to the plant the polynucleotide or polypeptide in such a manner that the sequence gains access to the interior of a cell of the plant. The methods of the invention do not depend on a particular method for introducing a sequence into a plant, only that the polynucleotide or polypeptides gains access to the interior of at least one cell of the plant. Methods for introducing polynucleotide or polypeptides into plants are known in the art including, but not limited to, stable transformation methods, transient transformation methods, and vim s-mediated methods.
  • “Stable transformation” is intended to mean that the nucleotide construct introduced into a plant integrates into the genome of the plant and is capable of being inherited by the progeny thereof. “Transient transformation” is intended to mean that a polynucleotide is introduced into the plant and does not integrate into the genome of the plant or a polypeptide is introduced into a plant.
  • Transformation protocols as well as protocols for introducing polypeptides or polynucleotide sequences into plants may vary depending on the type of plant or plant cell, i.e., monocot or dicot, targeted for transformation. Suitable methods of introducing polypeptides and polynucleotides into plant cells include microinjection (Crossway et al. (1986) Biotechniques 4:320-334), electroporation (Riggs et al. (1986) Proc. Natl. Acad. Sci. USA 83:5602-5606, Agrobacterium-mediated transformation (U.S. Pat. Nos. 5,563,055 and 5,981,840), direct gene transfer (Paszkowski et al. (1984) EMBO J. 3:2717-2722), and ballistic particle acceleration (see, for example, U.S. Pat. Nos. 4,945,050; 5,879,918; 5,886,244; and, 5,932,782; Tomes et al. (1995) in Plant Cell, Tissue, and Organ Culture: Fundamental Methods, ed. Gamborg and Phillips (Springer-Verlag, Berlin); McCabe et al. (1988) Biotechnology 6:923-926); and Lecl transformation (WO 00/28058). Also see Weissinger et al. (1988) Ann. Rev. Genet. 22:421-477; Sanford et al. (1987) Particulate Science and Technology 5:27-37 (onion); Christou et al. (1988) Plant Physiol. 87:671-674 (soybean); McCabe et al. (1988) Bio/Technology 6:923-926 (soybean); Finer and McMullen (1991) In Vitro Cell Dev. Biol. 27P:175-182 (soybean); Singh et al. (1998) Theor. Appl. Genet. 96:319-324 (soybean); Datta et al. (1990) Biotechnology 8:736-740 (rice); Klein et al. (1988) Proc. Natl. Acad. Sci. USA 85:4305-4309 (maize); Klein et al. (1988) Biotechnology 6:559-563 (maize); U.S. Pat. Nos. 5,240,855; 5,322,783; and, 5,324,646; Klein et al. (1988) Plant Physiol. 91:440-444 (maize); Fromm et al. (1990) Biotechnology 8:833-839 (maize); Hooykaas-Van Slogteren et al. (1984) Nature (London) 311:763-764; U.S. Pat. No. 5,736,369 (cereals); Bytebier et al. (1987) Proc. Natl. Acad. Sci. USA 84:5345-5349 (Liliaceae); De Wet et al. (1985) in The Experimental Manipulation of Ovule Tissues, ed. Chapman et al. (Longman, New York), pp. 197-209 (pollen); Kaeppler et al. (1990) Plant Cell Reports 9:415-418 and Kaeppler et al. (1992) Theor. Appl. Genet. 84:560-566 (whisker-mediated transformation); D'Halluin et al. (1992) Plant Cell 4:1495-1505 (electroporation); Li et al. (1993) Plant Cell Reports 12:250-255 and Christou and Ford (1995) Annals of Botany 75:407-413 (rice); Osjoda et al. (1996) Nature Biotechnology 14:745-750 (maize via Agrobacterium tumefaciens); all of which are herein incorporated by reference.
  • In specific embodiments, the silencing element sequences of the invention can be provided to a plant using a variety of transient transformation methods. Such transient transformation methods include, but are not limited to, the introduction of the protein or variants and fragments thereof directly into the plant or the introduction of the transcript into the plant. Such methods include, for example, microinjection or particle bombardment. See, for example, Crossway et al. (1986) Mol Gen. Genet. 202:179-185; Nomura et al. (1986) Plant Sci. 44:53-58; Hepler et al. (1994) Proc. Natl. Acad. Sci. 91: 2176-2180 and Hush et al. (1994) The Journal of Cell Science 107:775-784, all of which are herein incorporated by reference. Alternatively, polynucleotides can be transiently transformed into the plant using techniques known in the art. Such techniques include viral vector system and the precipitation of the polynucleotide in a manner that precludes subsequent release of the DNA. Thus, the transcription from the particle-bound DNA can occur, but the frequency with which it is released to become integrated into the genome is greatly reduced. Such methods include the use of particles coated with polyethylimine (PEI; Sigma #P3143).
  • In other embodiments, the polynucleotide of the invention may be introduced into plants by contacting plants with a virus or viral nucleic acids. Generally, such methods involve incorporating a nucleotide construct of the invention within a viral DNA or RNA molecule. Further, it is recognized that promoters of the invention also encompass promoters utilized for transcription by viral RNA polymerases. Methods for introducing polynucleotides into plants and expressing a protein encoded therein, involving viral DNA or RNA molecules, are known in the art. See, for example, U.S. Pat. Nos. 5,889,191, 5,889,190, 5,866,785, 5,589,367, 5,316,931, and Porta et al. (1996) Molecular Biotechnology 5:209-221; herein incorporated by reference.
  • Methods are known in the art for the targeted insertion of a polynucleotide at a specific location in the plant genome. In one embodiment, the insertion of the polynucleotide at a desired genomic location is achieved using a site-specific recombination system. See, for example, WO99/25821, WO99/25854, WO99/25840, WO99/25855, and WO99/25853, all of which are herein incorporated by reference. Briefly, the polynucleotide of the invention can be contained in transfer cassette flanked by two non-recombinogenic recombination sites. The transfer cassette is introduced into a plant having stably incorporated into its genome a target site which is flanked by two non-recombinogenic recombination sites that correspond to the sites of the transfer cassette. An appropriate recombinase is provided and the transfer cassette is integrated at the target site. The polynucleotide of interest is thereby integrated at a specific chromosomal position in the plant genome.
  • The cells that have been transformed may be grown into plants in accordance with conventional ways. See, for example, McCormick et al. (1986) Plant Cell Reports 5:81-84. These plants may then be grown, and either pollinated with the same transformed strain or different strains, and the resulting progeny having constitutive expression of the desired phenotypic characteristic identified. Two or more generations may be grown to ensure that expression of the desired phenotypic characteristic is stably maintained and inherited and then seeds harvested to ensure expression of the desired phenotypic characteristic has been achieved. In this manner, the present invention provides transformed seed (also referred to as “transgenic seed”) having a polynucleotide of the invention, for example, an expression cassette of the invention, stably incorporated into their genome.
  • As used herein, the term plant includes plant cells, plant protoplasts, plant cell tissue cultures from which plants can be regenerated, plant calli, plant clumps, and plant cells that are intact in plants or parts of plants such as embryos, pollen, ovules, seeds, leaves, flowers, branches, fruit, kernels, ears, cobs, husks, stalks, roots, root tips, anthers, and the like. Grain is intended to mean the mature seed produced by commercial growers for purposes other than growing or reproducing the species. Progeny, variants, and mutants of the regenerated plants are also included within the scope of the invention, provided that these parts comprise the introduced polynucleotides.
  • The present invention may be used for transformation of any plant species, including, but not limited to, monocots and dicots. Examples of plant species of interest include, but are not limited to, corn (Zea mays), Brassica sp. (e.g., B. napus, B. rapa, B. juncea), particularly those Brassica species useful as sources of seed oil, alfalfa (Medicago sativa), rice (Oryza sativa), rye (Secale cereale), sorghum (Sorghum bicolor, Sorghum vulgare), millet (e.g., pearl millet (Pennisetum glaucum), proso millet (Panicum miliaceum), foxtail millet (Setaria italica), finger millet (Eleusine coracana)), sunflower (Helianthus annuus), safflower (Carthamus tinctorius), wheat (Triticum aestivum), soybean (Glycine max), tobacco (Nicotiana tabacum), potato (Solanum tuberosum), peanuts (Arachis hypogaea), cotton (Gossypium barbadense, Gossypium hirsutum), sweet potato (Ipomoea batatus), cassava (Manihot esculenta), coffee (Coffea spp.), coconut (Cocos nucifera), pineapple (Ananas comosus), citrus trees (Citrus spp.), cocoa (Theobroma cacao), tea (Camellia sinensis), banana (Musa spp.), avocado (Persea americana), fig (Ficus casica), guava (Psidium guajava), mango (Mangifera indica), olive (Olea europaea), papaya (Carica papaya), cashew (Anacardium occidentale), macadamia (Macadamia integrifolia), almond (Prunus amygdalus), sugar beets (Beta vulgaris), sugarcane (Saccharum spp.), oats, barley, vegetables, ornamentals, and conifers.
  • Vegetables include tomatoes (Lycopersicon esculentum), lettuce (e.g., Lactuca sativa), green beans (Phaseolus vulgaris), lima beans (Phaseolus limensis), peas (Lathyrus spp.), and members of the genus Cucumis such as cucumber (C. sativus), cantaloupe (C. cantalupensis), and musk melon (C. melo). Ornamentals include azalea (Rhododendron spp.), hydrangea (Macrophylla hydrangea), hibiscus (Hibiscus rosasanensis), roses (Rosa spp.), tulips (Tulipa spp.), daffodils (Narcissus spp.), petunias (Petunia hybrida), carnation (Dianthus caryophyllus), poinsettia (Euphorbia pulcherrima), and chrysanthemum.
  • Conifers that may be employed in practicing the present invention include, for example, pines such as loblolly pine (Pinus taeda), slash pine (Pinus elliotii), ponderosa pine (Pinus ponderosa), lodgepole pine (Pinus contorta), and Monterey pine (Pinus radiata); Douglas-fir (Pseudotsuga menziesii); Western hemlock (Tsuga canadensis); Sitka spruce (Picea glauca); redwood (Sequoia sempervirens); true firs such as silver fir (Abies amabilis) and balsam fir (Abies balsamea); and cedars such as Western red cedar (Thuja plicata) and Alaska yellow-cedar (Chamaecyparis nootkatensis). In specific embodiments, plants of the present invention are crop plants (for example, corn, alfalfa, sunflower, Brassica, soybean, cotton, safflower, peanut, sorghum, wheat, millet, tobacco, etc.). In other embodiments, corn and soybean plants are optimal, and in yet other embodiments corn plants are optimal.
  • Other plants of interest include grain plants that provide seeds of interest, oil-seed plants, and leguminous plants. Seeds of interest include grain seeds, such as corn, wheat, barley, rice, sorghum, rye, etc. Oil-seed plants include cotton, soybean, safflower, sunflower, Brassica, maize, alfalfa, palm, coconut, etc. Leguminous plants include beans and peas. Beans include guar, locust bean, fenugreek, soybean, garden beans, cowpea, mungbean, lima bean, fava bean, lentils, chickpea, etc.
    • VIII. Methods of Use
  • The methods of the invention comprise methods for controlling a pest (i.e., pest from the Lepidoptera order, such as, Spodoptera frugiperda). The method comprises feeding to a pest a composition comprising a silencing element of the invention, wherein said silencing element, when ingested by a pest (i.e., pests from the Lepidoptera order, such as, Spodoptera frugiperda), reduces the level of a target polynucleotide of the pest and thereby controls the pest. The pest can be fed the silencing element in a variety of ways. For example, in one embodiment, the polynucleotide comprising the silencing element is introduced into a plant. As the Lepidoptera feeds on the plant or part thereof expressing these sequences, the silencing element is delivered to the pest. When the silencing element is delivered to the plant in this manner, it is recognized that the silencing element can be expressed constitutively or alternatively, it may be produced in a stage-specific manner by employing the various inducible or tissue-preferred or developmentally regulated promoters that are discussed elsewhere herein. In specific embodiments, the silencing element expressed in the roots, stalk or stem, leaf including pedicel, xylem and phloem, fruit or reproductive tissue, silk, flowers and all parts therein or any combination thereof.
  • In another method, a composition comprising at least one silencing element of the invention is applied to a plant. In such embodiments, the silencing element can be formulated in an agronomically suitable and/or environmentally acceptable carrier, which is preferably, suitable for dispersal in fields. In addition, the carrier can also include compounds that increase the half life of the composition. In specific embodiments, the composition comprising the silencing element is formulated in such a manner such that it persists in the environment for a length of time sufficient to allow it to be delivered to a pest. In such embodiments, the composition can be applied to an area inhabited by a pest. In one embodiment, the composition is applied externally to a plant (i.e., by spraying a field) to protect the plant from pests.
  • In certain embodiments, the constructs of the present invention can be stacked with any combination of polynucleotide sequences of interest in order to create plants with a desired trait. A trait, as used herein, refers to the phenotype derived from a particular sequence or groups of sequences. For example, the polynucleotides of the present invention may be stacked with any other polynucleotides encoding polypeptides having pesticidal and/or insecticidal activity, such as other Bacillus thuringiensis toxic proteins (described in U.S. Pat. Nos. 5,366,892; 5,747,450; 5,737,514; 5,723,756; 5,593,881; and Geiser et al. (1986) Gene 48:109), lectins (Van Damme et al. (1994) Plant Mol. Biol. 24:825, pentin (described in U.S. Pat. No. 5,981,722), and the like. The combinations generated can also include multiple copies of any one of the polynucleotides of interest. The polynucleotides of the present invention can also be stacked with any other gene or combination of genes to produce plants with a variety of desired trait combinations including, but not limited to, traits desirable for animal feed such as high oil genes (e.g., U.S. Pat. No. 6,232,529); balanced amino acids (e.g., hordothionins (U.S. Pat. Nos. 5,990,389; 5,885,801; 5,885,802; and 5,703,409); barley high lysine (Williamson et al. (1987) Eur. J. Biochem. 165:99-106; and WO 98/20122) and high methionine proteins (Pedersen et al. (1986) J. Biol. Chem. 261:6279; Kirihara et al. (1988) Gene 71:359; and Musumura et al. (1989) Plant Mol. Biol. 12:123)); increased digestibility (e.g., modified storage proteins (U.S. application Ser. No. 10/053,410, filed Nov. 7, 2001); and thioredoxins (U.S. application Ser. No. 10/005,429, filed Dec. 3, 2001)); the disclosures of which are herein incorporated by reference.
  • The polynucleotides of the present invention can also be stacked with traits desirable for disease or herbicide resistance (e.g., fumonisin detoxification genes (U.S. Pat. No. 5,792,931); avirulence and disease resistance genes (Jones et al. (1994) Science 266:789; Martin et al. (1993) Science 262:1432; Mindrinos et al. (1994) Cell 78:1089); acetolactate synthase (ALS) mutants that lead to herbicide resistance such as the S4 and/or Hra mutations; inhibitors of glutamine synthase such as phosphinothricin or basta (e.g., bar gene); and glyphosate resistance (EPSPS gene)); and traits desirable for processing or process products such as high oil (e.g., U.S. Pat. No. 6,232,529); modified oils (e.g., fatty acid desaturase genes (U.S. Pat. No. 5,952,544; WO 94/11516)); modified starches (e.g., ADPG pyrophosphorylases (AGPase), starch synthases (SS), starch branching enzymes (SBE), and starch debranching enzymes (SDBE)); and polymers or bioplastics (e.g., U.S. Pat. No. 5,602,321; beta-ketothiolase, polyhydroxybutyrate synthase, and acetoacetyl-CoA reductase (Schubert et al. (1988) J. Bacteriol. 170:5837-5847) facilitate expression of polyhydroxyalkanoates (PHAs)); the disclosures of which are herein incorporated by reference. One could also combine the polynucleotides of the present invention with polynucleotides providing agronomic traits such as male sterility (e.g., see U.S. Pat. No. 5,583,210), stalk strength, flowering time, or transformation technology traits such as cell cycle regulation or gene targeting (e.g., WO 99/61619, WO 00/17364, and WO 99/25821); the disclosures of which are herein incorporated by reference.
  • These stacked combinations can be created by any method including, but not limited to, cross-breeding plants by any conventional or TopCross methodology, or genetic transformation. If the sequences are stacked by genetically transforming the plants, the polynucleotide sequences of interest can be combined at any time and in any order. For example, a transgenic plant comprising one or more desired traits can be used as the target to introduce further traits by subsequent transformation. The traits can be introduced simultaneously in a co-transformation protocol with the polynucleotides of interest provided by any combination of transformation cassettes. For example, if two sequences will be introduced, the two sequences can be contained in separate transformation cassettes (trans) or contained on the same transformation cassette (cis). Expression of the sequences can be driven by the same promoter or by different promoters. In certain cases, it may be desirable to introduce a transformation cassette that will suppress the expression of the polynucleotide of interest. This may be combined with any combination of other suppression cassettes or overexpression cassettes to generate the desired combination of traits in the plant. It is further recognized that polynucleotide sequences can be stacked at a desired genomic location using a site-specific recombination system. See, for example, WO99/25821, WO99/25854, WO99/25840, WO99/25855, and WO99/25853, all of which are herein incorporated by reference.
  • Methods and compositions are further provided which allow for an increase in RNAi produced from the silencing element. In such embodiments, the methods and compositions employ a first polynucleotide comprising a silencing element for a target pest sequence operably linked to a promoter active in the plant cell; and, a second polynucleotide comprising a suppressor enhancer element comprising the target pest sequence or an active variant or fragment thereof operably linked to a promoter active in the plant cell. The combined expression of the silencing element with suppressor enhancer element leads to an increased amplification of the inhibitory RNA produced from the silencing element over that achievable with only the expression of the silencing element alone. In addition to the increased amplification of the specific RNAi species itself, the methods and compositions further allow for the production of a diverse population of RNAi species that can enhance the effectiveness of disrupting target gene expression. As such, when the suppressor enhancer element is expressed in a plant cell in combination with the silencing element, the methods and composition can allow for the systemic production of RNAi throughout the plant; the production of greater amounts of RNAi than would be observed with just the silencing element construct alone; and, the improved loading of RNAi into the phloem of the plant, thus providing better control of phloem feeding insects by an RNAi approach. Thus, the various methods and compositions provide improved methods for the delivery of inhibitory RNA to the target organism. See, for example, U.S. Provisional Application No. 61/021,676, entitled “Compositions and Methods for the Suppression of Target Polynucleotides”, filed Jan. 17, 2008 and herein incorporated by reference in its entirety.
  • As used herein, a “suppressor enhancer element” comprises a polynucleotide comprising the target sequence to be suppressed or an active fragment or variant thereof. It is recognize that the suppressor enhancer element need not be identical to the target sequence, but rather, the suppressor enhancer element can comprise a variant of the target sequence, so long as the suppressor enhancer element has sufficient sequence identity to the target sequence to allow for an increased level of the RNAi produced by the silencing element over that achievable with only the expression of the silencing element. Similarly, the suppressor enhancer element can comprise a fragment of the target sequence, wherein the fragment is of sufficient length to allow for an increased level of the RNAi produced by the silencing element over that achievable with only the expression of the silencing element. Thus, in specific embodiments, the suppressor enhancer element comprises a fragment or a variant of a polynucleotide encoding a juvenile hormone polypeptide, a vacuolar polypeptide, a cadherin polypeptide, a cuticle polypeptide, a translation initiation factor, a SARI polypeptide, an elongation factor, a phosphooligosaccharide, a myosin polypeptide, a potassium channel amino acid transporter, a potassium inwardly rectifier polypeptide, an amino acid transporter, a tubulin polypeptide, a ubiquitin polypeptide, small nuclear ribonucleoprotein, or any other polynucleotide fo interest disclosed herein. In still other embodiments, the suppressor enhancer element comprises a polynucleotide set forth in SEQ ID NO: 1-50 or an active variant or fragment thereof.
  • It is recognized that multiple suppressor enhancer elements from the same target sequence or from different target sequences, or from different regions of the same target sequence can be employed. For example, the suppressor enhancer elements employed can comprise fragments of the target sequence derived from different region of the target sequence (i.e., from the 3′UTR, coding sequence, intron, and/or 5′UTR). Further, the suppressor enhancer element can be contained in an expression cassette, as described elsewhere herein, and in specific embodiments, the suppressor enhancer element is on the same or on a different DNA vector or construct as the silencing element. The suppressor enhancer element can be operably linked to a promoter as disclosed herein. It is recognized that the suppressor enhancer element can be expressed constitutively or alternatively, it may be produced in a stage-specific manner employing the various inducible or tissue-preferred or developmentally regulated promoters that are discussed elsewhere herein.
  • In specific embodiments, employing both a silencing element and the suppressor enhancer element the systemic production of RNAi occurs throughout the entire plant. In further embodiments, the plant or plant parts of the invention have an improved loading of RNAi into the phloem of the plant than would be observed with the expression of the silencing element construct alone and, thus provide better control of phloem feeding insects by an RNAi approach. In specific embodiments, the plants, plant parts, and plant cells of the invention can further be characterized as allowing for the production of a diversity of RNAi species that can enhance the effectiveness of disrupting target gene expression.
  • In specific embodiments, the combined expression of the silencing element and the suppressor enhancer element increases the concentration of the inhibitory RNA in the plant cell, plant, plant part, plant tissue or phloem over the level that is achieved when the silencing element is expressed alone.
  • As used herein, an “increased level of inhibitory RNA” comprises any statistically significant increase in the level of RNAi produced in a plant having the combined expression when compared to an appropriate control plant. For example, an increase in the level of RNAi in the plant, plant part or the plant cell can comprise at least about a 1%, about a 1%-5%, about a 5%-10%, about a 10%-20%, about a 20%-30%, about a 30%-40%, about a 40%-50%, about a 50%-60%, about 60-70%, about 70%-80%, about a 80%-90%, about a 90%-100% or greater increase in the level of RNAi in the plant, plant part, plant cell, or phloem when compared to an appropriate control. In other embodiments, the increase in the level of RNAi in the plant, plant part, plant cell, or phloem can comprise at least about a 1 fold, about a 1 fold-5 fold, about a 5 fold-10 fold, about a 10 fold-20 fold, about a 20 fold-30 fold, about a 30 fold-40 fold, about a 40 fold-50 fold, about a 50 fold-60 fold, about 60 fold-70 fold, about 70 fold-80 fold, about a 80 fold-90 fold, about a 90 fold-100 fold or greater increase in the level of RNAi in the plant, plant part, plant cell or phloem when compared to an appropriate control. Methods to assay for an increase in the level of RNAi are discussed elsewhere herein.
  • The following examples are offered by way of illustration and not by way of limitation.
    • EXPERIMENTAL Example 1. Specific Target Genes and Silencing Elements that Cause Insecticidal Activity Against Spodoptera frugiperda
  • Disruption of insect gene function via RNAi can produce specific activity against target insects. This specificity is enhanced by delivery of the dsRNAs via transgenic plants. Identification of gene function in insects via RNAi has been largely limited to injection of dsRNAs. In fact, past experiments have indicated that insects are not capable of systemic RNAi response based on exposure to dsRNAs.
  • As described below, we have demonstrated acute activity of numerous dsRNA pairs through injection experiments and additionally have demonstrated insect antagonism through ingestion of dsRNAs. This evidence identifies several gene/primer pair combinations with clear insecticidal properties. The use of dsRNAs in transgenic plants also addresses the potential complication of heterologous protein expression and the possible risks of allergic reaction, non-target activity, and environmental- or bioaccumulation. The data presented below represents the first test of disruption of these particular genes resulting in insecticidal activity in whole organisms and the first report of insecticidal activity of dsRNAs against Spodoptera frugiperda.
  • The invention describes specific target genes and the dsRNA sequences causing insecticidal activity against the Lepidopteran Spodoptera frugiperda through RNA interference of the target gene's expression. Disruption of the genes targeted by the dsRNA sequences may be broadly insecticidal in numerous species. The specific dsRNA sequences display insecticidal activity upon ingestion and can be utilized with a transgenic plant mode of delivery. Table 1 provides the polynucleotide of non-limiting examples of target sequence from Spodoptera frugiperda, a brief description of the function of the protein encoded by the target sequence, and a SEQ ID NO. Table 2 provides a summary of primers used to suppress the target polynucleotides.
  • TABLE 1
    Target Polynucleotides from Spodoptera frugiperda.
    SEQ ID NO: 1
    >ise1c.pk002.m13 Juvenile hormone query
    CAAGCATCCAACATGGTATCCGACTTCAGGAAGAAGAAGCTCCTCCACGTGTTCAAGTCCTTCTTCGACACGGAC
    GGCAGCGGCAACATCGAGAAGGATGACTTCCTGATGGCCATCGAAAGGATAACCAAGACCAGAGGCTGGAAAGCT
    GGAGACGACAAATACAAATTTGTCGAGGAGACCCTATTGAAGATCTGGGACGGCATCCAGAAGGTCGCTGACGAG
    AACAAGGACGGACAGGTCAGCCAGGACGAGTGGATCGCTATGTGGGACAAGTACTCCAAGAACCCGTCCGAGGCG
    TTCGAGTGGCAGACCCTGTACTGCAAGTTCGCGTTCACTCTTGAAGACGCCAGCGACGATGGATCCATCGACAGC
    GAGGAGTTCTCCTCTGTGTACGCCTCCTTCGGCCTGGACAANGACGANGCTGTGGCTGCCTTCAAGAAAGATGGC
    TAACGGTAAGTCCGAAGTGTCCTGGGCTTGAGTTCCACGACCTGTGGAANGAGTACTTCTCATCCGGAAGACTNG
    AACGCTGCCGGCAAN
    SEQ ID NO: 2
    >ise1c.pk003.f7 Juvenile hormone query
    CCAACATGGTATCCGACTTCAGGAAGAAGAAGCTCCTCCACGTGTTCAAGTCCTTCTTCGACACGGACGGCAGCG
    GCAACATCGAGAAGGATGATTTCCTGATGGCCATCGAAAGGATAACCAAGACCAGAGGCTGGAAAGCTGGAGACA
    ACAAATACAAATTTGTCGAGGAAACCCTATTGAAGATCTGGGACGGCATCCAGAAGGTCGCTGACGAGAACAAGG
    ACGGACAGGTCAGCCAGGACGAGTGGATCGCTATGTGGGACAAGTACTCCAAGAACCCATCCGAGGCGTTCGAGT
    GGCAGACCCTGTACTGCAAGTTCGCGTTCACTCTTGAAGACGCCAGCGACGACGGATNCATCGACAGCGAAGAGT
    TCTCCTCTGTGTACGCCTCCTTCGGGCTGGACAANGGACGAGGCGGTGGCTGCCTTCAAGAAGATGNTAACGGTA
    AGTCCGAATGTCCTGGGGCTGAGTTTCAAGANCTGTTGGAAGGATACTTCTCAAC
    SEQ ID NO: 3
    >ise1c.pk005.a15 Juvenile hormone query
    CAACATGGTATCCGACTTCAGGAAGAATAAGCTCCTCCACGTGTTCAAGTCCTTCTTCGACACGGACGGCAGCGG
    CAACATCGAGAAGGATGACTTCCTGATGGCCATCGAAAGGATAACCAAGACCAGAGGCTGGAAAGCTGGAGACGA
    CAAATACAAATTTGTCGAGGAGACCCTATTGAAGATCTGGGACGGCATCCAGAAGGTCGCTGACGAGAACAAGGA
    CGGACAGGTCAGCCAGGACGAGTGGATCGCTATGTGGGACAAGTANTCCAAGAACCCGTCCGAGGCGTTCGAGTG
    GCAGACCCTGTACTGCAAGTTCGCGTTCACTCTTGAAGACGCCAGNGACGATGGATCCATCGACAGCGAGGAGTT
    CTCCTCTGTGTACGCCTCCTTCGGCCTGGACAAGG
    SEQ ID NO: 4
    >ise1c.pk006.d24 Juvenile hormone query
    GAGAGAGAGAGAGAGAGAGAACTAGTCTCGAGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTNGGAAANTAC
    TATTTTATTGTACCAACTGCCCCTTAACCTCATCTATGAGTCACCCATAAATGTTATTTTGGTAAAATGTTTGAC
    ACACTTCACACTAATATTTATAAATGTGAAAGTTTGTTTGTTTGAATGTTTGTATATTTGTCTGTCAATCACGCT
    GAAACCACTGTATAGAATTTGACCTAATTTGGTATACANACAGGGTATGAGCTGACTTGGGTGATAGGATACTTT
    TTATCCCACAGGAACGCGGGTAAAGTCCNTGGGCAGAAGCTAGTATGTAATAATTATNTCCCTCTACCTACCCTA
    TATGGGGGTGGACCGTCATGTTCTTTACNCNACAACCNGTTTGTCCACCTCNCCTTTAAAGTTTTGTNAG
    SEQ ID NO: 5
    >ise2c.pk009.i4 Juvenile hormone query
    GCACGAGGGCCGTGTCGACTTCGCACCAGTCCCCTATTTATTTACCTTGACAAAAATATGGCGCGCCTATTGTTT
    ATTGCGCCTATCCTGGCGTTGGCTATAATGCCAGTATACTTCTTATTCCTAAAGGGACCACCCCCACTACCCGAA
    CTAGATATGAACGAGTGGTGGGGCCCAGAGAAGCTAAAAGCAAAACCTGACACTAGTATAAAACCCTTTAAAATT
    GCTTTTGGAGACACTGTTGTAAAAGACTTAAAAGACCGTCTCAAACGTTCTCGGTCTTTCACTGCTCCGCTGGAG
    GGTGTGGCATTCCAGTACGGCTTCAACACTGCTCAGCTGGATGGTTGGCTGAAGTACTGGGCTAATGAGTATAAG
    TTCAAGGAGAGAGAGACCTTCCTCAACCAGTACCCTCAGTACAAAACCAATATCCAGGGTCTTGACATCCACTTC
    ATCAGGGTTACACCGAAGGTACCGGCAGGAGTGGAGGTGGTACCCATGCTACTCCTCCACGGCTGGCCAGGCTCT
    GTCAGGGAGTTCTACGAGGCTATTCCTCTCATCACAGCAGTCAGCAAGGACCGTGACTTCGCTGTGGAAGTCATC
    GTTCCAAGTCTACCTGGCTATGGATTCTCTGATGCCGCAGTTCGTCCCGGCnnnnnnnCCCCACAAATGnnn
    SEQ ID NO: 6
    >ise2c.pk001.d19 vacuolar query
    GCACGAGGCTTGGACGTGATGTTACCTGGGAATTCAACCCCTTGAATGTTAAGGTCGGCTCCCACATCACCGGAG
    GAGACTTGTACGGTATCGTACACGAGAACACATTGGTTAAGCACAAGATGTTGATCCCACCCAAGGCCAAGGGTA
    CCGTCACCTACGTCGCGCCCTCCGGCAACTACAAAGTCACTGACGTAGTGTTGGAGACGGAGTTCGACGGCGAGA
    AGGAGAAGTACACCATGTTGCAAGTATGGCCGGTGCGCCAGCCGCGCCCCGTCACTGAGAAGCTGTCCGCCAACC
    ACCCCCTGCTCACCGGACAGAGAGTGCTCGACTCTCTCTTCCCTTGTGTCCAGGGTGGTACCACGGCCATCCCCG
    GCGCCTTCGGTTGTGGCAAGACTGTCGTCTCACAGGCTCTGTCCAAGTACTCCAACTCTGACGTCATCATCTACG
    TCGGATGCGGTGAACGTGGTAACGAGATGTCTGAGGTACTGCGTGACTTCCCCGAGCTGACGGTGGAGATCGAGG
    GCATGACCGAGTCCATCATGAAGCGTACCGCGCTCGTCGCCAACACCTCCAACATGCCTGTAGCCGCCCGAGAGG
    CTTCCATCTACACCGGTATCACCCTCTCCGAGTACTTCCGTGACATGGGTTACAACGTGTCCATGATGGCTGACT
    CCACCTCTCGTTGGGCCG
    SEQ ID NO: 7
    >ise2c.pk001.e14 vacuolar query
    GCACGAGGCAGATAGTCATCACTGTTTTTGGGACCTGTnnnTACTCCCTCAATAAACCTACAAAATGGCCGAAAA
    CCCAATCTACGGACCCTTCTTTGGAGTTATGGGGGCGGCGTCTGCTATCATCTTTAGCGCGCTGGGAGCTGCCTA
    TGGAACTGCTAnGnCnnnnACCGGTATCGCCGCCATGTCGGTGATGCGGCCCGAGCTCATCATGAAGTCCAACAA
    CTACACCCTTTACAAGnGGTTCATCCACCTTGGCGCTGGTCTnnnCGTAAGTTTCTCCGGTCTAGCGnnnGGCnn
    SEQ ID NO: 8
    >ise2c.pk001.f20 vacuolar query
    GCACGAGGCTCACAGGCTCTGTCCAAGTACTCCAACTCTGACGTCATCATCTACGTCGGATGCGGTGAACGTGGT
    AACGAGATGTCTGAGGTACTGCGTGACTTCCCCGAGCTGACGGTGGAGATCGAGGGCATGACCGAGTCCATCATG
    AAGCGTACCGCGCTCGTCGCCAACACCTCCAACATGCCTGTAGCCGCCCGAGAGGCTTCCATCTACACCGGTATC
    ACCCTCTCCGAGTACTTCCGTGACATGGGTTACAACGTGTCCATGATGGCTGACTCCACCTCTCGTTGGGCCGAG
    GCTCTTCGTGAGATCTCnnnnCGTCTGGCTGAGATGCCTGCCGACTCGGGTTACCCCGCCTACCTGGGAGCCCGT
    CTGGCCTCGTTCTACGAGCGTGCCGGACGTGTGAAGTGCTTGGGTAACCCCGACAGGGAGGGCTCCGTGTCCATC
    GTGGGCGCCGTGTCGCCGCCCGGAGGTGACTTCTCCGACCCCGTGACGGCCGCCACGCTGGGTATCGTGCAGGTG
    TTCTGGGGGTTGGACAAGAAGCTCGCGCAGCGCAAGCACTTCCCCGCCATCAACTGGCTCATCTCCTACAGCAAG
    TACATGCGAGCGCTGGACGACTTCTATGAGAAGAACTACCCCGAGTTCGTGCCCCTCnnnnnCAAGGGTCAAGGA
    GATCCTGCAGnnn
    SEQ ID NO: 9
    >ise2c.pk010.h3 cadherin query
    GCACGAGGTATCTAAAACAGTGCGTCGTAATATATTCAAGATGTCTCGTCTTAGGTTTTGTTTTTTATTAGCAGT
    ACTATGCAGTTGTTTGCAGAATGGTTACGGTTTTACAACAGAAAAGCCAGTTACCCAGCATGTAGATCCTAAACC
    AGAAGTTCCTGAAACGTTGCCTGAAACAACACGAGTGCCTGCGCCGAGCTCGTCGACGGCAGCGCCGACCACACC
    AGCTCCGACACCGGCACCAACGCCAGCACCCACACCAGCTCCTACACCAGCTCCTACTCCAGCTCCTACCCCTGC
    GCCTACTCCTGCGCCTACTCCTGCGCCTACTCCTGCGCCTACCCCCGCACCTACACCAGCGCCCACTCCTGCTCC
    CACCCCAGCTCCCCTCCCCGCCCCCGACCAAGGCACATGGTCCTTCACTGATGAAAAGGCCAATCAGACATGCAT
    TGTGGCCCAATTCGCAGCCCAACTGAATGTCACATACACCAAGTTAGTGGAGAATGCAACGTCTCTATCGTACGT
    GAGGCTCAACGTGCCCGCGAACGCGTCGGTCCTCAACGGCAGCTGTTCGGACCCCGACCAATGGATCCAGATCAC
    CTGGAAGACCAACGACGACAGCGAGACGAACAACACCATGACCCTCGTGTACAACAAGAATGCCACCACCAAGnn
    CTACGGCCTG
    SEQ ID NO: 10
    >ise2c.pk011.a10 cuticle protein
    GCACGAGGGCGGTTTGAAGTGATCTAGTTCGTCAGAAAAAACACAGACCACGTTCACAATGAAATCGATGGTGGT
    GTTATTCGCTGTGTGCGCCGTGGCGTGCGGCTCCCTGGTGCCGCTGGCGCAGCCTCCTCATCACCCCGCCGTCGT
    GCTGGACCCGCACGGCCGCCCGCTCGACACCGCCGAGGTGATCAACGCCCGCGCCCTCCACCTGCAGGCTAAGGC
    CCTGGATGGACACTACGCTCCCCTCGCGCACGCTGCCGTCGTGCCTGTTGCCCACTCCGTGGTAGCCGCCCCCGC
    TGTGGTCGCCGCTCCCGCCGCCGTGTCCCACCAGTCCCGTGTGGATGTGCGCACCAGCCCCGCCATCGTGAGCCA
    CGCCGTCGCTGCTCCCGTAGTAGCCCACGGTGTCTACTCCGCTCCCCTGCTGGCCCACTCCGCTCTCGGCTACGC
    CGGTCACGGACACTACCTGAAGAAGCGCTCCCTGGGACACCTCGCCTACGCCGCTCCCGTCGTCGCCCACGTAGC
    TCCCTCCGCGGTGTCGCACCAGTCCCGCGTGGnCnTCGTCTCCAGCCnnnCTGTCGTGTCTCAnnnnnTnnnTnC
    CGTnnTGTCCCn
    SEQ ID NO: 11
    >ise2c.pk011.h12 cuticle protein
    GCACGAGGGGACGTTGAACGAAAGAAAATGCTACGCGTTACGATTTTAGCCGCAGTGGTGGTGTTCGCCTCAGGC
    GCGCCCCAGAACAACTTCATCTTCAAGAATGACATCACTCCTGAGGAAGCCCAGCAGTACCTCAAACAACTGCCG
    TTCACCTCACCCCAGCTCTCTGGACGCACCGCTGTACTGCCTCTGGTTCGCTACGACGACCCCAGGTTTCGTTCA
    GCTGAAGCTGGCCCAACCCTTGGACACTACTGGAAGAATGGACAGGAGATCCAGAACACAGAGGACTACTTAGAA
    GAGGTCTACAACGCGGCTCAATACCACGGCCAGGACGGTCTTGGCAACTACGCCTACGGTTATGAGACCCCTGAA
    TCTTCCAAGGTTGAGAACCGTGAAGGTTCCGGAGTCGTCCAAGGATCCTATGTGTACCAGGTTCCCGGAATGAAG
    GATCTCGTCnnGGTCCGTTACTGGGCTGACAGCCnnnnnTTCCACCAGnAnGACAATCTTCCCAAGGTTGAACTG
    AnnnCCGCTnnnnnnnnCCCGCTCT
    SEQ ID NO: 12
    >ise2c.pk001.d22 translation initiation factor
    GCACGAGGTATCACTCCTGACCGTATCTAAAACTCGGCACACAACACAATGGCTGACATCGAAGATACACATTTC
    GAGACCGGGGACTCCGGTGCCTCCGCCACCTTCCCTATGCAATGCTCGGCCCTGCGCAAGAACGGTTTCGTCATG
    CTTAAGGGTCGCCCCTGCAAAATCGTCGAGATGTCCACTTCCAAAACCGGAAAGCACGGCCACGCTAAAGTTCAC
    TTGGTTGGAATCGATATTTTTAACGGCAAGAAATACGAAGATATCTGCCCTTCCACCCACnnnCATGGACGTGCC
    CCACGTGAAGCGTGAGGACTACCAGCTCACCGATATCTCTGACGACGGCTACCTTACCCTCATGGCTGACAACGG
    CGATCTCCGCGAGGACCTCAAGATCCCAGACGGTGACCTCGGCACCCAGTTGCGTTCTGACTTCGATAGCGGCAA
    AGAGCTGTTGTGCACTGTGCTGAAGTCTTGCGGTGAGGAGTGTGTAATCGCAGTCAAGGCAAACACAGCTCTCGA
    CAAATAAACCAACTCAGCATTTATAGGGATATACATACATATAATTTTTTTACAATCAACAGCTCTTACATAAAT
    GTAAAACATAATACTATGTATAATTTAACATnnnnnATTATGGTGTGACGCGGTGCTGGCTTGTCGCCGTCCACT
    CCACCCCCGAAG
    SEQ ID NO: 13
    >ise2c.pk001.d9 translation initiation factor
    GCACGAGGCGCGATTGTAACATGTCGTATTCACCAGAAAGAAGATCAGAAGATTGGCCGGAAGATTCCAAAAATG
    GCCCGTCTAAGGATCAAGGCAACTATGATGGGCCTCCAGGAATGGAACCCCAAGGGGCACTTGATACAAACTGGC
    ACCAGGTCGTGGAAAGCTTTGACGACATGAATCTGAAGGAAGAATTGTTGAGAGGAATTTATGCTTACGGTTTTG
    AAAAGCCGTCTGCTATCCAACAACGCGCTATTATGCCTTGCATTCAAGGCCGTGATGTCATAGCTCAAGCCCAGT
    CTGGTACTGGGAAGACTGCTACCTTCTCTATTTCAATTCTTCAGCAAATCGATACCAGTATTCGTGAATGCCAAG
    CACTGATTTTGGCCCCTACTAGAGAGCTGGCTCAGCAGATCCAAAAGGTGGTGATTGCTCTTGGGGATCACTTGA
    ATGCTAAATGCCATGCTTGCATCGGCGGCACTAATnnnGCGCGAAGATGTTCGTCAGCTnnnnn
    SEQ ID NO: 14
    >ise2c.pk001.i23 translation initiation factor
    GCACGAGGGTCGTATTCACCAGAAAGAAGATCAGAAGATTGGCCGGAAGATTCCAAAAATGGCCCGTCTAAGGAT
    CAAGGCAACTATGATGGGCCTCCAGGAATGGAACCCCAAGGGGCACTTGATACAAACTGGCACCAGGTCGTGGAA
    AGCTTCGACGACATGAATCTGAAGGAAGAATTGTTGAGAGGAATTTATGCTTACGGTTTTGAAAAGCCGTCTGCT
    ATCCAACAACGCGCTATTATGCCTTGCATTCAAGGCCGTGATGTCATAGCTCAAGCCCAGTCTGGTACTGGGAAG
    ACTGCTACCTTCTCTATTTCAATTCTTCAGCAAATCGATACCAGTATTCGTGAATGCCAAGCACTGATTTTGGCC
    CCTACTAGAGAGCTGGCTCAGCAGATCCAAAAGGTGGTGATTGCTCTTGGGGATCACTTGAATGCTAAATGCCAT
    GCTTGCATCGGCGGCACTAATGTGCGCGAAGATGTTCGTCAGCTGGAGAGTGGTGTGCATGTGGTGGTGGGTACA
    CCTGGTCGCGTGTACGACATGATAACTCGTCGTGCTCTCCGTGCTAACACTATCAAGCTGTTTGTACTTGATGAA
    GCTGATGAAATGCTGTCAAGAGGATTTAAAGATCnn
    SEQ ID NO: 15
    >ise2c.pk001.l24 translation initiation factor
    GCACGAGGGCCATCCTGTCACACATCTACCACCACGCCCTGCACGATAACTGGTTCCAAGCTCGAGACTTGCTCT
    TGATGTCACACTTGCAAGAGACTGTTCAACATTCAGACCCGAGCACTCAGATTTTGTACAATCGTACTATGGCCA
    ATCTAGGTTTGTGCGCTTTTCGAAGGGGCAATGTTAAAGAAGCCCATGGCTGCCTAGCTGAACTGATGATGACTG
    GCAAACCCAAGGAACTGTTAGCTCAAGGTCTGCTACCTCAGCGTCAACACGAGCGTTCAAAGGAACAGGAAAAGA
    TAGAGAAGCAACGCCAAATGCCGTTCCACATGCACATCAACTTGGAACTGCTTGAATGTGTGTATTTAGTGTCTG
    CCATGCTGATTGAAATTCCATACATGGCCGCCCACGAATTCGATGCTCGCCGGCGCATGATTAGTAAGACTTTCT
    ATCAGAATTTGCGCGCAAGTGAGCGTCAGGCTTTGGTAGGCCCGCCCGAATCCATGCGTGAGCATGCTGTGGCTG
    CCGCCAGGGCGATGCGCCGCGGAGACTGGCGTGCTTGCCTCAATTTTATTGTnnnTGnnnAATGAAT
    SEQ ID NO: 16
    >ise2c.pk005.b9 translation initiation factor
    GCACGAGGCTGATAGCCACCTGCCAAATTATCTTGAAATATAACCATTCACTAAAATATTTAACGTAATTTAGTG
    GTTAATTCTAAACTTAATCATGGACGACGACATGGTATTTGATCCATCTTTAAAGAAAAAGAAGAAGAAGAAGAC
    CGGTTTCGACTTAGATGCCGCTCTCGCAGGCGAACAAGGTGAGAGCACGAGCGTGGAGGCGCCCGCTGGGTCGGG
    TGACGTCGACTTGCCTGAGGATGATAACCTCGATTTGGATAATTTTGGAAAGAAAAAGAAGAAGAAGAAGAAGGG
    AGTCTTCAACATGGAAGAACTTGAAAGTACGTTACCGGAAACACCTCCGGCCGAAGAGCCGGAACAGCAGGAGGA
    CGAAGTTATTGACGATTTAGATCTAGATATTGACTTCTCTAAAACGAAAAAGAAGAAGAAGAAGAAAAACATnnn
    AnGAGCTCGTCCTTGAAGATGACACCAAGGGAGAAGATCAAGAGAATGTCGAGGATGTTAGTGGTGATTTATGGA
    GCGGCACAGACCGTGACTACACGTACGACGAGCTACTAGAGCGAGTGTTCGACATCATGCGAGAAAAGAnnnnnA
    GCATGGTTT
    SEQ ID NO: 17
    >ise2c.pk002.m10 SAR1
    GCACGAGGCAGATTCATATTTCCATCGCTTATTCGTTGCTGAGAAAAATCGTCGGTTTTAGCGACGTAACATATT
    GCTAATAAGTGTGAAATATTGTGATAAACTTCCTTTTAGCATTAGTTAATCTAGTTCAATTTTAAATAATTCAAA
    ATGTTTATCTTGGATTGGTTCACTGGTGTTCTCGGATTCCTTGGTCTGTGGAAGAAATCAGGCAAGCTACTGTTC
    CTGGGACTGGACAATGCTGGCAAGACCACACTCCTGCACATGCTGAAGGATGACAGATTGGCGCAGCATGTACCC
    ACATTGCATCCCACGTCGGAGGAACTGTCAATAGGCAGTATGCGTTTCACGACGTTCGACTTGGGCGGGCATCAG
    CAGGCGCGGCGCGTGTGGCGCGACTACTTCCCGGCGGTGGACGCCATCGTGTTCCTGGTGGACGCGTGCGACCGC
    CCGCGCCTGCCCGAGTCCAAGGCCGAGCTGGACTCGCTGCTCACTGACGAGACGCTCAGCnnACTGCCCCGTGCT
    CATCCTCGGCAACAAGATCGACAAGCCCGGCGCAGCTAGTGAGGACGAGCTCCGTCAGTTCTTCAACCTGTACCA
    ACAGACCACTGGAnAnGnCAAAGTATCnAGnTCAnnnnT
    SEQ ID NO: 18
    >ise2c.pk001.c14 Elongation factor
    GCACGAGGGTCTATCTCGGATATTACACGTGGATTGTAATCCGTGACTAACCAAAAATGGGCAAGGAAAAGnnnC
    ACATTAACATTGTCGTCATTGGACACGTCGACTCCGGCAAGTCCACCACCACCGGTCACTTGATCTACAAATGCG
    GTGGTATCGACAAACGTACCATCGAGAAGTTCGAGAAGGnnnCCCAGGAAATGGGGTAAGGGTTCCTTCAAATAC
    GCCTGGGTATTGGACAAACTGAAGGCTGAGCGTGAACGTGGTATCACCATCGATATTGCTCTGTGGAAGTTCGAA
    ACCGCTAAATACTATGTCACCATCATTGACGCTCCCGGACACAGAGATTTCATCAAGAACATGATCACTGGAACT
    TCCCAGGCTGATTGCGCCGTACTCATTGTCGCCGCTGGTACCGGTGAGTTCGAGGCTGGTATCTCGAAGAACGGA
    CAGACCCGTGAGCACGCTCTGCTCGCTTTCACACTCGGTGTCAAGCAGCTGATTGTGGGCGTCAACAAAATGGAC
    TCCACTGAGCCCCCATACAGCGAATCCCGTTTCGAGGAAATCnnnnnnn
    SEQ ID NO: 19
    >ise2c.pk001.d16 Elongation factor
    GCACGAGGCGGATATTACACGTGGATTGTAATCCGTGACTAACCAAAAATGGGCAAGGAAAAGnTTCACATTAAC
    ATTGTCGTCATTGGACACGTCGACTCCGGCAAGTCCACCACCACCGGTCACTTGATCTACAAATGCGGTGGTATC
    GAnnnACGTACCATnnnnn
    SEQ ID NO: 20
    >ise2c.pk001.j9 myosin
    GCACGAGGCTCTAGTCCCGTCACCGTCGCCAGTAGGGGGCGCCACAAGAACAGAAAGAGAATTATTTCAAACTCC
    AATTATAACCTACTAGATAACTCCAAAAGTTCTGTCAGTTCTAACTTTAATTTAACGGGGACGTCAGAGTTTATG
    GATAGGACCGATAAGATAATATCGGACGCGACTGAGCTACAAGCAATGCAGAACTTTATCATGGAGAAGATTTAC
    GAAATGGAACCTAATGAGAAGAAGAAGCAATCTGAGGTCGACAGGGTATTCAAACACGCATTATTAGAATTCAAA
    GACAATTTAGTAGCGACGTACAGCATAGTGGAGACGCGGGGCTCTGCGCTGAAGTACAAGGATCTGATCGGCAAC
    TTCCTGCACGTCATGGAGACGGTTTGTGCCAGGGAGGGGTCCACGCTCTCCATCACCATGGGGGTCAACGCCTTT
    AGGGGTTTCATGGACGAGTTTATGAGCCAACATGACACTGATAAAGCTAGGACGnnnnGnnnAAGGATAAAAAGA
    nnnnnnTGGACGATCCAATACAATACAAAGGCCATACGTTCATACTGTCCATGATCAACATACCAAnnnnAGTGT
    GAGATCTGCAAGACTTTCTTCATGTGGCCCATAGAGCGGTCACTCATATGCCAGACGTGTAAACTTGCCTCGCAT
    AAnnnTnnnACACTA
    SEQ ID NO: 21
    >ise2c.pk001.b14 potassium channel amino acid transporter
    TGACTCCACAGTGGGACAAACTCATAGAGCTTGATGTGTGGTACGCTGCTGTGACCCAAGTGTTCTTCTCTCTGT
    CTGTGTGCACCGGTGCCATCATTATGTTCTCGTCCTACAATGGATTCAGACAAAATGTTTACAGAGACGCGATGA
    TTGTCACTACTTTGGACACCTTCACCAGTTTGTTATCCGGTTTCACGATCTTCGGTATCCTGGGTAACTTGGCGT
    ACGAGTTGGACAAAGATGTGGATGACGTCACTGGTTCTGCAGGAACTGGACTTGCCTTCATTTCATACCCTGACG
    CGATCTCCAAAACTTTCCAGCCACAGTTGTTCGCAGTGCTGTTCTTCTTGATGATGACGGTACTAGGTATCGGAT
    CAGCAGTTGCTTTACTTTCCACCATCAACACCGTGATGATGGACGCGTTCCCTCGCATCAAGACCATCTACATGT
    CCGCCTTCTGCTGCACTATTGGATTTGCCATCGGTCTCATTTACGTCACACCTGGTGGCCAATATATTCTCGAGC
    TGGTGGATTACTTCGGTGGAACCTTCCTGATTCTCTTCTGTGCTATCGCTGAAATTATTGGTGTATTCTGGATTT
    ACGGCTTGGAGnnnTATGCCTGGATATTGAGTACATGTTGGGAGTTAAACTTCTTCTACTGGnnnTnnTGTTGGG
    GCGTTATTATGCCTGCCATGATGATnACCGnnnnnn
    SEQ ID NO: 22
    >ise2c.pk003.f2 potassium inwardly rectifier...
    GCACGAGGGTAAACAGATTTTAACACTACATTAATTTGTTCTAGAGTTAAATGTATTAATTCCGACTTAAAAACA
    GTGCTTGTGATAAGTGAACACAAATTATTGAGCAATGACTGACTTTATAAAACAATATTTCAAGGAACAATATGA
    AATAAATGAAAAAATGCTTTCGAAAATTGACGCGGATCTGCGAACCTGCGGAGCACACTTAGTAGCAGTGAAGTT
    AATGGTGACTGCCCTCGAGTTGAAAATGACTTCGATGAAGACAATGTATCAGGATCTAATGGAACTCAGAGAAAT
    AATCGTTCTTTTAAATCCACACTTGAAGAAACCGAGATAATAATACAATACAGTAAGGTTAACGAATACTATCTT
    TTAATTTCCTTAAATTATGTTCATAAAAATGATTAAGTTGTTTAGCTGAACACAGTGGTGTACTGACAGGATAGG
    TTTCATTAAACTTTGCATAATCGATCAGAAAACCGTGCTTTTCTTTTTTGTACTCGACCATTTCAATAAAGCGAT
    GACCCCATAGGATTnnnnTGGGTGGTGTAGCTCGACTTCGCTTGGACAGGCTGACCAGTTGATTCTATAGTGCCT
    TCAAACACTACGAnnATTTCCATAT
    SEQ ID NO: 23
    >ise2c.pk005.l20 amino acid transporter
    GCACGAGGATTTTCTTAAAACGGTACTGCAGCAAAAAGACGGCATTGAAGGTGGACTCGGTCTGCCTATCTGGTA
    CCTGGTGGTTTGTCTGTTCGGGTCATGGTTTATCATCTTCGTGATTGTGTCCCGAGGTGTAAAGAGTTCCGGTAA
    AGCTGCATACTTCTTGGCTCTCTTCCCCTACGTTGTGATGCTCATTTTGCTTATAACGACCTCTATTCTGCCCGG
    AGCCGGCACCGGCATTCTTTTCTTCCTGACTCCACAGTGGGACAAACTCATAGAGCTTGATGTGTGGTACGCTGC
    CGTGACCCAAGTGTTCTTCTCTCTGTCTGTGTGCACCGGTGCCATCATTATGTTCTCGTCCTACAATGGATTCAG
    ACAAAATGTTTACAGAGACGCGATGATTGTCACTACTTTGGACACCTTCACCAGTTTGTTATCCGGTTTCACGAT
    CTTnnnTATCCTnnnTAACTTG
    SEQ ID NO: 24
    >ise2c.pk001.d1 tubulin
    GCACGAGGCCGGTCTTCAGGGCTTCCTTATCTTCCACTCCTTCGGTGGAGGTACTGGATCTGGTTTCACTTCCCT
    CCTGATGGAGCGACTCTCCGTGGACTACGGCAAGAAGTCCAAGCTGGAGTTCGCCATCTACCCGGCGCCTCAGGT
    GTCCACCGCTGTCGTGGAGCCCTACAACTCCATCCTCACCACCCACACCACCCTTGAGCACTCCGACTGCGCCTT
    CATGGTCGACAACGAGGCCATCTACGACATCTGCCGCCGCAACCTCGACATCGAGCGCCCCACGTACACCAACCT
    GAACCGTCTCATCGGGCAGATCGTGTCCTCCATCACGGCCTCCCTGCGCTTCGACGGCGCCCTCAACGTCGATCT
    TACCGAGTTCCAGACCAACTTGGTGCCCTACCCCCGTATCCACTTCCCTCTGGTCACATACGCCCCGGTCATCTC
    TGCCGAGAAGGCGTACCACGAGCAGCTGTCGGTGGCTGAAATCACCAACGCATGCTTCGAGCCCGCCAACCAGAT
    GGTCAAGTGCGACCCTCGTCACGGCAAGTACATGGCTnnnnTGCATGTTGTACCGTGGTGACGTCGTCCCCAAGG
    ACGTGAACGCCGCCATCGCCACCATCAAGACCAAGCGTACCATCCAGnnnCGTCnnTTGGTGTCCnnCnnnGTnnn
    SEQ ID NO: 25
    >ise2c.pk001.k6 tubulin
    GCACGAGGATTCGTTTGGCAAGCCTCTTAACCGGTCGCGCTGAACGACGACTGATATTTAATTAATTTATATTCT
    ACGTTAAGTTCAACAAAACTCAATTCAAAATGCGTGAGTGCATCTCAGTACACGTTGGACAAGCCGGAGTCCAGA
    TCGGTAATGCCTGCTGGGAATTATATTGCCTTGAGCATGGAATCCAGCCTGACGGCCAGATGCCCACAGACAAGA
    CCGTGGGCGGTGGTGATGACTCCTTCAACACCTTCTTCAGCGAGACCGGTGCCGGCAAGCACGTCCCCAGGGCTG
    TGTTTGTTGACTTGGAACCCACAGTAGTTGATGAGGTCCGCACTGGCACATACAGACAGTTGTTTCATCCAGAAC
    AACTTATCACTGGTAAGGAAGATGCGGCCAACAACTACGCCCGTGGTCACTACACCATCGGCAAGGAAATCGTAG
    ACCTAGTCCTCGACCGCATCCGTAAGCTCGCCGACCAGTGCACCGGTCTCCAGGGCTTCCTTATCTTCCACnnnn
    nTCGGTGnnnnnACTGGGATCTGGTTTCACTTCCCTCCTGATGGAGCGACTCTCCGTGGACTACGGCAAGAAGTn
    nAAGCTGGAGTTCGCCATCTnnnCnGCnnCTCnnnnnTCnnnnnnCTGTC
    SEQ ID NO: 26
    >ise2c.pk001.l2 tubulin
    TTCGGCACGAGGGGCAAGCCTCTTAACCGGTCGCGCTGAACGACGACTGATATTTAATTAATTTATATTCTACGT
    TAAGTTCAACAAAACTCAATTCAAAATGCGTGAGTGCATCTCAGTACACGTTGGACAAGCCGGAGTCCAGATCGG
    TAATGCCTGCTGGGAATTATATTGCCTTGAGCATGGAATCCAGCCTGATGGCCAGATGCCCACAGACAAGACCGT
    GGGCGGTGGTGATGACTCCTTCAACACCTTCTTCAGCGAGACCGGTGCCGGCAAGCACGTCCCCAGGGCTGTGTT
    TGTTGACTTGGAACCCACAGTAGTTGATGAGGTCCGCACTGGCACATACAGACAGTTGTTTCATCCAGAACAACT
    TATCACTGGTAAGGAAGATGCGGCCAACAACTACGCCCGTGGTCACTACACCATCGGCAAGGAAATCGTAGACCT
    AGTCCTCGACCGCATCCGTAAGCTCGCCGACCAGTGCACCGGTCTCCAGGGCTTCCTTATCTTCCACTCCnnnCn
    GTGGAGnTnnnTGGATCTGGTTTCACTTCCCTCCTGATGGAGCGACTCTCCGTGGACTACGGCAAGAAGTnnAAG
    CTGGAGTTCGCCATCTAnnnn
    SEQ ID NO: 27
    >ise2c.pk002.b4 ubiquitin
    GCACGAGGATCAAAGAGTTACGAACCGTCACCATACTGAAGGAGATACCATTCGTCGTGCCATTCTCAACACGCG
    TCCTTATATTCCAAGGACTTTTAGCGAGAGAGAAGCACGACCACTGGTACGAAATGACGAACTTCAACGAGGGGC
    CCTCGATCAACATCAGTGTTCGAAGGACGCATTTATATGAAGATGCATTTGATAAACTTAGTCCGGATAATGAAC
    CTGATTTGAAGTTGAAACTTCGCGTGCAACTGATCAACCAGGCCGGTGCGGAGGAAGCTGGTGTCGACGGCGGTG
    GACTATTCCGAGAGTTTCTTTCTGAGCTCTTAAAATCTGCATTTGATCCGAACAGGGGTCTGTTCCGGCTGACAA
    TAGACAACATGTTGTATCCGAACCCCGCCGTACATCTACTGTACGATGACTTCCCCATGCACTACTACTTCGTCG
    GCAGGATGCTGGGAAAGGCGATGTACGAGAACCTGTTGGTGGAGCTGCCGCTGGCGGAGTTCTTCCTGGGCAAGC
    TGTGCGGCTGCGGGGAGGCCGACGTGCACGCGCTGGCCTCGCTCGACCCCGCGCTGCACCGCGGGTTGTTACTAC
    TC
    SEQ ID NO: 28
    >ise2c.pk001.j16 small nuclear ribonucleoprotein
    GCACGAGGGCCGGCCGCCGTGTTCGTGCCGTCCCGCCGGGCCGCGCGCCTACTGGCCGCCGACCTGCTGGCGCTG
    GCCGCGGCGCACGCGCAGCCCGCCGCCTTCCTGCGCGCGCGCCCCGACGTGCTGCAGCCCTTCCTCAAGAGGATC
    AACGACAAGATGCTGAAGGAGACGGTGGCTGCGGGCGTGGCGTACCTGCACGAGGGCGTGGACCCGGCGGAnnGG
    CGCCTGGTGCAACAACTGCTGGAGTCGGGCGCGCTGGCGCTCTGCGTCGTGGCCGCCGAGCTGGCCTGGGGACT
    SEQ ID NO: 29
    >ise2c.pk006.h23 small nuclear ribonucleoprotein
    GCACGAGGCGAAGATAAAGGTCGCGTGTGGACCTTAGGTTTAAGTTTATTATTAAATAATTTAGCCTAAACATAA
    GTCATGGCCAATAACGACAACTTTGCACAAGATGTTACTGATAATCAACTAAATGGAAATGCCGAAAATGGTGGT
    GGCGATACGCAAGAACATAATAGTGCCGAAGCCCCTGGGCGTGATGATGACAGAAAACTTTTTGTCGGAGGCCTG
    AGCTGGGAAACCACAGACAAGGAGTTACGTGACCACTTCAGTGCATATGGTGAGATTGAGAGCATCAATGTCAAG
    ACTGATCCAAACACTGGCAGATCAAGAGGATTTGCCTTTATTGTGTTCAAGGCACCAGATTCAATAGACAAAGTG
    ATGGCTGCTGGAGAGCACACTATTAACAACAAAAAAGTTGATCCGAAAAAAGCAAAGGCTAGACATGGAAAGATC
    TTTGTTGGTGGTCTTAGCAGTGAAATATCAGATGATGAGATCAAAAACTTCTTCAGTAATTTTGGAACAATAATT
    GAAGTCGAGATGCCCTTTGACAAAACCAAGAATCAGnnnAAGGGATTCTGCTTTATAACATTCGAGTCTGAACAG
    GTGGTCAATGAGCTGCTGAnnnCn
    SEQ ID NO: 30
    >ise2c.pk006.m8
    GCACGAGGCGCGTGTGGACCTTAGGTTTAAGTTTATTATTAAATAATTTAGCCTAAACATAAGTCATGGCCAATA
    ACGACAACTTTGCACAAGATGTTACTGATAATCAACTAAATGGAAATGCCGAAAATGGTGGTGGCGATACGCAAG
    AACATAATAGTGCCGAAGCCCCTGGGCGTGATGATGACAGAAAACTTTTTGTCGGAGGCCTGAGCTGGGAAACCA
    CAGACAAGGAGTTACGTGACCACTTCAGTGCATATGGTGAGATTGAGAGCATCAATGTCAAGACTGATCCAAACA
    CTGGCAGATCAAGAGGATTTGCCTTTATTGTGTTCAAGGCACCAGATTCAATAGACAAAGTGATGGCTGCTGGAG
    AGCACACTATTAACAACAAAAAAGTTGATCCGAAAAAAGCAAAGGCTAGACATGGAAAGATCTTTGTTGGTGGTC
    TTAGCAGTGAAATATCAGATGATGAGATCAAAAACTTCTTCAGTAATTTTGGAACAATAATTGAAGTCGAGATGC
    CCTTTGACAAAACTAAGAATCAGAGGAAGGGATTCTGCTTTATAACATTCGAGTCTGAACAGGTGGTCAATGAGC
    TGCTGAnGACTCCTAAGCAGnnnATTGGTGGCAnnnnnnnCGAC
    SEQ ID NO: 31
    >ise2c.pk001.a23
    GCACGAGGATGAAGTTGGCTCTGACACTCTTGGCTCTGGCGGCGGTGGCCACCGCTAAAAACATCAACGTCGAGG
    ATGCCATCGACCTAGAGGACATCACCGCCTACGGATACTTGGCTAAGATCGGTAAACCTCTTGCCGACGAAATCC
    GCAAAGCTGAGGAGGCAGAGAGCGCATCCAGAATTGTTGGTGGTCAGGCCTCCAGCCTCGGACAGTTCCCCTACC
    AGGCTGGTCTTCTCGCTGACTTCTCCGCTGGCCAAGGTGTGTGTGGTGGTTCCTTGGTGCGTGCCAACCGTGTTC
    TTACTGCTGCTCACTGCTGGTTCGATGGCCAGAACCAGGCCTGGAGATTCACCGTTGTTCTTGGCTCCATCCGTT
    TGTTCTCCGGTGGTACCAGAGTTCAAACCTCCAACGTTGTTATGCATGGAAGCTGGAACCCCAGTAACATCCGTA
    ATGACGTCGCCATGATCAGGCTGAACTCCAACGTTGGTCTTTCAAACACCATTGCACTCATCGCTCTGCCCAGCG
    GTAGCCAGCTCAACGAAAACTTCGCCGGTGAAAACGCCGTCGCnnnCTGGATTCG
    SEQ ID NO: 32
    >ise2c.pk001.a7
    GCACGAGGATCAAAATGAAACTGTTCCTCGCAGTCGTGTGCTTGGCCGTTGCCGCATCCGCGGTGGAGATTGGAG
    TTCCGTCTCAGGAAAACCCAGTCTTTGGCTACCATCAAAACTTCGGTATTGCCGAAGCTGCCAGGATCAAGAAGG
    CTGAGGAAGAAACCAGCCCTAGCGCCCAGAGGATCGTCGGAGGATCTGTCACTGACATTTCCAACGTCCCTTACC
    AGGCTGGTCTCGTGATCCAAGTTTTGGTCATCTTCCAATCCGTGTGCGGTGGTTCCATCATCTCCCACAACCGCA
    TCGTGACCGCTGCTCACTGCAACTGGGACGGTTCTATCACCGCTAACTCTTTCACCGTCGTACTTGGCTCCAACT
    TCCTCTTCTCCGGCGGTAACCGCATCACCACCAGAGATGTTGTCATGCACCCCAACTGGACCCCAACCACCGCTG
    CCAACGACATTGCTGTCCTCCGCATTAGCTCCGTTACTTTCACCAACGTGATCCAGCCCATCGCTCTGCCCAGCG
    GCAACGAGCTCAACAACGACTTCGTCAACTGGAACGCTATCGCTTCCGGATACGGTCTTACCGCTGATGGTGCTA
    ACATCGGTACTACCCAACGTGTCAGCTCCGTGGTACTCCCCGTGATCnnnnnnCGCCAGnnCGCTACCGTnnnnnn
    SEQ ID NO: 33
    >ise2c.pk004.c4
    GCACGAGGAATCTTAGTTACATTGGAGTGACTTTTATTTATCAATAACATTTTTATTTGAAGACTCAGTACGTAT
    TATCGCGTAGTTCAACAGAGTTGCTAGTGTAGTTTTCTGAAAGTTGCCATCTTGCTTTTGCAACTTTTAAATATA
    AAAGTCTTATTAGATCGTTTTTACTACCGATAAATTTACTAAAAATATAAAAGTGCAATTTACAATTACTCTGTT
    AGTGTCAGTTTGTGTGAATTTGTCGTAGTTATAAAAGGACACTGTATTGATTTTGTCAATCAGTTTGACGCATGC
    GCTCATTGGGTGCCGTAAAAAAGGGTTGGCCAACATTCCGAACAGTGTCGTTCCGGTCGCCGTTGTCGTGGTGTC
    GGTGAAGTTAGTGGTGGAATTTTTACGTGTATAACATCAAAAAATGGCGTCTGGTGTGACAGTTTCGGACGCGTG
    CAAAACGACGTACGAGGAGATTAAGAAAGACAAGAAGCACCGCTACGTGGTGTTCTACATCAGGGATGAGAAACA
    AATTGACGTAGAGACCGTCGGCGAACGTAACGCGGAATACGATCAGTTCCTTGAGGATCTGCAGnnnGGTGGCAC
    CGGnnAGTGCn
    SEQ ID NO: 34
    >ise2c.pk004.l4
    GCACGAGGCTGATATCTAATCTTAGTTACATTGGATTGACTTTTATTTATCAATAACATTTTTATTTGAAGACTC
    AGTACGTATTATCGCGTAGTTCAACGGAGTTGCTAGTGTAGTTTTCTGAAAGTTGCCATCTTGCTTTTGCAACTT
    TTAAATATAAAAGTCTTATTAGATCGTTTTTACTACCGATAAATTTATCAAAAATATAAAAGTGCAATTTACAAT
    TACTCTGTTAGTGTCAGTTTGTGTGAATTTGTCTTAGTTATAAAAGGACACTGTATTGATTTTGTCAATCAGTTT
    GACGCATGCGCTCATTGGGTGCCGTAAAAAAGGGTTGGCCAACATTCCGAACAGTGTCGTTCCGGTCGCCGTTGT
    CGTGGTGTCGGTGAAGTTAGTGGTGGAATTTTTACGTGTATAACATCAAAAAATGGCGTCTGGTGTGACAGTTTC
    GGACGCGTGCAAAACGACGTACGAGGAGATTAAGAAAGACAAGAAGnnnCCGCTACGTGGTGTTCTACATCAGGG
    ATGAGAAACAAATTGACGTAGAGACCGTCGGCGAACGTAACGCGGAATACGATCAGTTCCTTGAGGATCTGCAGA
    AGGGTGGCACCGGAGAGTGCAGATATGGCCTCTTCGACTTCGAGTACACGCACCAGTGCCAAGGCACGTCGnnn
    SEQ ID NO: 35
    >ise2c.pk004.n19
    GCACGAGGCCTCGTGCCGCGCGAATAGACAGTTTTGTGTGCACAATGTTGATCCTTTGGCTAAATATCATCGCAA
    TAATTTGTGTCATACCCTACGCAAATGGAGAAGGAAGGGTTGCAATAGCGCATTTACAATCGCTAAAGTCAGTGA
    CTGGTCAAATTCAATTTACGGAGACGGCAAAAGGGCTTCATGTCGAAGGAGTTATATTTGGTTTACCACCCGGTG
    CCTACGGGTTTCACGTTCACGAATTAGGAGATGTTGCACCTGGTTGCGACCAGGCGGGCCGGCACTTCAACCCTG
    AGGGATCCACCCACGGTGGCAGGAACTCCACCGTACGCCATGTCGGTGACCTCGGAAATGTAGTGTTCGTTAGCG
    AGCGAGCCGCTTATGCTACAGTAGACTTTGTAGATAGTCTATTGGCACTTCAAGGACGTAATAGTATATTGGGGC
    GCTCTTTGGTCTTGCATGAACAAACGGATGACCTAGGTTTGGGAGGAAACGCGACGTCTTTGACTACAGGTAACT
    CGGGGCCCCGGATAGCATGTGGTGCTATTGGAATCAAATCACCTTATGACCCTTGGAATGCTGCTAGCTCTATGT
    CTCCGTCGATGCTACTATTTATCACATCTTTAACTTTATTTACTTTAnnnTnnnAAnTnnnnGTATnAGTATTTA
    ATTTnnnnn
    SEQ ID NO: 36
    >ise2c.pk005.f21
    GCACGAGGCTTCCACATACGCGAATAGACAGTTTTGTGTGCACAATGTTGGTCCTTTGGCTAAATATCATCGCAA
    TAATTTGTGTCATACCCTACGCAAATGGAGAAGGAAGGGTTGCAATAGCGCATTTACAATCGCTAAAGTCAGTGA
    CTGGTCAAATTCAATTTACGGAGACGGCAAAAGGGCTTCATGTCGAAGGAGTTATATTTGGTTTACCACCCGGTG
    CCTACGGGTTTCATGTTCACGAATTAGGAGATGTTGCACCTGGTTGCGACCAGGCGGGCCGGCACTTCAACCCTG
    AGGGATCCAACCACGGTGGCnnnnnCTCCACCGTGCGCCATGTCGGTGACCTCnnAAATGTAGTGnTTGTTAGCG
    AGCGAGCCGCTTATGCTACAGTnnnCn
    SEQ ID NO: 37
    >ise2c.pk010.h5
    GCACGAGGGTCGAGAGATACGGTGCGCACATAGCAACAATATCAAAGTACAAAGGTCAGTAACTATGAGTGGTAA
    ATTGTTAAAAACTCTAATCCTTGGGGCACCTGCTTCAGGCAAGGGGACTATATCGTCTCGGATAGTGAAGAAATA
    TGCTGTGGCACACGTGTCCAGTGGGGACAAGCTGAGGGACCACATTGAGAAACAAACTGACCTAGGTAAAGAAGT
    CAAAAAGTACTTGAATGAAGGGAAACTTGTACCTGATGATGTCATGATAAAGTTTATGATCACAGAATTAAAAAA
    AGTTGAAGATAAACCATGGCTACTGGATGGATTCCCGAGGACTGTGGGACAGGCTGATGCTTTGTGGAAGGTACA
    ACCTGTTGATGTAGTAGnnnnnTTAGTAGTGCCTTTTGAGGTAATCATAGACAGAGTGAnnnAnCGCTGGGTGCA
    CTTGCCTTCGGGCCGAGTGTATAACATTGGCTTCAACACTCCTAAAGTGGAAGGTAAGGATGATGAGACAGGTGA
    GGACTTGGTTCAGAGACCTGACGACAAGCCAGAGGCTGTGCGCAAGCGGCTGGAGATCTATGAGAGTGTGACGAG
    GCCAGTCATAGAGTTCTAnnnnGCTAA
    SEQ ID NO: 38
    >ise2c.pk001.c18
    TGCTGCTGCTGGAAGCTGGGCCCAACCCTCCCGAGGAGAGCATTATACCAGGCTTAAGACAAACCTTGAAAGAAA
    CGCCCTACGACTGGAACTTCACCACCATTGACGACGGGGTCACGAGCCAGGCGCTGGCGGGCCACGTGCAGAGAC
    AGCCGCGGGGCAAGATGCTGGGCGGCAGCGGCTCGCTCAACGACATGGTGTACGCGCGGGGCCACCCCGAGGACT
    ACTACGAGTGGGCCGACATCGCCGGCGACGTCTGGAACTGGACCAACGTGCTGGACTACTTCAAGCGGACGGAGC
    ACATGACGGACGCCAATATCGTTCACAACnnnnAGCTCATGCAGTACCACGGCACGGnnnnnnCCATnnnnnnnT
    nnnGnnnCCAnTnnnnnnnn
    SEQ ID NO: 39
    >ise2c.pk004.p1
    GCACGAGGGGAAAACATGGGAAGGAGGTCGCATCAAGATGTTAGTGCTCGACTTGAACTGCCCGGTCGTTGGAGA
    CGACTGCAAAGACAGCCGCAAGAAGTTGCTTGTGGACTACTTCCATACAAACCTGCATACCCAGAACTTCTACGC
    GTTCCGCTTCTTTATCTGCGAAGTGTTGAACTTCATCAACGTCGTGGGCCAGATCTTCTTCATGGACTTTTTCCT
    GGACGGCGAGTTCTCCACGTACGGCAGTGACGTGGTCAGTTTCACCGAGATGGAGCCCGAGGAGCGTGTGGACCC
    GATGGCTAGAGTGTTCCCGAAAGTGACCAAGTGCACCTTCCACAAATACGGTCCTTCAGGAACCGTGCAGAAGTT
    CGACGGTCTGTGCGTGCTGCCATTGAACATCGTCAATGAAAAGATCTACGTGTTCCTGTGGTTCTGGTTTATGAT
    CCTGTCGATCCTGAGTGGAATTTCGCTGATTTACCGCATGGCCGTGGTGGCTGGACCGCGCGTGCGCCTGTACCT
    GCTGCGTGCGCGCAGCCGCCTGGCCCCGCnnnCGCnnnnnGnnnn
    SEQ ID NO: 40
    >ise2c.pk005.p13
    GCACGAGGATTTTAATAGCTATTATGACTTTACAGACTAGACGGATCAAGGCCATGCCTCTCGCTTGCATACTCA
    CCATCCGCACATACCGTATTGCGGTATGTCAATAAGTTGCAAATAATGTCTGTTCAGTTTTACAAGGATAAGATC
    AGCAGTATTTGCGAACTGTACCTACTACTAAGCTGATAATGTAATAATTAAACTTTATTATTGAAATAGATATGT
    ATAATTGACATCTTTCTCAAATGGGTGTCAATACTGCCAACTCTATTACCACAATTTCTTTTCGTATTTGCTTTT
    ATACTGAGCCTGATGACGTACTGTACTTTTTATTAGAATTTAATTTTTCTTATTTTTCTTACTACGTAGTCATTA
    AATCTGAGAAATTAAAAATTACTAATTTAGAACTCCCAAATTCTGAATGAGGTTCTAAAAAGTTGTTAGGAATAC
    TAAATACCATTTTACCAACATAAATCTAATTTCGTTACTTAAAATATTAAATGTATAATGAAATGTCTATGATAA
    GTGTTTACTATCTTTATATCGACAAAATTTATTTTCCATGTTTTAAAATTTATTTTTCAGATGTTTTGACGTGAT
    AAGTTTGTATTTTATCAATATCTGATAGTCGAGAGTTAnnnAnTATTG
    SEQ ID NO: 41
    >ise2c.pk001.f12
    GCACGAGGGAGGAGAGGTGGTGGCTGGCTTCCTTGCAAACGAAGCGTCGTAAATTACATCTTATTTGTAAATTTT
    AATAAAAATTTGATCGTTAAACGATCGAATCAGTAGTGATTTAAGTGCTCAAGCAGTTTCACATCCAATCGACAA
    TGAGTTCGAGTGTATGCTACAAGTGTAACCGGACAGGGCACTTCGCCCGCGAGTGCACCCAGGGTGGTGTTGCCG
    CTCGTGACTCTGGTTTCAACCGTCAGCGCGAAAAGTGCTTCAAGTGCAACCGCGCTGGGCACTTCGCTCGGGATT
    GCAAGGAGGAGGCCGACCGTTGCTACAGATGTAACGGCACGGGACACATAGCGCGTGAGTGCGCGCAAAGTCCGG
    ACGAGCCGTCGTGTTACACTTGCAACAAGACCGGGCACATCGCACGGAACTGCCCAGAGGGCGGGCGCGACAGCT
    CCAACCAGACCTGCTACAACTGCAACAAGTCCGGCCACATCTCACGCAACTGCCCCGACGGCACCAAGACTTGTT
    ACGTGTGCGGAAAGCCCGGACACATCTCCCGCGATTGCGATGAGGAGCGGAACTAACACACGCCTCTTCGCGACT
    GCCTATATATAnnnTAAACTATGTATATTATGATGCCACGCACGGACGATAAGCAAAGGACGCGATACGCGACAC
    TAGATCGTAAGACCACACGACTGTATGnnnnTAATGCAACG
    SEQ ID NO: 42
    >ise2c.pk001.n21
    GCACGAGGATAATAAACGTTAATATTTAACAAGTTGAAAAGTTTGTCTTTCAATTTGTGATTTTGTAAAGATCAT
    TCTATGGAATGGACAGTTTGCTATCTGTGAAACATCCATTAGCTTTGTGTTGAGAGCAGAGGTCGCGGCGGCGGG
    GTGATGCGGCCATGGCTTCGCGGCGCGTGACGCGCAAGTGGGAGGTGTTCGCGGGACGGAACCGATTCTGGTGCG
    ACGGCCGCCTCATGACGGCGCCGCACCCCGGCGTGTTCCTGCTCACGCTCGCGCTCATCTGCGGCACGTGCGCCC
    TGCACTTCGCCTTCGACTGCCCCTTCCTGGCCGTGCGCGTGTCGCCCGCCGTGCCCGCGGCCGGCGCCGCGCTGT
    GCGCGCTGACGCTGGCGGCGCTGCTGCGCACGGCGCTGTCCGACCCCGGCATCATCCCGCGCGCCGCCGCGGCCG
    AGGCGGCGGCGCTGGAGGCGGnG
    SEQ ID NO: 43
    >ise2c.pk004.e20
    CGCGCACGTCGCTCnnCAAGCCCGCTGCAGCGCCGGCCAAGCCCGCCCCCGCGGCGGCGCGCGCCACCAGTGCGA
    CCAGCCGCGCGGCCCCCGCGGCCCGGCCGGCCCCCAAGTCCGCAGTAGGCGCAGCGCGGCCCGCAGCACAAAAGA
    CAGATGCGGCCGCCAAACCCGCGGCGACCCGGGTTGCGGCTCCGCGTCCCGCGCTGTCGGCGCCCAGGCCCCAGC
    CTAAGCCGGCAGACAAGAAGCCAGTACCGAATGGTGACGTGAAAGACTCCAAGCCAGCCGCGCGGCCCGCGCCCC
    GGCCGGCCGCGGCCGCGCGCCCCGCGCCGCGCCCCACTCCCCGCGCCCCCGCCGCACnGGTCGCACCCACTACTn
    nnnnGAGTGCCCCCAAGCCGGCGCCGCGTGCTCCCCTGGACAAGCAGAGCnnnGACCTCGCTAACAAACGCATCn
    nnGnCAnGGCAGCACCGCCTAGGACTGCTCCCCCTAAGACGACAACGACGACAACAGGnnnnnnnnnnnnnGTnn
    CGAAGnnnnn
    SEQ ID NO: 44
    >ise2c.pk005.n11
    GCACGAGGCTATAACAAGCAGCATATAAAAATGAAATTCTTGCTGTCTTTCGCTGCCGTCATCGCCGTGGCCGCC
    GCTGGCCTGGTGCCCGTTGGACCCGCCGGCCCTGCGCCCGCTCCTGAGGCCCCTGAGGTCTTCGAGCCCGTCGCT
    ATTGGACCCGCTGTCATTGACTCCTTCGAGCCCATCGCCATCGGACCCGCTATCATCGACTCCTTCGAGCCCATC
    GCCATCGGACCCGCTATTGTTCCATCTCCCGAGCCCGTCGCCATCGGACCCGCCATCATTGAGAGCCCAGAGCCC
    GTTGCTGTCGGACCTGCATGGATTGACTTCCCCCTGCCCGACGGTGGTGCTGCCGTTGCCCCCGTTGAGCCCTCT
    CCCGTGGCTGTTATCCCCGGTCCCGTGTCCACTGAGGTTGCTTCAGGCACTCCCCTCGTTCAGATCATCCTGAAC
    ATCAACnnnnnnTCTGCTGACGTTAGCCCCGTTGCTGTnGGCCCCGCTGTCGAGnnnACACCCGTGCACGTTGTG
    GACTCTGCCCCTGAACCCGTCCACGTTGTGnnnnnnGCCCCnnnnnCnATCnnnnnGTCGn
    SEQ ID NO: 45
    >ise2c.pk003.l14
    GCACGAGGCTTAGAGTAAGCATAGGTGTATTTATGTATTGAGTCGGAAGAAGCAATGGACGATCCAAATAGGATG
    ATGGCGCATAGCGGCGGGCTTATGGGGCCGCAGGGCTACGGCCTGCCTGGCGGCGAGGGAACTCCAACCGCAGGC
    GAAGGTGAAGCCCGCAAGCAAGATATTGGTGAAATATTGCAACAGATCATGAATATTACAGATCAAAGTCTTGAT
    GAAGCGCAAGCGAGAAAACATACTCTCAACTGTCACAGAATGAAGCCTGCCCTATTTTCAGTGTTGTGTGAAATC
    AAAGAGAAAACAGTGCTGTCCCTCCGCAACACGCAAGAGGAGGAGCCCCCAGATCCCCAGCTGATGCGCTTGGAC
    AACATGCTCATAGCCGAGGGGGTCGCTGGCCCTGAAAAGGGTGGTGGTGCGGGCGCTGCAGCTTCGGCATCAGCT
    GCTGCTGGTGAATGGGACAATGCCATCGAGCACTCTGACTACCGTGCGAAGTTGGCGCAGATCCGCCAGATCTAC
    CACCAGGAGCTGGACAAGTATGAGAATGCTTGTAATGnnnnnnCCACCCACGTGATGAACTTACTCCGCGAGCAG
    AGCCGCACCAGGCCTATCACAnn
    SEQ ID NO: 46
    >ise2c.pk003.e24
    GCACGAGGCCAGGTTTGAGAAAAACGCTTAAACTGCCACAAAATCCCGTTCTCGAAGAAGCACTTTTCACTTATT
    AATAAGTAACTTGTGTAAAATGTGGTTTAAATGTGTATTTTACTAAACCTCAATAAATATATTTATATCAAAATA
    TTTTTTTTCTATACTGTATTATTTATTCCTATAGTACATATTATAATCCGAACGCTCCGTGAGTCCGAACAGGGG
    TAATTTTTTGGTAGTTCGGATTATCGAGGCTCTACTGTATACCTACTTTTTGTTAAAATATTTTAGTCTTATATA
    CGACTTCCTAACTAATCCATATCTCTTAGAGCTTTCGAATATCCATTTGCCTTTTTCTTAAAAAGATTAATAACT
    ATTTATATATATCCCAAATATATAAAAACAACCACTCCAATTATTATTATTCAAATATGACAAACTAGATAGAAT
    GTCCCAAGAAATTTGCAAAAAAGTAATGTTCAAATTATTAACCGAAGAACGAATTnnnGAGTGTATAATATTATA
    CAGACATTTAGAAATTTTTAATAGGCTCCAATCGCATGAGAGGTCGCTTTAAAATTCGGCATTGGTGTGTGCGTT
    GCAATTTAATCTTTAACACCCnnn
    SEQ ID NO: 47
    >ise2c.pk005.l5
    GCACGAGGGGACGTGTTTACAATTTACTTTCGTGCTCGTGTGATTTTAATTAAAACAGTGCTAAGTGCTCTAGGA
    CGCTGAATAACTGATATTTGTTTTAAAAGTTGATATAAATTAATCACAATGAATAGAGATAAACGAGAACCAGAG
    TATCCAACGGAGTTGGAGTCTCAATTCGTAATGCGTTTACCTGAGGAGCCTGCAAAAGTTTTGAGAGAAGTGTTG
    AAATCCGGAGAGAACCTGAAAAACAGACTGACGATACAAATAGAAAACGACATGCGCACGGGCGAGGTAAGGTTT
    GATCACTGGTTGATGCACGCCAAGATCGTGGATCTACCAACCATCATAGAATCTCTAAAAACGATCGACAACAAG
    AGTTTCTACAAAACAGCAGATATATGCCAAATGATGATTTGTAAAGAAGAACCTGACCAACCATCCACAGAGGAA
    GAGTCACCAGCTAAAAATAAGAAAAAAGATCCATACAAAGTTGACAAAAAGTTCCTATGGCCACACGGCATCACA
    CCGCCTACGAAGAACGTACGGAAGCGTCGATTTAGAAAAACCCTTAAAAAGAAATATGTAGAAGCACCAGAAATT
    GAAAAGGAAGTGAAGAGGCTGCTGAGnGCAnnCnATGAGGCTGTTAGTGTTAACTGGGAGGTCATCAAnnnnnnn
    GAT
    SEQ ID NO: 48
    >ise2c.pk006.k12
    GCACGAGGGTCGAATGGAACATGGCGGTGCTAGGCAGGATGTGCATAAGTTTTTGATTTTTGCATTTTTAACGAG
    TTGCTTATATCAGTTAGCTTTCTAAATAATTTCTGACTTATTTCGTGTGTTATAATATTTGTTATAGTGTAAAAG
    CTTATCCACCCCAGGAATTTCCTATCTGGACTTACTTAGTTCTGCAATGAAAATTATTATTCGTTGGTAGTGTAA
    AAATAATTGTGACAAATATATCACTTTGCTTCAGTGTGCCGTGTTGGTCATGGCTACGCTCCTCCAAGAGAATGG
    TATAAAGGAGTTAAGCAAAGTTGTGCCTAACCGTGGTATATCCTCACATAGTGTAACAAATCATATGGTGCCTGA
    TCATGAATATTGCGAAGCTGGGTCAACTAGCACGTCACAGATGAAGTGTACCGATACAAGTGAGGCGATGGCGCC
    ACCCGCCGCCATTGAAGAAGAGGAGGATACACCAGAAATAGATATAATGATAAACAATGTTGTGTGCAGTTTTAG
    TGTTAAGTGCCACCTGAACCTTAGACAGATAGCATTnnnTGGTGTGAACGTTGAATTTCGCCGCGAGAACGGCAT
    GGTAACTATGAAGTTACGGCGTCCATACACTACTGCGTCCATCTGGTCGTCCGGCCGCGTGACGTGCACTGGTGC
    AACCAGCG
    SEQ ID NO: 49
    >ise2c.pk010.i8
    GCACGAGGGAATATTGCGAAGCTGGGTCAACTAGCACGTCACAGATGAAGTGTACCGATACAAGTGAGGCGATGG
    CGCCACCCGCCGCCATTGAAGAAGAGGAGGATACACCAGAAATAGATATAATGATAAACAATGTTGTGTGCAGTT
    TTAGTGTTAAGTGCCACCTGAACCTTAGACAGATAGCATTAAATGGTGTGAACGTTGAATTTCGCCGCGAGAACG
    GCATGGTAACTATGAAGTTACGGCGTCCATACACTACTGCGTCCATCTGGTCGTCCGGCCGCGTGACGTGCACTG
    GTGCAACCAGCGAGGACCAGGCGAAGGTTGCCGCACGACGGTATGCGCGCGCCCTTCAGAAGCTCGGCTTCCAAG
    TGCGTTTCCGCAATTTCCGTGTAGTCAATGTATTAGGCACCTGTCGGATGCCGTTTGGTATAAGGATCATATCTT
    TTTCGAAAAAATACAAGGAAGCAGACTATGAACCTGAGCTCCATCCTGGAGTCACATATAAGTTATACAATCCTA
    AAGCCACACTCAAGATATTCTCCACTGGTGGTGTGACTATCACAGCTCGGAGTGTGAGTGACGTTCAGTCAGCCG
    TGGAACGCATCTTCCCTTTGnTGTACGAGTTCCGCAAGCCTCnnnnACCGGCAnnnnA
    SEQ ID NO: 50
    >ise2c.pk010.b12
    GCACGAGGGTACCAAAAGCTCTTTTCATTGCAGCTGAAGGGTCACTGCAACTTGGCCAATCAGAATTAGCATTGA
    AACTATTCAAAGAACTAAAACAAGAAGGAATGGAAATCAGGCAACATTTCTATTGGCCTTTGTTAGTTCAGAAGG
    CAAAGGAAAATGATGAGGAAGGCCTCTTGCAAATTTTAAAAGAAATGAGCAGCAATGACTTTACTGTTACTGGAG
    AAGCGTTAAGAGACTATGTTATCCCTTACTTGATAAAAAAAGATTCTCCACAGAATGTCTTACTTAAACTTCAAA
    TTGCAAATGTACCAACAATCCATGCTGCAAGAAATCTAATGGTTGATCTTTTGGATTCTGGAGACATAAAAGGCG
    CAGCGGAAATAGCTCTGCAATATAGACCTTGGGGCAACTACTCTCTTGTTGCCAGGTCCCTCATCAATGCAGTGA
    ATAAGACAAAAGATGTAGAATCGTTTGCTAAAATTCTTCATGCTATAAGCAGTAAACCTTTGTCACAGGGTGAAG
    AAGATGTTGCTGCCAACAATGAGGAAGGTCAAAGTGATGAAAATAATGATATTCATGAAGTCGGCCGTATTGTGA
    GGTCGTCTGCCAAGAGTTTGGCTAAACCAGACTTAATAGnAAnnnnTTTAGA
  • TABLE 2
    List of dsRNA primers. (Note: the sense RNA primer sequence
    and the antisense RNA primer sequences shown in table 2
    were generated with 2 thymine residues at the 3′ end.)
    Primer # Target Gene ID Seq ID Target
    0075 juvenile ise1c.pk002.m13 AACATGGTATCCGACTTC
    hormone diol AGGAA
    kinase
    0076 juvenile ise1c.pk002.m13 AAGGTCGCTGACGAGAA
    hormone diol CAAGGA
    kinase
    0077 juvenile ise1c.pk002.m13 AAGTGTCCTGGGCTTGAG
    hormone diol TTCCA
    kinase
    0078 juvenile ise1c.pk003.f7 AAGAAGAAGCTCCTCCA
    hormone diol CGTGTT
    kinase
    0079 juvenile ise1c.pk003.f7 AAGGTCGCTGACGAGAA
    hormone diol CAAGGA
    kinase
    0080 juvenile ise1c.pk003.f7 AATGTCCTGGGGCTGAGT
    hormone diol TTCAA
    kinase
    0081 juvenile ise1c.pk005.a15 AAGAATAAGCTCCTCCA
    hormone diol CGTGTT
    kinase
    0082 juvenile ise1c.pk005.a15 AATTTGTCGAGGAGACC
    hormone diol CTATTG
    kinase
    0083 juvenile ise1c.pk005.a15 AAGTTCGCGTTCACTCTT
    hormone diol GAAGA
    kinase
    0084 ribosomal ise1c.pk006.d24 AACTGCCCCTTAACCTCA
    protein L18a TCTAT
    0085 ribosomal ise1c.pk006.d24 AATCACGCTGAAACCAC
    protein L18a TGTATA
    0086 epoxide ise2c.pk009.i4 AAAATATGGCGCGCCTA
    hydrolase TTGTTT
    0087 epoxide ise2c.pk009.i4 AACGTTCTCGGTCTTTCA
    hydrolase CTGCT
    0088 epoxide ise2c.pk009.i4 AAGTCATCGTTCCAAGTC
    hydrolase TACCT
    0089 V-ATPase A ise2c.pk001.d19 AACCCCTTGAATGTTAAG
    subunit GTCGG
    0090 V-ATPase A ise2c.pk001.d19 AAGTACACCATGTTGCA
    subunit AGTATG
    0091 V-ATPase A ise2c.pk001.d19 AACGTGTCCATGATGGCT
    subunit GACTC
    0092 H+-ATPase V- ise2c.pk001.e14 AAACCTACAAAATGGCC
    type subunit GAAAAC
    0093 H+-ATPase V- ise2c.pk001.e14 AATCTACGGACCCTTCTT
    type subunit TGGAG
    0094 V-ATPase A ise2c.pk001.f20 AACTCTGACGTCATCATC
    subunit TACGT
    0095 V-ATPase A ise2c.pk001.f20 AAGTGCTTGGGTAACCCC
    subunit GACAG
    0096 V-ATPase A ise2c.pk001.f20 AACTGGCTCATCTCCTAC
    subunit AGCAA
    0097 novel sequence ise2c.pk010.h3 AAACAGTGCGTCGTAAT
    ATATTC
    0098 novel sequence ise2c.pk010.h3 AAGGCACATGGTCCTTCA
    CTGAT
    0099 novel sequence ise2c.pk010.h3 AACACCATGACCCTCGTG
    TACAA
    0100 Larval cuticle ise2c.pk007.k24 AACGAGGCCGGATCTCTT
    protein LCP-17 AAGCA
    0101 Larval cuticle ise2c.pk007.k24 AACTTCACACATAACTAG
    protein LCP-17 ACAAA
    0102 Larval cuticle ise2c.pk007.k24 AATGCGTGGCGATTTCAA
    protein LCP-17 ACTTA
    0103 transcriptional ise2c.pk011.a10 AAAAAACACAGACCACG
    repressor TTCACA
    0104 transcriptional ise2c.pk011.a10 AATCGATGGTGGTGTTAT
    repressor TCGCT
    0105 novel sequence ise2c.pk011.h12 AAAGAAAATGCTACGCG
    TTACGA
    0106 novel sequence ise2c.pk011.h12 AACCCTTGGACACTACTG
    GAAGA
    0107 novel sequence ise2c.pk011.h12 AAGGATCCTATGTGTACC
    AGGTT
    0108 translation ise2c.pk001.d22 AAACTCGGCACACAACA
    initiation factor CAATGG
    5A
    0109 translation ise2c.pk001.d22 AATACGAAGATATCTGC
    initiation factor CCTTCC
    5A
    0110 translation ise2c.pk001.d22 AATCAACAGCTCTTACAT
    initiation factor AAATG
    5A
    0111 eukaryotic ise2c.pk001.d9 AAAGAAGATCAGAAGAT
    initiation factor TGGCCG
    eIF-4A
    0112 eukaryotic ise2c.pk001.d9 AAAAGCCGTCTGCTATCC
    initiation factor AACAA
    eIF-4A
    0113 eukaryotic ise2c.pk001.d9 AATGCTAAATGCCATGCT
    initiation factor TGCAT
    eIF-4A
    0114 eukaryotic ise2c.pk001.i23 AAGATCAGAAGATTGGC
    initiation factor CGGAAG
    4A
    0115 eukaryotic ise2c.pk001.i23 AATTCTTCAGCAAATCGA
    initiation factor TACCA
    4A
    0116 eukaryotic ise2c.pk001.i23 AAATGCTGTCAAGAGGA
    initiation factor TTTAAA
    4A
    0117 RNA ise2c.pk001.l24 AAGCTCGAGACTTGCTCT
    polymerase TGATG
    sigma subunit
    SigE
    0118 RNA ise2c.pk001.l24 AACTGTTAGCTCAAGGTC
    polymerase TGCTA
    sigma subunit
    SigE
    0119 RNA ise2c.pk001.l24 AAGACTTTCTATCAGAAT
    polymerase TTGCG
    sigma subunit
    SigE
    0120 translation ise2c.pk005.b9 AAACTTAATCATGGACG
    initiation factor ACGACA
    2, subunit 2 beta
    0121 translation ise2c.pk005.b9 AAAGAAGAAGAAGAAGA
    initiation factor AGGGAG
    2, subunit 2 beta
    0122 translation ise2c.pk005.b9 AAGATCAAGAGAATGTC
    initiation factor GAGGAT
    2, subunit 2 beta
    0123 putative sar1 ise2c.pk002.m10 AAAATCGTCGGTTTTAGC
    protein GACGT
    0124 putative sar1 ise2c.pk002.m10 AACTGTCAATAGGCAGT
    protein ATGCGT
    0125 putative sar1 ise2c.pk002.m10 AACCTGTACCAACAGAC
    protein CACTGG
    0126 elongation factor ise2c.pk001.c14 AACCAAAAATGGGCAAG
    1-alpha GAAAAG
    0127 elongation factor ise2c.pk001.c14 AACGTGGTATCACCATCG
    1-alpha ATATT
    0128 elongation factor ise2c.pk001.c14 AACAAAATGGACTCCAC
    1-alpha TGAGCC
    0129 elongation ise2c.pk001.d16 AATCCGTGACTAACCAA
    factor-1alpha F2 AAATGG
    0130 elongation ise2c.pk001.d16 AACATTGTCGTCATTGGA
    factor-lalpha F3 CACGT
    0131 Oligosaccharyl ise2c.pk005.h3 AATTTGTGAGACTGGTGG
    transferase 48 kDa CCGAA
    subunit
    0132 Oligosaccharyl ise2c.pk005.h3 AATCTGATTGTATTCGCC
    transferase 48 kDa CCCTC
    subunit
    0133 Oligosaccharyl ise2c.pk005.h3 AACACTCTAGTTCTGCCT
    transferase 48 kDa ATTCT
    subunit
    0134 Myosin ise2c.pk001.d21 AACACACATCACAATGG
    regulatory light CGGATA
    chain
    0135 Myosin ise2c.pk001.d21 AAGGATGGCATCATCGG
    regulatory light CAAGAA
    chain
    0136 Myosin ise2c.pk001.d21 AAAGGCTTCATCGACAC
    regulatory light CGCGAA
    chain
    0137 novel sequence ise2c.pk001.j9 AAACTCCAATTATAACCT
    ACTAG
    0138 novel sequence ise2c.pk001.j9 AAGTACAAGGATCTGAT
    CGGCAA
    0139 novel sequence ise2c.pk001.j9 AAGACTTTCTTCATGTGG
    CCCAT
    0140 novel sequence ise2c.pk002.f12 AAACAAAGTATCGCCTA
    CACCGC
    0141 novel sequence ise2c.pk002.f12 AATAGCGTCGATCTTCAA
    CGACT
    0142 potassium ise2c.pk001.b14 AACTCATAGAGCTTGATG
    coupled amino TGTGG
    acid transporter
    0143 potassium ise2c.pk001.b14 AAGATGTGGATGACGTC
    coupled amino ACTGGT
    acid transporter
    0144 potassium ise2c.pk001.b14 AACCTTCCTGATTCTCTT
    coupled amino CTGTG
    acid transporter
    0145 inwardly ise2c.pk003.f2 AACAGTGCTTGTGATAA
    rectifying K+ GTGAAC
    channel protein
    0146 inwardly ise2c.pk003.f2 AAGTTAATGGTGACTGCC
    rectifying K+ CTCGA
    channel protein
    0147 inwardly ise2c.pk003.f2 AATAAAGCGATGACCCC
    rectifying K+ ATAGGA
    channel protein
    0148 potassium ise2c.pk005.l20 AAACGGTACTGCAGCAA
    coupled amino AAAGAC
    acid transporter
    0149 potassium ise2c.pk005.l20 AAGCTGCATACTTCTTGG
    coupled amino CTCTC
    acid transporter
    0150 potassium ise2c.pk005.l20 AAATGTTTACAGAGACG
    coupled amino CGATGA
    acid transporter
    0151 alpha tubulin ise2c.pk001.d1 AACGTCGATCTTACCGAG
    TTCCA
    0152 tubulin alpha ise2c.pk001.k6 AATTCAAAATGCGTGAG
    chain TGCATC
    0153 tubulin alpha ise2c.pk001.k6 AAATCGTAGACCTAGTCC
    chain TCGAC
    0154 tubulin alpha ise2c.pk001.l2 AAACTCAATTCAAAATG
    chain CGTGAG
    0155 tubulin alpha ise2c.pk001.l2 AACTTATCACTGGTAAGG
    chain AAGAT
    0156 ubiquitin kinase ise2c.pk002.b4 AAGAGTTACGAACCGTC
    ACCATA
    0157 ubiquitin kinase ise2c.pk002.b4 AAACTTAGTCCGGATAAT
    GAACC
    0158 ubiquitin kinase ise2c.pk002.b4 AAGGCGATGTACGAGAA
    CCTGTT
    0159 nuclear ise2c.pk001.j16 AACGACAAGATGCTGAA
    ribonucleoprotein GGAGAC
    200 kDa
    Helicase
    0160 Sqd protein ise2c.pk006.h23 AAGATAAAGGTCGCGTG
    Homologue TGGACC
    (RNA binding)
    0161 Sqd protein ise2c.pk006.h23 AATGTCAAGACTGATCC
    Homologue AAACAC
    (RNA binding)
    0162 Sqd protein ise2c.pk006.h23 AACATTCGAGTCTGAAC
    Homologue AGGTGG
    (RNA binding)
    0163 pre-mRNA- ise2c.pk006.m8 AACATAAGTCATGGCCA
    binding protein ATAACG
    0164 pre-mRNA- ise2c.pk006.m8 AAGAACATAATAGTGCC
    binding protein GAAGCC
    0165 pre-mRNA- ise2c.pk006.m8 AAACACTGGCAGATCAA
    binding protein GAGGAT
    0166 pre-mRNA- ise2c.pk006.m8 AAGATCTTTGTTGGTGGT
    binding protein CTTAG
    0167 pre-mRNA- ise2c.pk006.m8 AACAGGTGGTCAATGAG
    binding protein CTGCTG
    0168 chymotrypsin- ise2c.pk001.a23 AAGTTGGCTCTGACACTC
    like; protease TTGGC
    0169 chymotrypsin- ise2c.pk001.a23 AAATCCGCAAAGCTGAG
    like; protease GAGGCA
    0170 chymotrypsin- ise2c.pk001.a23 AACCGTGTTCTTACTGCT
    like; protease GCTCA
    0171 chymotrypsin- ise2c.pk001.a23 AACGTTGTTATGCATGGA
    like; protease AGCTG
    0172 chymotrypsin- ise2c.pk001.a23 AAAACTTCGCCGGTGAA
    like; protease AACGCC
    0173 chymotrypsinogen; ise2c.pk001.a7 AAATGAAACTGTTCCTCG
    protease CAGTC
    0174 chymotrypsinogen; ise2c.pk001.a7 AAGAAGGCTGAGGAAGA
    protease AACCAG
    0175 chymotrypsinogen; ise2c.pk001.a7 AACTCTTTCACCGTCGTA
    protease CTTGG
    0176 chymotrypsinogen; ise2c.pk001.a7 AACGACATTGCTGTCCTC
    protease CGCAT
    0177 chymotrypsinogen; ise2c.pk001.a7 AACATCGGTACTACCCA
    protease ACGTGT
    0178 actin- ise2c.pk004.c4 AAGACTCAGTACGTATTA
    depolymerizing TCGCG
    0179 actin- ise2c.pk004.c4 AAGTTGCCATCTTGCTTT
    depolymerizing TGCAA
    0180 actin- ise2c.pk004.c4 AATCAGTTTGACGCATGC
    depolymerizing GCTCA
    0181 actin- ise2c.pk004.c4 AATGGCGTCTGGTGTGAC
    depolymerizing AGTTT
    0182 actin- ise2c.pk004.c4 AACGCGGAATACGATCA
    depolymerizing GTTCCT
    0183 actin ise2c.pk004.l4 AAGACTCAGTACGTATTA
    depolymerizing TCGCG
    factor
    0184 actin ise2c.pk004.l4 AAGTTGCCATCTTGCTTT
    depolymerizing TGCAA
    factor
    0185 actin ise2c.pk004.l4 AATCAGTTTGACGCATGC
    depolymerizing GCTCA
    factor
    0186 actin ise2c.pk004.l4 AAAAATGGCGTCTGGTG
    depolymerizing TGACAG
    factor
    0187 actin ise2c.pk004.l4 AATACGATCAGTTCCTTG
    depolymerizing AGGAT
    factor
    0188 dismutase; ise2c.pk004.n19 AATAATTTGTGTCATACC
    superoxide CTACG
    0189 dismutase; ise2c.pk004.n19 AAGTCAGTGACTGGTCA
    superoxide AATTCA
    0190 dismutase; ise2c.pk004.n19 AATTAGGAGATGTTGCA
    superoxide CCTGGT
    0191 dismutase; ise2c.pk004.n19 AACAAACGGATGACCTA
    superoxide GGTTTG
    0192 dismutase; ise2c.pk004.n19 AATGCTGCTAGCTCTATG
    superoxide TCTCC
    0193 superoxide ise2c.pk005.f21 AATTTGTGTCATACCCTA
    dismutase CGCAA
    0194 superoxide ise2c.pk005.f21 AAAAGGGCTTCATGTCG
    dismutase AAGGAG
    0195 superoxide ise2c.pk005.f21 AATTAGGAGATGTTGCA
    dismutase CCTGGT
    0196 adenylate kinase ise2c.pk010.h5 AAAGGTCAGTAACTATG
    isozyme 3 AGTGGT
    0197 adenylate kinase ise2c.pk010.h5 AAGAAATATGCTGTGGC
    isozyme 3 ACACGT
    0198 adenylate kinase ise2c.pk010.h5 AACTTGTACCTGATGATG
    isozyme 3 TCATG
    0199 adenylate kinase ise2c.pk010.h5 AACATTGGCTTCAACACT
    isozyme 3 CCTAA
    0200 adenylate kinase ise2c.pk010.h5 AAGCGGCTGGAGATCTA
    isozyme 3 TGAGAG
    0201 ecdysone ise2c.pk001.c18 AACCCTCCCGAGGAGAG
    oxidase CATTAT
    0202 ecdysone ise2c.pk001.c18 AACGCCCTACGACTGGA
    oxidase ACTTCA
    0203 ecdysone ise2c.pk001.c18 AACTGGACCAACGTGCT
    oxidase GGACTA
    0204 innexin-2 ise2c.pk004.p1 AAAACATGGGAAGGAGG
    TCGCAT
    0205 innexin-2 ise2c.pk004.p1 AAGTTGCTTGTGGACTAC
    TTCCA
    0206 innexin-2 ise2c.pk004.p1 AACGTCGTGGGCCAGAT
    CTTCTT
    0207 innexin-2 ise2c.pk004.p1 AATACGGTCCTTCAGGA
    ACCGTG
    0208 innexin-2 ise2c.pk004.p1 AATTTCGCTGATTTACCG
    CATGG
    SEQ ID NO
    Target/sense/
    Primer # Sense strand Antisense strand antisense
    0075 CAUGGUAUCCGACUUCAGG CCUGAAGUCGGAUA 51/52/53
    CCAUG
    0076 GGUCGCUGACGAGAACAAG CUUGUUCUCGUCAG 54/55/56
    CGACC
    0077 GUGUCCUGGGCUUGAGUUC GAACUCAAGCCCAG 57/58/59
    GACAC
    0078 GAAGAAGCUCCUCCACGUG CACGUGGAGGAGCU 60/61/62
    UCUUC
    0079 GGUCGCUGACGAGAACAAG CUUGUUCUCGUCAG 63/64/65
    CGACC
    0080 UGUCCUGGGGCUGAGUUUC GAAACUCAGCCCCA 66/67/68
    GGACA
    0081 GAAUAAGCUCCUCCACGUG CACGUGGAGGAGCU 69/70/71
    UAUUC
    0082 UUUGUCGAGGAGACCCUAU AUAGGGUCUCCUCG 72/73/74
    ACAAA
    0083 GUUCGCGUUCACUCUUGAA UUCAAGAGUGAACG 75/76/77
    CGAAC
    0084 CUGCCCCUUAACCUCAUCU AGAUGAGGUUAAGG 78/79/80
    GGCAG
    0085 UCACGCUGAAACCACUGUA UACAGUGGUUUCAG 81/82/83
    CGUGA
    0086 AAUAUGGCGCGCCUAUUGU ACAAUAGGCGCGCC 84/85/86
    AUAUU
    0087 CGUUCUCGGUCUUUCACUG CAGUGAAAGACCGA 87/88/89
    GAACG
    0088 GUCAUCGUUCCAAGUCUAC GUAGACUUGGAACG 90/91/92
    AUGAC
    0089 CCCCUUGAAUGUUAAGGUC GACCUUAACAUUCA 93/94/95
    AGGGG
    0090 GUACACCAUGUUGCAAGUCA UACUUGCAACAUGG 96/97/98
    UGUAC
    0091 CGUGUCCAUGAUGGCUGACC GUCAGCCAUCAUGG  99/100/101
    ACACG
    0092 ACCUACAAAAUGGCCGAACA UUUCGGCCAUUUUG 102/103/104
    UAGGU
    0093 UCUACGGACCCUUCUUUGG CCAAAGAAGGGUCC 105/106/107
    GUAGA
    0094 CUCUGACGUCAUCAUCUAC GUAGAUGAUGACGU 108/109/110
    CAGAG
    0095 GUGCUUGGGUAACCCCGAC GUCGGGGUUACCCA 111/112/113
    AGCAC
    0096 CUGGCUCAUCUCCUACAGC GCUGUAGGAGAUGA 114/115/116
    GCCAG
    0097 ACAGUGCGUCGUAAUAUAU AUAUAUUACGACGC 117/118/119
    ACUGU
    0098 GGCACAUGGUCCUUCACUG CAGUGAAGGACCAU 120/121/122
    GUGCC
    0099 CACCAUGACCCUCGUGUAC GUACACGAGGGUCA 123/124/125
    UGGUG
    0100 CGAGGCCGGAUCUCUUAAG CUUAAGAGAUCCGG 457/458/459
    CCUCG
    0101 CUUCACACAUAACUAGACA UGUCUAGUUAUGUG 460/461/462
    UGAAG
    0102 UUAGAAAUUAUAAGCCCAG CUGGGCUUAUAAUU 463/464/465
    UCUAA
    0103 AAAACACAGACCACGUUCA UGAACGUGGUCUGU 126/127/128
    GUUUU
    0104 UCGAUGGUGGUGUUAUUCG CGAAUAACACCACC 129/130/131
    AUCGA
    0105 AGAAAAUGCUACGCGUUAC GUAACGCGUAGCAU 132/133/134
    UUUCU
    0106 CCCUUGGACACUACUGGAA UUCCAGUAGUGUCC 135/136/137
    AAGGG
    0107 GGAUCCUAUGUGUACCAGG CCUGGUACACAUAG 138/139/140
    GAUCC
    0108 ACUCGGCACACAACACAAU AUUGUGUUGUGUGC 141/142/143
    CGAGU
    0109 UACGAAGAUAUCUGCCCUU AAGGGCAGAUAUCU 144/145/146
    UCGUA
    0110 UCAACAGCUCUUACAUAAA UUUAUGUAAGAGCU 147/148/149
    GUUGA
    0111 AGAAGAUCAGAAGAUUGGC GCCAAUCUUCUGAU 150/151/152
    CUUCU
    0112 AAGCCGUCUGCUAUCCAAC GUUGGAUAGCAGAC 153/154/155
    GGCUU
    0113 UGCUAAAUGCCAUGCUUGC GCAAGCAUGGCAUU 156/157/158
    UAGCA
    0114 GAUCAGAAGAUUGGCCGGA UCCGGCCAAUCUUC 159/160/161
    UGAUC
    0115 UUCUUCAGCAAAUCGAUAC GUAUCGAUUUGCUG 162/163/164
    AAGAA
    0116 AUGCUGUCAAGAGGAUUUA UAAAUCCUCUUGAC 165/166/167
    AGCAU
    0117 GCUCGAGACUUGCUCUUGA UCAAGAGCAAGUCU 168/169/170
    CGAGC
    0118 CUGUUAGCUCAAGGUCUGC GCAGACCUUGAGCU 171/172/173
    AACAG
    0119 GACUUUCUAUCAGAAUUUG CAAAUUCUGAUAGA 174/175/176
    AAGUC
    0120 ACUUAAUCAUGGACGACGA UCGUCGUCCAUGAU 177/178/179
    UAAGU
    0121 AGAAGAAGAAGAAGAAGGG CCCUUCUUCUUCUU 180/181/182
    CUUCU
    0122 GAUCAAGAGAAUGUCGAGG CCUCGACAUUCUCU 183/184/185
    UGAUC
    0123 AAUCGUCGGUUUUAGCGAC GUCGCUAAAACCGA 186/187/188
    CGAUU
    0124 CUGUCAAUAGGCAGUAUGC GCAUACUGCCUAUU 189/190/191
    GACAG
    0125 CCUGUACCAACAGACCACU AGUGGUCUGUUGGU 192/193/194
    ACAGG
    0126 CCAAAAAUGGGCAAGGAAA UUUCCUUGCCCAUU 195/196/197
    UUUGG
    0127 CGUGGUAUCACCAUCGAUA UAUCGAUGGUGAUA 198/199/200
    CCACG
    0128 CAAAAUGGACUCCACUGAG CUCAGUGGAGUCCA 201/202/203
    UUUUG
    0129 UCCGUGACUAACCAAAAAU AUUUUUGGUUAGUC 204/205/206
    ACGGA
    0130 CAUUGUCGUCAUUGGACAC GUGUCCAAUGACGA 207/208/209
    CAAUG
    0131 UUUGUGAGACUGGUGGCCG CGGCCACCAGUCUC 421/422/423
    ACAAA
    0132 UCUGAUUGUAUUCGCCCCC GGGGGCGAAUACAA 424/425/426
    UCAGA
    0133 CACUCUAGUUCUGCCUAUU AAUAGGCAGAACUA 427/428/429
    GAGUG
    0134 CACACAUCACAAUGGCGGA UCCGCCAUUGUGAU 430/431/432
    GUGUG
    0135 GGAUGGCAUCAUCGGCAAG CUUGCCGAUGAUGC 433/434/435
    CAUCC
    0136 AGGCUUCAUCGACACCGCG CGCGGUGUCGAUGA 436/437/438
    AGCCU
    0137 ACUCCAAUUAUAACCUACU AGUAGGUUAUAAUU 210/211/212
    GGAGU
    0138 GUACAAGGAUCUGAUCGGC GCCGAUCAGAUCCU 213/214/215
    UGUAC
    0139 GACUUUCUUCAUGUGGCCC GGGCCACAUGAAGA 216/217/218
    AAGUC
    0140 ACAAAGUAUCGCCUACACC GGUGUAGGCGAUAC 439/440/441
    UUUGU
    0141 UAGCGUCGAUCUUCAACGA UCGUUGAAGAUCGA 442/443/444
    CGCUA
    0142 CUCAUAGAGCUUGAUGUGU ACACAUCAAGCUCU 219/220/221
    AUGAG
    0143 GAUGUGGAUGACGUCACUG CAGUGACGUCAUCC 222/223/224
    ACAUC
    0144 CCUUCCUGAUUCUCUUCUG CAGAAGAGAAUCAG 225/226/227
    GAAGG
    0145 CAGUGCUUGUGAUAAGUGA UCACUUAUCACAAG 228/229/230
    CACUG
    0146 GUUAAUGGUGACUGCCCUC GAGGGCAGUCACCA 231/232/233
    UUAAC
    0147 UAAAGCGAUGACCCCAUAG CUAUGGGGUCAUCG 234/235/236
    CUUUA
    0148 ACGGUACUGCAGCAAAAAG CUUUUUGCUGCAGU 237/238/239
    ACCGU
    0149 GCUGCAUACUUCUUGGCUC GAGCCAAGAAGUAU 240/241/242
    GCAGC
    0150 AUGUUUACAGAGACGCGAU AUCGCGUCUCUGUA 243/244/245
    AACAU
    0151 CGUCGAUCUUACCGAGUUC GAACUCGGUAAGAU 246/247/248
    CGACG
    0152 UUCAAAAUGCGUGAGUGCA UGCACUCACGCAUU 249/250/251
    UUGAA
    0153 AUCGUAGACCUAGUCCUCG CGAGGACUAGGUCU 252/253/254
    ACGAU
    0154 ACUCAAUUCAAAAUGCGUG CACGCAUUUUGAAU 255/256/257
    UGAGU
    0155 CUUAUCACUGGUAAGGAAG CUUCCUUACCAGUG 258/259/260
    AUAAG
    0156 GAGUUACGAACCGUCACCA UGGUGACGGUUCGU 261/262/263
    AACUC
    0157 ACUUAGUCCGGAUAAUGAA UUCAUUAUCCGGAC 264/265/266
    UAAGU
    0158 GGCGAUGUACGAGAACCUG CAGGUUCUCGUACA 267/268/269
    UCGCC
    0159 CGACAAGAUGCUGAAGGAG CUCCUUCAGCAUCU 270/271/272
    UGUCG
    0160 GAUAAAGGUCGCGUGUGGA UCCACACGCGACCU 273/274/275
    UUAUC
    0161 UGUCAAGACUGAUCCAAAC GUUUGGAUCAGUCU 276/277/278
    UGACA
    0162 CAUUCGAGUCUGAACAGGU ACCUGUUCAGACUC 279/280/281
    GAAUG
    0163 CAUAAGUCAUGGCCAAUAA UUAUUGGCCAUGAC 282/283/284
    UUAUG
    0164 GAACAUAAUAGUGCCGAAG CUUCGGCACUAUUA 285/286/287
    UGUUC
    0165 ACACUGGCAGAUCAAGAGG CCUCUUGAUCUGCC 288/289/290
    AGUGU
    0166 GAUCUUUGUUGGUGGUCUU AAGACCACCAACAA 291/292/293
    AGAUC
    0167 CAGGUGGUCAAUGAGCUGC GCAGCUCAUUGACC 294/295/296
    ACCUG
    0168 GUUGGCUCUGACACUCUUG CAAGAGUGUCAGAG 297/298/299
    CCAAC
    0169 AUCCGCAAAGCUGAGGAGG CCUCCUCAGCUUUG 300/301/302
    CGGAU
    0170 CCGUGUUCUUACUGCUGCU AGCAGCAGUAAGAA 303/304/305
    CACGG
    0171 CGUUGUUAUGCAUGGAAGC GCUUCCAUGCAUAA 306/307/308
    CAACG
    0172 AACUUCGCCGGUGAAAACG CGUUUUCACCGGCG 309/310/311
    AAGUU
    0173 AUGAAACUGUUCCUCGCAG CUGCGAGGAACAGU 312/313/314
    UUCAU
    0174 GAAGGCUGAGGAAGAAACC GGUUUCUUCCUCAG 315/316/317
    CCUUC
    0175 CUCUUUCACCGUCGUACUU AAGUACGACGGUGA 318/319/320
    AAGAG
    0176 CGACAUUGCUGUCCUCCGC GCGGAGGACAGCAA 321/322/323
    UGUCG
    0177 CAUCGGUACUACCCAACGU ACGUUGGGUAGUAC 324/325/326
    CGAUG
    0178 GACUCAGUACGUAUUAUCG CGAUAAUACGUACU 327/328/329
    GAGUC
    0179 GUUGCCAUCUUGCUUUUGC GCAAAAGCAAGAUG 330/331/332
    GCAAC
    0180 UCAGUUUGACGCAUGCGCU AGCGCAUGCGUCAA 333/334/335
    ACUGA
    0181 UGGCGUCUGGUGUGACAGU ACUGUCACACCAGA 336/337/338
    CGCCA
    0182 CGCGGAAUACGAUCAGUUC GAACUGAUCGUAUU 339/340/341
    CCGCG
    0183 GACUCAGUACGUAUUAUCG CGAUAAUACGUACU 342/343/344
    GAGUC
    0184 GUUGCCAUCUUGCUUUUGC GCAAAAGCAAGAUG 345/346/347
    GCAAC
    0185 UCAGUUUGACGCAUGCGCU AGCGCAUGCGUCAA 348/349/350
    ACUGA
    0186 AAAUGGCGUCUGGUGUGAC GUCACACCAGACGC 351/352/353
    CAUUU
    0187 UACGAUCAGUUCCUUGAGG CCUCAAGGAACUGA 354/355/356
    UCGUA
    0188 UAAUUUGUGUCAUACCCUA UAGGGUAUGACACA 357/358/359
    AAUUA
    0189 GUCAGUGACUGGUCAAAUU AAUUUGACCAGUCA 360/361/362
    CUGAC
    0190 UUAGGAGAUGUUGCACCUG CAGGUGCAACAUCU 363/364/365
    CCUAA
    0191 CAAACGGAUGACCUAGGUU AACCUAGGUCAUCC 366/367/368
    GUUUG
    0192 UGCUGCUAGCUCUAUGUCU AGACAUAGAGCUAG 369/370/371
    CAGCA
    0193 UUUGUGUCAUACCCUACGC GCGUAGGGUAUGAC 372/373/374
    ACAAA
    0194 AAGGGCUUCAUGUCGAAGG CCUUCGACAUGAAG 375/376/377
    CCCUU
    0195 UUAGGAGAUGUUGCACCUG CAGGUGCAACAUCU 378/379/380
    CCUAA
    0196 AGGUCAGUAACUAUGAGUG CACUCAUAGUUACU 381/382/383
    GACCU
    0197 GAAAUAUGCUGUGGCACAC GUGUGCCACAGCAU 384/385/386
    AUUUC
    0198 CUUGUACCUGAUGAUGUCA UGACAUCAUCAGGU 387/388/389
    ACAAG
    0199 CAUUGGCUUCAACACUCCU AGGAGUGUUGAAGC 390/391/392
    CAAUG
    0200 GCGGCUGGAGAUCUAUGAG CUCAUAGAUCUCCA 393/394/395
    GCCGC
    0201 CCCUCCCGAGGAGAGCAUU AAUGCUCUCCUCGG 396/397/398
    GAGGG
    0202 CGCCCUACGACUGGAACUU AAGUUCCAGUCGUA 399/400/401
    GGGCG
    0203 CUGGACCAACGUGCUGGAC GUCCAGCACGUUGG 402/403/404
    UCCAG
    0204 AACAUGGGAAGGAGGUCGC GCGACCUCCUUCCC 405/406/407
    AUGUU
    0205 GUUGCUUGUGGACUACUUC GAAGUAGUCCACAA 408/409/410
    GCAAC
    0206 CGUCGUGGGCCAGAUCUUC GAAGAUCUGGCCCA 411/412/413
    CGACG
    0207 UACGGUCCUUCAGGAACCG CGGUUCCUGAAGGA 415/416/417
    CCGUA
    0208 UUUCGCUGAUUUACCGCAU AUGCGGUAAAUCAGU 418/419/420
    CGAAA

    Droplet Feeding Assay for Evaluation of 21 Mer dsRNA Insecticidal Properties Against the Fall Armyworm Spodoptera frugiperda
  • 10 nanoMole quantities of 21 mer desalted primers were purchased from Proligo (Sigma Aldrich, St. Louis, Miss.). The lyophilized sample is solubilized in nuclease free water at a 100 uMolar concentration. The stock solution was then diluted in 20% sucrose containing blue McCormick food coloring. 0.5 ul droplets of this solution were dispensed in a circle in a parafilm-lined 65 mm petridish. Sucrose blanks were used as controls. Between 20 and 30 neonate fall armyworms were then added to the middle of the droplet circle and the petri dish sealed with parafilm. After two hours, the neonates with blue digestive tracts were removed and placed on standard multispecies lepidopteran insect diet. Insects were evaluated at 48, 72, and 96 hours post challenge for mortality and growth inhibition.
  • Serial dilution assays starting with a high dose of 20 uM and including 10, 5, 2.5, 1.25, 0.6, and 0 uMolar concentrations were also performed in this manner.
  • TABLE 3
    Rep 1 Rep 2
    72 H 72 H
    Primer Insects ave. Insects ave. Combined
    # Target gene treated weight treated weight ave.
    75 juvenile hormone diol kinase 9 10 11 11 11
    83 juvenile hormone diol kinase 15 14 14 12 13
    91 V-ATPase A subunit 14 14 11 15 14
    99 conserved hypothetical 16 15 19 16 16
    protein
    107 novel sequence (cuticular 16 14 13 15 14
    protein?)
    115 Eukaryotic initiation factor 4A 16 9 18 14 12
    123 putative sar1 protein 16 15 16 17 16
    131 Oligosaccharyl transferase 17 13 14 15 14
    48 kDa subunit
    139 myosin protein 13 15 16 18 17
    147 inwardly rectifying K+ 15 11 15 16 14
    channel protein
    155 alpha tubulin chain 15 10 16 19 15
    sucrose control 14 17 15 18 18
    • Sucrose Droplet Feeding Assay.
  • Neonate larvae were fed 25 uMolar dsRNAs. Treated insects were weighed en masse at 72 hours and compared to sucrose controls. 2 replicates of the experiment were averaged.
  • Injection Feeding Assay for Evaluation of 21 Mer dsRNA Insecticidal Properties Against the Fall Armyworm Spodoptera frugiperda
  • Second instar fall armyworm were injected using a micromanipulator and microinjection needles pulled on a Sutter Instrument (Novato, Calif.) P-2000 horizontal needle puller. The needle was back loaded with dsRNA solution. Initial injection experiments employed a concentration of 2 ug/ul (see Table X). This rate produced high mortality across all primers tested. Subsequent assays were performed with lower concentrations. Blue McCormick food coloring was included in the dsRNA solution to better visualize the injection process. Prior to injection, the insects were affixed to a microscope slide using a glue stick (Office Depot, Delray Beach, Fla.). The injection needle was connected to a 20 ml hypodermic syringe via Teflon tubing. The injection needle was then mounted on a Leitz micromanipulator. The dsRNA solution was dispensed from the microinjection needle by pressing on the plunger of the 20 ml syringe. Injection volumes were variable but averaged approximately 250 nL (based on injection of approximately 20 insects injected from a 5 ul volume loaded into the needle). Following injection, insects were removed from the microscope slide with the aid of a moistened fine camelhair brush. The insects were then placed on multispecies diet and were evaluated for mortality at 24 and 48 hours. Water injections were used as controls. Silencer® Negative Control #1, 2, and 3 siRNA control primers from Ambion (Austin, Tex.) were also included as negative controls.
  • TABLE 4
    Primer # Target gene No. injected Alive Dead
    75 juvenile hormone diol kinase 6 0 6
    83 juvenile hormone diol kinase 6 0 6
    91 V-ATPase A subunit 8 3 5
    99 conserved hypothetical sequence 8 0 8
    107 novel sequence (cuticular protein 8 0 8
    115 Eukaryotic initiation factor 4A 8 0 8
    123 putative sar1 protein 8 1 8
    131 Oligosaccharyl transferase 8 2 8
    48 kDa subunit
    147 inwardly rectifying K+ channel 8 1 7
    protein
    Water 8 7 1
    Microinjection of dsRNAs [2 ug/ul].


    Microinjection Assay using 0.7 ug/ul dose of dsRNA 21 mers. Note; On some occasions, the mortality was lower at 48 hours than at 24 hours. This is due to moribund insects recovering at the later time point.
    Topical Diet Assay for Evaluation of 21 Mer dsRNA Insecticidal Properties Against the Fall Armyworm Spodoptera frugiperda
  • The term “topical diet assay” refers to assays where artificial diets are pipetted into microtiter plates and the dsRNA solution is dispensed on the surface of the diet. In the dsRNA experiments, 100 ul of diet was dispensed per well. The surface of the well was then treated with 10 ul of a dsRNA solution of varying concentrations. The plates were then infested with 1 neonate fall armyworm per well and sealed with mylar. The mylar seal was punctured with a small insect pin to allow for air exchange. Plates were then stored in a growth chamber at 28 C and the assay was scored for stunting or mortality at 4 days. Table 6-12 represents several experiments using this method. Table 13 provides a summary of the data.
  • In topical assay #1, the primers that previously showed activity in injection assays were tested in a FAW topical diet assay. These results are shown in Table 6. A 50 uMolar solution (0.66 ug/ul) was used as the test concentration. 5 ul of this sample was loaded onto the top of 100 ul of diet producing a final concentration of 2.5 uMolar or 30 ppm. In addition to A1-A11 (A12 is a negative control), the other samples are those with no known human orthologs. The plate was infested with aprox. 5 neonates/well. The scoring period was 72 hours.
  • In topical assay #2, primers were tested in a FAW topical diet assay, and the results are shown in table 7. In this experiment, the 2.7 ug/ul stock was diluted to a starting concentration of 0.67 ug/ul. 2 fold serial dilution was carried out to produce stocks of 0.32 ug/ul and 0.16 ug/ul. 5 ul of these stocks were added to the 100 ul of diet producing final concentrations of 30, 15, and 8 ppm in diet. The scoring period was 72 hours.
  • In topical assay #3, primers were tested in a FAW topical diet assay, and the results are shown in table 8. In this experiment, the 2.7 ug/ul stock was diluted to a starting concentration of 0.67 ug/ul. 2 fold serial dilution was carried out to produce stocks of 0.32 ug/ul and 0.16 ug/ul. 5 ul of these stocks were added to the 100 ul of diet producing final concentrations of 30, 15, and 8 ppm in diet. This is a replicate of the previous experiment. The scoring period was 72 hours.
  • In topical assay #4, primers were tested in a FAW topical diet assay, and the results are shown in table 9. In this experiment, the 2.7 ug/ul stock was diluted to a starting concentration of 0.67 ug/ul. 2 fold serial dilution was carried out to produce stocks of 0.32 ug/ul and 0.16 ug/ul. 5 ul of these stocks were added to the 100 ul of diet producing final concentrations of 30, 15, and 8 ppm in diet. The scoring period was 72 hours.
  • A summary of the topical assay data shown in tables 6-9 appears in Table 10.
  • In topical assay #5, primers were tested in a FAW topical diet assay and the results are shown in Table 11. 50 ul of 0.16 ug/ul primers were mixed with 50 ul water and then serially diluted. 10 ul of the sample then added to the wells. Therefore the first concentration was 10 ul×0.08 ug/ul=0.8 ug total dsRNA/100 ul diet=8 ppm. This was ½ the rate of previous experiments (assays #1-4) where 5 ul of 0.32 showed activity. The scoring period was 72 hours. A score of “S” indicates clear stunting compared to untreated controls. A score of “ss” indicates live insects but exhibiting severe stunting defined as little or no growth beyond the neonate body size.
  • In topical assay #6, primers were tested in a FAW topical diet assay and the results are shown in Table 12. The first rate is 10 ul of the 0.16 ug/ul primer stock. From there, 50 ul of 0.16 ug/ul primer mixed with 50 ul water and then serially diluted. 10 ul of the sample was then added to the wells. Therefore first concentration was 10 ul×0.16 ug/ul=1.6 ug total dsRNA/100 ul diet=16 ppm. The scoring period was 72 hours.
  • TABLE 6
    SEQ ID NO
    Target
    region/
    sense/
    Sample seq id gene id Target sequence forward reverse 30 ppm antisense
    0075 ise1c.pk002.m13 Juvenile AACATGGTATCCGACTTC CAUGGUAUCCGACUU CCUGAAGUCGGAU 51/52/53
    hormone AGGAA CAGG ACCAUG
    query
    0083 ise1c.pk005.a15 Juvenile AAGTTCGCGTTCACTCTT GUUCGCGUUCACUCU UUCAAGAGUGAAC + 75/76/77
    hormone GAAGA UGAA GCGAAC
    query
    0085 ise1c.pk006.d24 Juvenile AATCACGCTGAAACCAC UCACGCUGAAACCAC UACAGUGGUUUCA + 81/82/83
    hormone TGTATA UGUA GCGUGA
    query
    0086 ise2c.pk009.i4 Juvenile AAAATATGGCGCGCCTA AAUAUGGCGCGCCUA ACAAUAGGCGCGC 84/85/86
    hormone TTGTTT UUGU CAUAUU
    query
    0088 ise2c.pk009.i5 Juvenile AAGTCATCGTTCCAAGTC GUCAUCGUUCCAAGU GUAGACUUGGAAC + 90/91/92
    hormone TACCT CUAC GAUGAC
    query
    0089 ise2c.pk001.d19 vacuolar query AACCCCTTGAATGTTAAG CCCCUUGAAUGUUAA GACCUUAACAUUC + 93/94/95
    GTCGG GGUC AAGGGG
    0091 ise2c.pk001.d20 vacuolar query AACGTGTCCATGATGGCT CGUGUCCAUGAUGGC GUCAGCCAUCAUG + 99/100/101
    GACTC UGAC GACACG
    0094 ise2c.pk001.f20 vacuolar query AACTCTGACGTCATCATC CUCUGACGUCAUCAU GUAGAUGAUGAC + 108/109/110
    TACGT CUAC GUCAGAG
    0095 ise2c.pk001.f21 vacuolar query AAGTGCTTGGGTAACCCC GUGCUUGGGUAACCC GUCGGGGUUACCC + 111/112/113
    GACAG CGAC AAGCAC
    0099 ise2c.pk010.h3 cadherin query AACACCATGACCCTCGTG CACCAUGACCCUCGU GUACACGAGGGUC 123/124/125
    TACAA GUAC AUGGUG
    0107 ise2c.pk011.h12 cuticle AAGGATCCTATGTGTACC GGAUCCUAUGUGUAC CCUGGUACACAUA + 138/139/140
    protein AGGTT CAGG GGAUCC
    0115 ise2c.pk001.i23 Translation AATTCTTCAGCAAATCGA UUCUUCAGCAAAUCG GUAUCGAUUUGCU 162/163/164
    initiation TACCA AUAC GAAGAA
    factor
    0123 ise2c.pk002.m10 SAR1 AAAATCGTCGGTTTTAGC AAUCGUCGGUUUUAG GUCGCUAAAACCG 186/187/188
    GACGT CGAC ACGAUU
    0131 ise2c.pk005.h3 phosphooligo- AATTTGTGAGACTGGTGG UUUGUGAGACUGGUG CGGCCACCAGUCU 421/422/423
    saccha- CCGAA GCCG CACAAA
    ride . . .
    0139 ise2c.pk001.j9 Myosin AAGACTTTCTTCATGTGG GACUUUCUUCAUGUG GGGCCACAUGAAG 216/217/218
    CCCAT GCCC AAAGUC
    0147 ise2c.pk003.f2 Potassium AATAAAGCGATGACCCC UAAAGCGAUGACCCC CUAUGGGGUCAUC + 234/235/236
    inwardly ATAGGA AUAG GCUUUA
    rectifying
    protein
    0155 ise2c.pk001.12 Tubulin AACTTATCACTGGTAAGG CUUAUCACUGGUAAG CUUCCUUACCAGU 258/259/260
    AAGAT GAAG GAUAAG
    (Note: the sense RNA primer sequence and the antisen RNA primer sequences shown in table 6 were generated with 2 thymine residues at the 3′ end.)
  • TABLE 7
    SEQ ID NO
    Target region/
    sense/
    Sample seq id gene id Target sequence forward reverse 30 ppm antisense
    0075 ise1c.pk002.m13 Juvenile AACATGGTATCCGAC CAUGGUAUCCGACUUC CCUGAAGUCGGAU 51/52/53
    hormone TTCAGGAA AGG ACCAUG
    query
    0076 AAGGTCGCTGACGA GGUCGCUGACGAGAAC CUUGUUCUCGUCA 54/55/56
    GAACAAGGA AAG GCGACC
    0077 AAGTGTCCTGGGCTT GUGUCCUGGGCUUGAG GAACUCAAGCCCA 57/58/59
    GAGTTCCA UUC GGACAC
    0078 ise1c.pk003.f7 Juvenile AAGAAGAAGCTCCT GAAGAAGCUCCUCCAC CACGUGGAGGAGC 60/61/62
    hormone CCACGTGTT GUG UUCUUC
    query
    0079 AAGGTCGCTGACGA GGUCGCUGACGAGAAC CUUGUUCUCGUCA 63/64/65
    GAACAAGGA AAG GCGACC
    0080 AATGTCCTGGGGCTG UGUCCUGGGGCUGAGU GAAACUCAGCCCCA 66/67/68
    AGTTTCAA UUC GGACA
    0081 ise1c.pk005.a15 Juvenile AAGAATAAGCTCCTC GAAUAAGCUCCUCCAC CACGUGGAGGAGC 69/70/71
    hormone CACGTGTT GUG UUAUUC
    query
    0082 AATTTGTCGAGGAG UUUGUCGAGGAGACCC AUAGGGUCUCCUC 72/73/74
    ACCCTATTG UAU GACAAA
    0083 AAGTTCGCGTTCACT GUUCGCGUUCACUCUU UUCAAGAGUGAAC + 75/76/77
    CTTGAAGA GAA GCGAAC
    0084 ise1c.pk006.d24 Juvenile AACTGCCCCTTAACC CUGCCCCUUAACCUCA AGAUGAGGUUAAG 78/79/80
    hormone TCATCTAT UCU GGGCAG
    query
    0085 AATCACGCTGAAAC UCACGCUGAAACCACU UACAGUGGUUUCA 81/82/83
    CACTGTATA GUA GCGUGA
    0086 ise2c.pk009.i4 Juvenile AAAATATGGCGCGC AAUAUGGCGCGCCUAU ACAAUAGGCGCGC 84/85/86
    hormone CTATTGTTT UGU CAUAUU
    query
    0087 AACGTTCTCGGTCTT CGUUCUCGGUCUUUCA CAGUGAAAGACCG 87/88/89
    TCACTGCT CUG AGAACG
    0088 AAGTCATCGTTCCAA GUCAUCGUUCCAAGUC GUAGACUUGGAAC 90/91/92
    GTCTACCT UAC GAUGAC
    0089 ise2c.pk001.d19 vacuolar AACCCCTTGAATGTT CCCCUUGAAUGUUAAG GACCUUAACAUUC 93/94/95
    query AAGGTCGG GUC AAGGGG
    0090 AAGTACACCATGTTG GUACACCAUGUUGCAA UACUUGCAACAUG 96/97/98
    CAAGTATG GUA GUGUAC
    0091 AACGTGTCCATGATG CGUGUCCAUGAUGGCU GUCAGCCAUCAUG 99/100/101
    GCTGACTC GAC GACACG
    0092 ise2c.pk001.e14 vacuolar AAACCTACAAAATG ACCUACAAAAUGGCCG UUUCGGCCAUUUU 102/103/104
    query GCCGAAAAC AAA GUAGGU
    0093 AATCTACGGACCCTT UCUACGGACCCUUCUU CCAAAGAAGGGUC 105/106/107
    CTTTGGAG UGG CGUAGA
    0094 ise2c.pk001.f20 vacuolar AACTCTGACGTCATC CUCUGACGUCAUCAUC GUAGAUGAUGACG 108/109/110
    query ATCTACGT UAC UCAGAG
    0095 AAGTGCTTGGGTAAC GUGCUUGGGUAACCCC GUCGGGGUUACCC 111/112/113
    CCCGACAG GAC AAGCAC
    0096 AACTGGCTCATCTCC CUGGCUCAUCUCCUAC GCUGUAGGAGAUG 114/115/116
    TACAGCAA AGC AGCCAG
    0097 ise2c.pk010.h3 cadherin AAACAGTGCGTCGT ACAGUGCGUCGUAAUA aUAUAUUACGACG 117/118/119
    query AATATATTC UAU CACUGU
    0098 AAGGCACATGGTCCT GGCACAUGGUCCUUCA CAGUGAAGGACCA + 120/121/122
    TCACTGAT CUG UGUGCC
    0099 AACACCATGACCCTC CACCAUGACCCUCGUG GUACACGAGGGUC 123/124/125
    GTGTACAA UAC AUGGUG
    0100 ise2c.pk007.k24 cuticle AACGAGGCCGGATC CGAGGCCGGAUCUCUU CUUAAGAGAUCCG 457/458/459
    protein TCTTAAGCA AAG GCCUCG
    0101 AACTTCACACATAAC CUUCACACAUAACUAG UGUCUAGUUAUGU 460/461/462
    TAGACAAA ACA GUGAAG
    0102 AATGCGTGGCGATTT UUAGAAAUUAUAAGCC CUGGGCUUAUAAU 463/464/465
    CAAACTTA CAG UUCUAA
    0103 ise2c.pk011.a10 cuticle AAAAAACACAGACC AAAACACAGACCACGU UGAACGUGGUCUG + 126/127/128
    protein ACGTTCACA UCA UGUUUU
    0104 AATCGATGGTGGTGT UCGAUGGUGGUGUUAU CGAAUAACACCACC + 129/130/131
    TATTCGCT UCG AUCGA
    0105 ise2c.pk011.h12 cuticle AAAGAAAATGCTAC AGAAAAUGCUACGCGU GUAACGCGUAGCA 132/133/134
    protein GCGTTACGA UAC UUUUCU
    0106 AACCCTTGGACACTA CCCUUGGACACUACUG UUCCAGUAGUGUC + 135/136/137
    CTGGAAGA GAA CAAGGG
    0107 AAGGATCCTATGTGT GGAUCCUAUGUGUACC CCUGGUACACAUA 138/139/140
    ACCAGGTT AGG GGAUCC
    0108 ise2c.pk001.d22 translation AAACTCGGCACACA ACUCGGCACACAACAC AUUGUGUUGUGUG 141/142/143
    initiation ACACAATGG AAU CCGAGU
    factor
    0109 AATACGAAGATATCT UACGAAGAUAUCUGCC AAGGGCAGAUAUC + 144/145/146
    GCCCTTCC CUU UUCGUA
    0110 AATCAACAGCTCTTA UCAACAGCUCUUACAU UUUAUGUAAGAGC 147/148/149
    CATAAATG AAA UGUUGA
    0111 ise2c.pk001.d9 translation AAAGAAGATCAGAA AGAAGAUCAGAAGAUU GCCAAUCUUCUGA 150/151/152
    initiation GATTGGCCG GGC UCUUCU
    factor
    0112 AAAAGCCGTCTGCTA AAGCCGUCUGCUAUCC GUUGGAUAGCAGA + 153/154/155
    TCCAACAA AAC CGGCUU
    0113 AATGCTAAATGCCAT UGCUAAAUGCCAUGCU GCAAGCAUGGCAU 156/157/158
    GCTTGCAT UGC UUAGCA
    0114 ise2c.pk001.i23 translation AAGATCAGAAGATT GAUCAGAAGAUUGGCC UCCGGCCAAUCUUC + 159/160/161
    initiation GGCCGGAAG GGA UGAUC
    factor
    0115 ATTCTTCAGCAAAT UUCUUCAGCAAAUCGA GUAUCGAUUUGCU 162/163/164
    CGATACCA UAC GAAGAA
    0116 AAATGCTGTCAAGA AUGCUGUCAAGAGGAU UAAAUCCUCUUGA 165/166/167
    GGATTTAAA UUA CAGCAU
    0117 ise2c.pk001.124 translation AAGCTCGAGACTTGC GCUCGAGACUUGCUCU UCAAGAGCAAGUC 168/169/170
    initiation TCTTGATG UGA UCGAGC
    factor
    0118 AACTGTTAGCTCAAG CUGUUAGCUCAAGGUC GCAGACCUUGAGC 171/172/173
    GTCTGCTA UGC UAACAG
    0119 AAGACTTTCTATCAG GACUUUCUAUCAGAAU CAAAUUCUGAUAG + 174/175/176
    AATTTGCG UUG AAAGUC
    0120 ise2c.pk005.b9 translation AAACTTAATCATGGA ACUUAAUCAUGGACGA UCGUCGUCCAUGA 177/178/179
    initiation CGACGACA CGA UUAAGU
    factor
    0121 AAAGAAGAAGAAGA AGAAGAAGAAGAAGAA CCCUUCUUCUUCUU + 180/181/182
    AGAAGGGAG GGG CUUCU
    0122 AAGATCAAGAGAAT GAUCAAGAGAAUGUCG CCUCGACAUUCUCU + 183/184/185
    GTCGAGGAT AGG UGAUC
    0123 ise2c.pk002.m10 SAR1 AAAATCGTCGGTTTT AAUCGUCGGUUUUAGC GUCGCUAAAACCG 186/187/188
    AGCGACGT GAC ACGAUU
    0124 AACTGTCAATAGGC CUGUCAAUAGGCAGUA GCAUACUGCCUAU 189/190/191
    AGTATGCGT UGC UGACAG
    0125 AACCTGTACCAACA CCUGUACCAACAGACC AGUGGUCUGUUGG + 192/193/194
    GACCACTGG ACU UACAGG
    0126 ise2c.pk001.c14 Elongation AACCAAAAATGGGC CCAAAAAUGGGCAAGG UUUCCUUGCCCAU + 195/196/197
    factor AAGGAAAAG AAA UUUUGG
    0127 AACGTGGTATCACCA CGUGGUAUCACCAUCG UAUCGAUGGUGAU + 198/199/200
    TCGATATT AUA ACCACG
    0128 AACAAAATGGACTC CAAAAUGGACUCCACU CUCAGUGGAGUCC 201/202/203
    CACTGAGCC GAG AUUUUG
    0129 ise2c.pk001.d16 Elongation AATCCGTGACTAACC UCCGUGACUAACCAAA AUUUUUGGUUAGU + 204/205/206
    factor AAAAATGG AAU CACGGA
    0130 AACATTGTCGTCATT CAUUGUCGUCAUUGGA GUGUCCAAUGACG 207/208/209
    GGACACGT CAC ACAAUG
    0131 ise2c.pk005.h3 phospho- AATTTGTGAGACTGG UUUGUGAGACUGGUGG CGGCCACCAGUCUC 421/422/423
    oligo- TGGCCGAA CCG ACAAA
    saccha-
    ride . . .
    0132 AATCTGATTGTATTC UCUGAUUGUAUUCGCC GGGGGCGAAUACA 424/245/426
    GCCCCCTC CCC AUCAGA
    0133 AACACTCTAGTTCTG CACUCUAGUUCUGCCU AAUAGGCAGAACU 427/228/429
    CCTATTCT AUU AGAGUG
    0134 ise2c.pk001.d21 myosin AACACACATCACAA CACACAUCACAAUGGC UCCGCCAUUGUGA 430/431/432
    TGGCGGATA GGA UGUGUG
    0135 AAGGATGGCATCAT GGAUGGCAUCAUCGGC CUUGCCGAUGAUG 433/434/435
    CGGCAAGAA AAG CCAUCC
    0136 AAAGGCTTCATCGAC AGGCUUCAUCGACACC CGCGGUGUCGAUG 436/437/438
    ACCGCGAA GCG AAGCCU
    0137 ise2c.pk001.j9 myosin AAACTCCAATTATAA ACUCCAAUUAUAACCU AGUAGGUUAUAAU 210/211/212
    CCTACTAG ACU UGGAGU
    0138 AAGTACAAGGATCT GUACAAGGAUCUGAUC GCCGAUCAGAUCC + 213/214/215
    GATCGGCAA GGC UUGUAC
    0139 AAGACTTTCTTCATG GACUUUCUUCAUGUGG GGGCCACAUGAAG 216/217/218
    TGGCCCAT CCC AAAGUC
    0140 ise2c.pk002.f12 myosin AAACAAAGTATCGC ACAAAGUAUCGCCUAC GGUGUAGGCGAUA 439/440/441
    CTACACCGC ACC CUUUGU
    0141 AATAGCGTCGATCTT UAGCGUCGAUCUUCAA UCGUUGAAGAUCG 442/443/444
    CAACGACT CGA ACGCUA
    0142 ise2c.pk001.b14 potassium AACTCATAGAGCTTG CUCAUAGAGCUUGAUG ACACAUCAAGCUC 219/220/221
    channel ATGTGTGG UGU UAUGAG
    amino acid
    transporter
    0143 AAGATGTGGATGAC GAUGUGGAUGACGUCA CAGUGACGUCAUC 221/223/224
    GTCACTGGT CUG CACAUC
    0144 AACCTTCCTGATTCT CCUUCCUGAUUCUCUU CAGAAGAGAAUCA 225/226/227
    CTTCTGTG CUG GGAAGG
    0145 ise2c.pk003.f2 potassium AACAGTGCTTGTGAT CAGUGCUUGUGAUAAG UCACUUAUCACAA + 228/229/230
    inwardly AAGTGAAC UGA GCACUG
    recti-
    fier . . .
    0146 AAGTTAATGGTGACT GUUAAUGGUGACUGCC GAGGGCAGUCACC + 231/232/233
    GCCCTCGA CUC AUUAAC
    0147 AATAAAGCGATGAC UAAAGCGAUGACCCCA CUAUGGGGUCAUC + 234/235/236
    CCCATAGGA UAG GCUUUA
    0148 ise2c.pk005.120 amino acid AAACGGTACTGCAG ACGGUACUGCAGCAAA CUUUUUGCUGCAG + 237/238/239
    transporter CAAAAAGAC AAG UACCGU
    0149 AAGCTGCATACTTCT GCUGCAUACUUCUUGG GAGCCAAGAAGUA + 240/241/242
    TGGCTCTC CUC UGCAGC
    0150 AAATGTTTACAGAG AUGUUUACAGAGACGC AUCGCGUCUCUGU 243/244/245
    ACGCGATGA GAU AAACAU
    0151 ise2c.pk001.d1 tubulin AACGTCGATCTTACC CGUCGAUCUUACCGAG GAACUCGGUAAGA + 246/247/248
    GAGTTCCA UUC UCGACG
    0152 ise2c.pk001.k6 tubulin AATTCAAAATGCGTG UUCAAAAUGCGUGAGU UGCACUCACGCAU 249/250/251
    AGTGCATC GCA UUUGAA
    0153 AAATCGTAGACCTA AUCGUAGACCUAGUCC CGAGGACUAGGUC + 252/253/254
    GTCCTCGAC UCG UACGAU
    0154 ise2c.pk001.12 tubulin AAACTCAATTCAAA ACUCAAUUCAAAAUGC CACGCAUUUUGAA + 255/256/257
    ATGCGTGAG GUG UUGAGU
    0155 AACTTATCACTGGTA CUUAUCACUGGUAAGG CUUCCUUACCAGU 258/259/260
    AGGAAGAT AAG GAUAAG
    0156 ise2c.pk002.b4 ubiquitin AAGAGTTACGAACC GAGUUACGAACCGUCA UGGUGACGGUUCG 261/262/263
    GTCACCATA CCA UAACUC
    0157 AAACTTAGTCCGGAT ACUUAGUCCGGAUAAU UUCAUUAUCCGGA + 264/265/266
    AATGAACC GAA CUAAGU
    0158 AAGGCGATGTACGA GGCGAUGUACGAGAAC CAGGUUCUCGUAC + 267/268/269
    GAACCTGTT CUG AUCGCC
    0159 ise2c.pk001.j16 small AACGACAAGATGCT CGACAAGAUGCUGAAG CUCCUUCAGCAUCU + 270/271/272
    nuclear GAAGGAGAC GAG UGUCG
    ribonucleo-
    protein
    0160 ise2c.pk006.h23 small AAGATAAAGGTCGC GAUAAAGGUCGCGUGU UCCACACGCGACCU 273/274/275
    nuclear GTGTGGACC GGA UUAUC
    ribonucleo-
    protein
    0161 AATGTCAAGACTGAT UGUCAAGACUGAUCCA GUUUGGAUCAGUC 276/277/278
    CCAAACAC AAC UUGACA
    0162 AACATTCGAGTCTGA CAUUCGAGUCUGAACA ACCUGUUCAGACU + 279/280/281
    ACAGGTGG GGU CGAAUG
    (Note: the sense RNA primer sequence and the antisense RNA primer sequences shown in table 7 were generated with 2 thymine residues at the 3′ end.)
  • TABLE 8
    SEQ ID NO
    Target region/
    sense/
    Sample seq id gene id Target sequence forward reverse 30 ppm antisense
    0075 ise1c.pk002.m13 Juvenile AACATGGTATCCGAC CAUGGUAUCCGACUUC CCUGAAGUCGGAU 51/52/53
    hormone TTCAGGAA AGG ACCAUG
    query
    0076 AAGGTCGCTGACGA GGUCGCUGACGAGAAC CUUGUUCUCGUCA 54/55/56
    GAACAAGGA AAG GCGACC
    0077 AAGTGTCCTGGGCTT GUGUCCUGGGCUUGAG GAACUCAAGCCCA 57/58/59
    GAGTTCCA UUC GGACAC
    0078 ise1c.pk003.f7 Juvenile AAGAAGAAGCTCCT GAAGAAGCUCCUCCAC CACGUGGAGGAGC 60/61/62
    hormone CCACGTGTT GUG UUCUUC
    query
    0079 AAGGTCGCTGACGA GGUCGCUGACGAGAAC CUUGUUCUCGUCA 63/64/65
    GAACAAGGA AAG GCGACC
    0080 AATGTCCTGGGGCTG UGUCCUGGGGCUGAGU GAAACUCAGCCCCA + 66/67/68
    AGTTTCAA UUC GGACA
    0081 ise1c.pk005.a15 Juvenile AAGAATAAGCTCCTC GAAUAAGCUCCUCCAC CACGUGGAGGAGC + 69/70/71
    hormone CACGTGTT GUG UUAUUC
    query
    0082 AATTTGTCGAGGAG UUUGUCGAGGAGACCC AUAGGGUCUCCUC 72/73/74
    ACCCTATTG UAU GACAAA
    0083 AAGTTCGCGTTCACT GUUCGCGUUCACUCUU UUCAAGAGUGAAC NT 75/76/77
    CTTGAAGA GAA GCGAAC
    0084 ise1c.pk006.d24 Juvenile AACTGCCCCTTAACC CUGCCCCUUAACCUCA AGAUGAGGUUAAG + 78/79/80
    hormone TCATCTAT UCU GGGCAG
    query
    0085 AATCACGCTGAAAC UCACGCUGAAACCACU UACAGUGGUUUCA 81/82/83
    CACTGTATA GUA GCGUGA
    0086 ise2c.pk009.i4 Juvenile AAAATATGGCGCGC AAUAUGGCGCGCCUAU ACAAUAGGCGCGC 84/85/86
    hormone CTATTGTTT UGU CAUAUU
    query
    0087 AACGTTCTCGGTCTT CGUUCUCGGUCUUUCA CAGUGAAAGACCG 87/88/89
    TCACTGCT CUG AGAACG
    0088 AAGTCATCGTTCCAA GUCAUCGUUCCAAGUC GUAGACUUGGAAC 90/91/92
    GTCTACCT UAC GAUGAC
    0089 ise2c.pk001.d19 vacuolar AACCCCTTGAATGTT CCCCUUGAAUGUUAAG GACCUUAACAUUC + 93/94/95
    query AAGGTCGG GUC AAGGGG
    0090 AAGTACACCATGTTG GUACACCAUGUUGCAA UACUUGCAACAUG 96/97/98
    CAAGTATG GUA GUGUAC
    0091 AACGTGTCCATGATG CGUGUCCAUGAUGGCU GUCAGCCAUCAUG + 99/100/101
    GCTGACTC GAC GACACG
    0092 ise2c.pk001.e14 vacuolar AAACCTACAAAATG ACCUACAAAAUGGCCG UUUCGGCCAUUUU 102/103/104
    query GCCGAAAAC AAA GUAGGU
    0093 AATCTACGGACCCTT UCUACGGACCCUUCUU CCAAAGAAGGGUC 105/106/107
    CTTTGGAG UGG CGUAGA
    0094 ise2c.pk001.f20 vacuolar AACTCTGACGTCATC CUCUGACGUCAUCAUC GUAGAUGAUGACG 108/109/110
    query ATCTACGT UAC UCAGAG
    0095 AAGTGCTTGGGTAAC GUGCUUGGGUAACCCC GUCGGGGUUACCC 111/112/113
    CCCGACAG GAC AAGCAC
    0096 AACTGGCTCATCTCC CUGGCUCAUCUCCUAC GCUGUAGGAGAUG 114/115/116
    TACAGCAA AGC AGCCAG
    0097 ise2c.pk010.h3 cadherin AAACAGTGCGTCGT ACAGUGCGUCGUAAUA AUAUAUUACGACG 117/118/119
    query AATATATTC UAU CACUGU
    0098 AAGGCACATGGTCCT GGCACAUGGUCCUUCA CAGUGAAGGACCA 120/121/122
    TCACTGAT CUG UGUGCC
    0099 AACACCATGACCCTC CACCAUGACCCUCGUG GUACACGAGGGUC 123/124/125
    GTGTACAA UAC AUGGUG
    0100 ise2c.pk007.k24 cuticle AACGAGGCCGGATC CGAGGCCGGAUCUCUU CUUAAGAGAUCCG 457/458/459
    protein TCTTAAGCA AAG GCCUCG
    0101 AACTTCACACATAAC CUUCACACAUAACUAG UGUCUAGUUAUGU 460/461/462
    TAGACAAA ACA GUGAAG
    0102 AATGCGTGGCGATTT UUAGAAAUUAUAAGCC CUGGGCUUAUAAU 463/464/465
    CAAACTTA CAG UUCUAA
    0103 ise2c.pk011.a10 cuticle AAAAAACACAGACC AAAACACAGACCACGU UGAACGUGGUCUG 126/127/128
    protein ACGTTCACA UCA UGUUUU
    0104 AATCGATGGTGGTGT UCGAUGGUGGUGUUAU CGAAUAACACCACC + 129/130/131
    TATTCGCT UCG AUCGA
    0105 ise2c.pk011.h12 cuticle AAAGAAAATGCTAC AGAAAAUGCUACGCGU GUAACGCGUAGCA 132/133/134
    protein GCGTTACGA UAC UUUUCU
    0106 AACCCTTGGACACTA CCCUUGGACACUACUG UUCCAGUAGUGUC 135/136/137
    CTGGAAGA GAA CAAGGG
    0107 AAGGATCCTATGTGT GGAUCCUAUGUGUACC CCUGGUACACAUA 138/139/140
    ACCAGGTT AGG GGAUCC
    0108 ise2c.pk001.d22 translation AAACTCGGCACACA ACUCGGCACACAACAC AUUGUGUUGUGUG + 141/142/143
    initiation ACACAATGG AAU CCGAGU
    factor
    0109 AATACGAAGATATCT UACGAAGAUAUCUGCC AAGGGCAGAUAUC + 144/145/146
    GCCCTTCC CUU UUCGUA
    0110 AATCAACAGCTCTTA UCAACAGCUCUUACAU UUUAUGUAAGAGC + 147/148/149
    CATAAATG AAA UGUUGA
    0111 ise2c.pk001.d9 translation AAAGAAGATCAGAA AGAAGAUCAGAAGAUU GCCAAUCUUCUGA 150/151/152
    initiation GATTGGCCG GGC UCUUCU
    factor
    0112 AAAAGCCGTCTGCTA AAGCCGUCUGCUAUCC GUUGGAUAGCAGA 153/154/155
    TCCAACAA AAC CGGCUU
    0113 AATGCTAAATGCCAT UGCUAAAUGCCAUGCU GCAAGCAUGGCAU + 156/157/158
    GCTTGCAT UGC UUAGCA
    0114 ise2c.pk001.i23 translation AAGATCAGAAGATT GAUCAGAAGAUUGGCC UCCGGCCAAUCUUC + 159/160/161
    initiation GGCCGGAAG GGA UGAUC
    factor
    0115 AATTCTTCAGCAAAT UUCUUCAGCAAAUCGA GUAUCGAUUUGCU NT 162/163/164
    CGATACCA UAC GAAGAA
    0116 AAATGCTGTCAAGA AUGCUGUCAAGAGGAU UAAAUCCUCUUGA 165/166/167
    GGATTTAAA UUA CAGCAU
    0117 ise2c.pk001.i24 translation AAGCTCGAGACTTGC GCUCGAGACUUGCUCU UCAAGAGCAAGUC + 168/169/170
    initiation TCTTGATG UGA UCGAGC
    factor
    0118 AACTGTTAGCTCAAG CUGUUAGCUCAAGGUC GCAGACCUUGAGC + 171/172/173
    GTCTGCTA UGC UAACAG
    0119 AAGACTTTCTATCAG GACUUUCUAUCAGAAU CAAAUUCUGAUAG 174/175/176
    AATTTGCG UUG AAAGUC
    0120 ise2c.pk005.b9 translation AAACTTAATCATGGA ACUUAAUCAUGGACGA UCGUCGUCCAUGA 177/178/179
    initiation CGACGACA CGA UUAAGU
    factor
    0121 AAAGAAGAAGAAGA AGAAGAAGAAGAAGAA CCCUUCUUCUUCUU + 180/181/182
    AGAAGGGAG GGG CUUCU
    0122 AAGATCAAGAGAAT GAUCAAGAGAAUGUCG CCUCGACAUUCUCU + 183/184/185
    GTCGAGGAT AGG UGAUC
    0123 ise2c.pk002.m10 SAR1 AAAATCGTCGGTTTT AAUCGUCGGUUUUAGC GUCGCUAAAACCG + 186/187/188
    AGCGACGT GAC ACGAUU
    0124 AACTGTCAATAGGC CUGUCAAUAGGCAGUA GCAUACUGCCUAU + 189/190/191
    AGTATGCGT UGC UGACAG
    0125 AACCTGTACCAACA CCUGUACCAACAGACC AGUGGUCUGUUGG + 192/193/194
    GACCACTGG ACU UACAGG
    0126 ise2c.pk001.c14 Elongation AACCAAAAATGGGC CCAAAAAUGGGCAAGG UUUCCUUGCCCAU + 195/196/197
    factor AAGGAAAAG AAA UUUUGG
    0127 AACGTGGTATCACCA CGUGGUAUCACCAUCG UAUCGAUGGUGAU + 198/199/200
    TCGATATT AUA ACCACG
    0128 AACAAAATGGACTC CAAAAUGGACUCCACU CUCAGUGGAGUCC + 201/202/203
    CACTGAGCC GAG AUUUUG
    0129 ise2c.pk001.d16 Elongation AATCCGTGACTAACC UCCGUGACUAACCAAA AUUUUUGGUUAGU + 204/205/206
    factor AAAAATGG AAU CACGGA
    0130 AACATTGTCGTCATT CAUUGUCGUCAUUGGA GUGUCCAAUGACG + 207/208/209
    GGACACGT CAC ACAAUG
    0131 ise2c.pk005.h3 phospho- AATTTGTGAGACTGG UUUGUGAGACUGGUGG CGGCCACCAGUCUC 421/422/423
    oligo- TGGCCGAA CCG ACAAA
    saccha-
    ride . . .
    0132 AATCTGATTGTATTC UCUGAUUGUAUUCGCC GGGGGCGAAUACA 424/425/426
    GCCCCCTC CCC AUCAGA
    0133 AACACTCTAGTTCTG CACUCUAGUUCUGCCU AAUAGGCAGAACU 427/428/429
    CCTATTCT AUU AGAGUG
    0134 ise2c.pk001.d21 myosin AACACACATCACAA CACACAUCACAAUGGC UCCGCCAUUGUGA 430/431/432
    TGGCGGATA GGA UGUGUG
    0135 AAGGATGGCATCAT GGAUGGCAUCAUCGGC CUUGCCGAUGAUG 433/434/435
    CGGCAAGAA AAG CCAUCC
    0136 AAAGGCTTCATCGAC AGGCUUCAUCGACACC CGCGGUGUCGAUG 436/437/438
    ACCGCGAA GCG AAGCCU
    0137 ise2c.pk001.j9 myosin AAACTCCAATTATAA ACUCCAAUUAUAACCU AGUAGGUUAUAAU 210/211/212
    CCTACTAG ACU UGGAGU
    0138 AAGTACAAGGATCT GUACAAGGAUCUGAUC GCCGAUCAGAUCC 213/214/215
    GATCGGCAA GGC UUGUAC
    0139 AAGACTTTCTTCATG GACUUUCUUCAUGUGG GGGCCACAUGAAG 216/217/218
    TGGCCCAT CCC AAAGUC
    0140 ise2c.pk002.f12 myosin AAACAAAGTATCGC ACAAAGUAUCGCCUAC GGUGUAGGCGAUA 439/440/441
    CTACACCGC ACC CUUUGU
    0141 AATAGCGTCGATCTT UAGCGUCGAUCUUCAA UCGUUGAAGAUCG 442/443/444
    CAACGACT CGA ACGCUA
    0142 ise2c.pk001.b14 potassium AACTCATAGAGCTTG CUCAUAGAGCUUGAUG ACACAUCAAGCUC 219/220/221
    channel ATGTGTGG UGU UAUGAG
    amino acid
    transporter
    0143 AAGATGTGGATGAC GAUGUGGAUGACGUCA CAGUGACGUCAUC + 221/223/224
    GTCACTGGT CUG CACAUC
    0144 AACCTTCCTGATTCT CCUUCCUGAUUCUCUU CAGAAGAGAAUCA + 225/226/227
    CTTCTGTG CUG GGAAGG
    0145 ise2c.pk003.f2 potassium AACAGTGCTTGTGAT CAGUGCUUGUGAUAAG UCACUUAUCACAA + 228/229/230
    inwardly AAGTGAAC UGA GCACUG
    recti-
    fier . . .
    0146 AAGTTAATGGTGACT GUUAAUGGUGACUGCC GAGGGCAGUCACC + 231/232/233
    GCCCTCGA CUC AUUAAC
    0147 AATAAAGCGATGAC UAAAGCGAUGACCCCA CUAUGGGGUCAUC + 234/235/236
    CCCATAGGA UAG GCUUUA
    0148 ise2c.pk005.l20 amino acid AAACGGTACTGCAG ACGGUACUGCAGCAAA CUUUUUGCUGCAG + 237/238/239
    transporter CAAAAAGAC AAG UACCGU
    0149 AAGCTGCATACTTCT GCUGCAUACUUCUUGG GAGCCAAGAAGUA + 240/241/242
    TGGCTCTC CUC UGCAGC
    0150 AAATGTTTACAGAG AUGUUUACAGAGACGC AUCGCGUCUCUGU + 243/244/245
    ACGCGATGA GAU AAACAU
    0151 ise2c.pk001.d1 tubulin AACGTCGATCTTACC CGUCGAUCUUACCGAG GAACUCGGUAAGA + 246/247/248
    GAGTTCCA UUC UCGACG
    0152 ise2c.pk001.k6 tubulin AATTCAAAATGCGTG UUCAAAAUGCGUGAGU UGCACUCACGCAU 249/250/251
    AGTGCATC GCA UUUGAA
    0153 AAATCGTAGACCTA AUCGUAGACCUAGUCC CGAGGACUAGGUC + 252/253/254
    GTCCTCGAC UCG UACGAU
    0154 ise2c.pk001.l2 tubulin AAACTCAATTCAAA ACUCAAUUCAAAAUGC CACGCAUUUUGAA + 255/256/257
    ATGCGTGAG GUG UUGAGU
    0155 AACTTATCACTGGTA CUUAUCACUGGUAAGG CUUCCUUACCAGU 258/259/260
    AGGAAGAT AAG GAUAAG
    0156 ise2c.pk002.b4 ubiquitin AAGAGTTACGAACC GAGUUACGAACCGUCA UGGUGACGGUUCG + 261/262/263
    GTCACCATA CCA UAACUC
    0157 AAACTTAGTCCGGAT ACUUAGUCCGGAUAAU UUCAUUAUCCGGA + 264/265/266
    AATGAACC GAAt CUAAGU
    0158 AAGGCGATGTACGA GGCGAUGUACGAGAAC CAGGUUCUCGUAC + 267/268/269
    GAACCTGTT CUG AUCGCC
    0159 ise2c.pk001.j16 small AACGACAAGATGCT CGACAAGAUGCUGAAG CUCCUUCAGCAUCU + 270/271/272
    nuclear GAAGGAGAC GAG UGUCG
    ribonucleo-
    protein
    0160 ise2c.pk006.h23 small AAGATAAAGGTCGC GAUAAAGGUCGCGUGU UCCACACGCGACCU + 273/274/275
    nuclear GTGTGGACC GGA UUAUC
    ribonucleo-
    protein
    0161 AATGTCAAGACTGAT UGUCAAGACUGAUCCA GUUUGGAUCAGUC + 276/277/278
    CCAAACAC AAC UUGACA
    0162 AACATTCGAGTCTGA CAUUCGAGUCUGAACA ACCUGUUCAGACU + 279/280/281
    ACAGGTGG GGUt CGAAUG
    (Note: the sense RNA primer sequence and the antisense RNA primer sequences shown in table 8 were generated with 2 thymine residues at the 3′ end.)
  • TABLE 9
    SEQ ID
    NO
    Target
    region/
    30 15 8 sense/
    Sample seq id gene id Target sequence forward reverse ppm ppm ppm antisense
    0075 AAGGTCGCTGACGA GGUCGCUGACG CUUGUUCUCGUCA 51/52/53
    GAACAAGGA AGAACAAG GCGACC
    0076 AAGTGTCCTGGGCTT GUGUCCUGGGC GAACUCAAGCCCA + 54/55/56
    GAGTTCCA UUGAGUUC GGACAC
    0077 ise1c.pk003.f7 Juvenile AAGAAGAAGCTCCT GAAGAAGCUCC CACGUGGAGGAGC 57/58/59
    hormone query CCACGTGTT UCCACGUG UUCUUC
    0078 AAGGTCGCTGACGA GGUCGCUGACG CUUGUUCUCGUCA 60/61/62
    GAACAAGGA AGAACAAG GCGACC
    0079 AATGTCCTGGGGCT UGUCCUGGGGC GAAACUCAGCCCC 63/64/65
    GAGTTTCAA UGAGUUUC AGGACA
    0080 ise1c.pk005.a15 Juvenile AAGAATAAGCTCCT GAAUAAGCUCC CACGUGGAGGAGC + + 66/67/68
    hormone query CCACGTGTT UCCACGUG UUAUUC
    0081 AATTTGTCGAGGAG UUUGUCGAGGA AUAGGGUCUCCUC 69/70/71
    ACCCTATTG GACCCUAU GACAAA
    0082 AAGTTCGCGTTCACT GUUCGCGUUCA UUCAAGAGUGAA NT 72/73/74
    CTTGAAGA CUCUUGAA CGCGAAC
    0083 ise1c.pk006.d24 Juvenile AACTGCCCCTTAACC CUGCCCCUUAAC AGAUGAGGUUAA 75/76/77
    hormone query TCATCTAT CUCAUCUtt GGGGCAG
    0084 AATCACGCTGAAAC UCACGCUGAAA UACAGUGGUUUC + 78/79/80
    CACTGTATA CCACUGUAtt AGCGUGA
    0085 ise2c.pk009.i4 Juvenile AAAATATGGCGCGC AAUAUGGCGCG ACAAUAGGCGCGC 81/82/83
    hormone query CTATTGTTT CCUAUUGU CAUAUU
    0086 AACGTTCTCGGTCTT CGUUCUCGGUC CAGUGAAAGACCG 84/85/86
    TCACTGCT UUUCACUG AGAACG
    0087 AAGTCATCGTTCCAA GUCAUCGUUCC GUAGACUUGGAA + 87/88/89
    GTCTACCT AAGUCUAC CGAUGAC
    0088 ise2c.pk001.d19 vacuolar query AACCCCTTGAATGTT CCCCUUGAAUG GACCUUAACAUUC + 90/91/92
    AAGGTCGG UUAAGGUC AAGGGG
    0089 AAGTACACCATGTT GUACACCAUGU UACUUGCAACAUG 93/94/95
    GCAAGTATG UGCAAGUA GUGUAC
    0090 AACGTGTCCATGAT CGUGUCCAUGA GUCAGCCAUCAUG NT 96/97/98
    GGCTGACTC UGGCUGAC GACACG
    0091 ise2c.pk001.e14 vacuolar query AAACCTACAAAATG ACCUACAAAAU UUUCGGCCAUUUU 99/100/101
    GCCGAAAAC GGCCGAAA GUAGGU
    0092 AATCTACGGACCCTT UCUACGGACCC CCAAAGAAGGGUC + 102/103/104
    CTTTGGAG UUCUUUGG CGUAGA
    0093 ise2c.pk001.f20 vacuolar query AACTCTGACGTCATC CUCUGACGUCA GUAGAUGAUGAC 105/106/107
    ATCTACGT UCAUCUAC GUCAGAG
    0094 AAGTGCTTGGGTAA GUGCUUGGGUA GUCGGGGUUACCC 108/109/110
    CCCCGACAG ACCCCGAC AAGCAC
    0095 AACTGGCTCATCTCC CUGGCUCAUCU GCUGUAGGAGAU 111/112/113
    TACAGCAA CCUACAGC GAGCCAG
    0096 ise2c.pk010.h3 cadherin query AAACAGTGCGTCGT ACAGUGCGUCG AUAUAUUACGAC 114/115/116
    AATATATTC UAAUAUAU GCACUGU
    0097 AAGGCACATGGTCC GGCACAUGGUC CAGUGAAGGACCA 117/118/119
    TTCACTGAT CUUCACUG UGUGCC
    0098 AACACCATGACCCT CACCAUGACCCU GUACACGAGGGUC NT 120/121/122
    CGTGTACAA CGUGUAC AUGGUG
    0099 ise2c.pk007.k24 cuticle protein AACGAGGCCGGATC CGAGGCCGGAU CUUAAGAGAUCCG 123/124/125
    TCTTAAGCA CUCUUAAG GCCUCG
    0100 AACTTCACACATAA CUUCACACAUA UGUCUAGUUAUG 457/458/459
    CTAGACAAA ACUAGACA UGUGAAG
    0101 AATGCGTGGCGATTT UUAGAAAUUAU CUGGGCUUAUAA 460/461/462
    CAAACTTA AAGCCCAG UUUCUAA
    0102 ise2c.pk011.a10 cuticle protein AAAAAACACAGACC AAAACACAGAC UGAACGUGGUCU 463/464/465
    ACGTTCACA CACGUUCA GUGUUUU
    0103 AATCGATGGTGGTG UCGAUGGUGGU CGAAUAACACCAC + 126/127/128
    TTATTCGCT GUUAUUCG CAUCGA
    0104 ise2c.pk011.h12 cuticle protein AAAGAAAATGCTAC AGAAAAUGCUA GUAACGCGUAGCA 129/130/131
    GCGTTACGA CGCGUUAC UUUUCU
    0105 AACCCTTGGACACT CCCUUGGACAC UUCCAGUAGUGUC + 132/133/134
    ACTGGAAGA UACUGGAA CAAGGG
    0106 AAGGATCCTATGTGT GGAUCCUAUGU CCUGGUACACAUA NT 135/136/137
    ACCAGGTT GUACCAGG GGAUCC
    0107 ise2c.pk001.d22 translation AAACTCGGCACACA ACUCGGCACAC AUUGUGUUGUGU 138/139/140
    initiationx ACACAATGG AACACAAU GCCGAGU
    factor
    0108 AATACGAAGATATC UACGAAGAUAU AAGGGCAGAUAU + 141/142/143
    TGCCCTTCC CUGCCCUU CUUCGUA
    0109 AATCAACAGCTCTTA UCAACAGCUCU UUUAUGUAAGAG + 144/145/146
    CATAAATG UACAUAAA CUGUUGA
    0110 ise2c.pk001.d9 translation AAAGAAGATCAGAA AGAAGAUCAGA GCCAAUCUUCUGA 147/148/149
    initiation GATTGGCCG AGAUUGGC UCUUCU
    factor
    0111 AAAAGCCGTCTGCT AAGCCGUCUGC GUUGGAUAGCAG 150/151/152
    ATCCAACAA UAUCCAAC ACGGCUU
    0112 AATGCTAAATGCCA UGCUAAAUGCC GCAAGCAUGGCAU + 153/154/155
    TGCTTGCAT AUGCUUGC UUAGCA
    0113 ise2c.pk001.i23 translation AAGATCAGAAGATT GAUCAGAAGAU UCCGGCCAAUCUU + 156/157/158
    initiation GGCCGGAAG UGGCCGGA CUGAUC
    factor
    0114 AATTCTTCAGCAAAT UUCUUCAGCAA GUAUCGAUUUGC NT 159/160/161
    CGATACCA AUCGAUAC UGAAGAA
    0115 AAATGCTGTCAAGA AUGCUGUCAAG UAAAUCCUCUUGA + 162/163/164
    GGATTTAAA AGGAUUUA CAGCAU
    0116 ise2c.pk001.l24 translation AAGCTCGAGACTTG GCUCGAGACUU UCAAGAGCAAGUC + 165/166/167
    initiation CTCTTGATG GCUCUUGA UCGAGC
    factor
    0117 AACTGTTAGCTCAA CUGUUAGCUCA GCAGACCUUGAGC + 168/169/170
    GGTCTGCTA AGGUCUGC UAACAG
    0118 AAGACTTTCTATCAG GACUUUCUAUC CAAAUUCUGAUA 171/172/173
    AATTTGCG AGAAUUUG GAAAGUC
    0119 ise2c.pk005.b9 translation AAACTTAATCATGG ACUUAAUCAUG UCGUCGUCCAUGA 174/175/176
    initiation ACGACGACA GACGACGA UUAAGU
    factor
    0120 AAAGAAGAAGAAGA AGAAGAAGAAG CCCUUCUUCUUCU + 177/178/179
    AGAAGGGAG AAGAAGGG UCUUCU
    0121 AAGATCAAGAGAAT GAUCAAGAGAA CCUCGACAUUCUC + + + 180/181/182
    GTCGAGGAT UGUCGAGG UUGAUC
    0122 ise2c.pk002.m10 SAR1 AAAATCGTCGGTTTT AAUCGUCGGUU GUCGCUAAAACCG NT 183/184/185
    AGCGACGT UUAGCGAC ACGAUU
    0123 AACTGTCAATAGGC CUGUCAAUAGG GCAUACUGCCUAU + 186/187/188
    AGTATGCGT CAGUAUGC UGACAG
    0124 AACCTGTACCAACA CCUGUACCAAC AGUGGUCUGUUG + 189/190/191
    GACCACTGG AGACCACU GUACAGG
    0125 ise2c.pk001.c14 Elongation AACCAAAAATGGGC CCAAAAAUGGG UUUCCUUGCCCAU + 192/193/194
    factor AAGGAAAAG CAAGGAAA UUUUGG
    0126 AACGTGGTATCACC CGUGGUAUCAC UAUCGAUGGUGA + 195/196/197
    ATCGATATT CAUCGAUA UACCACG
    0127 AACAAAATGGACTC CAAAAUGGACU CUCAGUGGAGUCC + 198/199/200
    CACTGAGCC CCACUGAG AUUUUG
    0128 ise2c.pk001.d16 Elongation AATCCGTGACTAAC UCCGUGACUAA AUUUUUGGUUAG + 201/202/203
    factor CAAAAATGG CCAAAAAU UCACGGA
    0129 AACATTGTCGTCATT CAUUGUCGUCA GUGUCCAAUGACG 204/205/206
    GGACACGT UUGGACAC ACAAUG
    0130 ise2c.pk005.h3 phospho- AATTTGTGAGACTG UUUGUGAGACU CGGCCACCAGUCU NT 207/208/209
    oligo- GTGGCCGAA GGUGGCCG CACAAA
    saccharide . . .
    0131 AATCTGATTGTATTC UCUGAUUGUAU GGGGGCGAAUAC 421/422/423
    GCCCCCTC UCGCCCCC AAUCAGA
    0132 AACACTCTAGTTCTG CACUCUAGUUC AAUAGGCAGAAC 424/425/426
    CCTATTCT UGCCUAUU UAGAGUG
    0133 ise2c.pk001.d21 myosin AACACACATCACAA CACACAUCACA UCCGCCAUUGUGA 427/428/429
    TGGCGGATA AUGGCGGA UGUGUG
    0134 AAGGATGGCATCAT GGAUGGCAUCA CUUGCCGAUGAUG 430/431/432
    CGGCAAGAA UCGGCAAG CCAUCC
    0135 AAAGGCTTCATCGA AGGCUUCAUCG CGCGGUGUCGAUG 433/434/435
    CACCGCGAA ACACCGCG AAGCCU
    0136 ise2c.pk001.j9 myosin AAACTCCAATTATA ACUCCAAUUAU AGUAGGUUAUAA 436/437/438
    ACCTACTAG AACCUACU UUGGAGU
    0137 AAGTACAAGGATCT GUACAAGGAUC GCCGAUCAGAUCC 210/211/212
    GATCGGCAA UGAUCGGC UUGUAC
    0138 AAGACTTTCTTCATG GACUUUCUUCA GGGCCACAUGAAG NT 213/214/215
    TGGCCCAT UGUGGCCC AAAGUC
    0139 ise2c.pk002.f12 myosin AAACAAAGTATCGC ACAAAGUAUCG GGUGUAGGCGAU 216/217/218
    CTACACCGC CCUACACC ACUUUGU
    0140 AATAGCGTCGATCTT UAGCGUCGAUC UCGUUGAAGAUC 439/440/441
    CAACGACT UUCAACGA GACGCUA
    0141 ise2c.pk001.b14 potassium AACTCATAGAGCTT CUCAUAGAGCU ACACAUCAAGCUC 442/443/444
    channel GATGTGTGG UGAUGUGU UAUGAG
    amino
    acid
    transporter
    0142 AAGATGTGGATGAC GAUGUGGAUGA CAGUGACGUCAUC 219/220/221
    GTCACTGGT CGUCACUG CACAUC
    0143 AACCTTCCTGATTCT CCUUCCUGAUU CAGAAGAGAAUC + 222/223/224
    CTTCTGTG CUCUUCUG AGGAAGG
    0144 ise2c.pk003.f2 potassium AACAGTGCTTGTGAT CAGUGCUUGUG UCACUUAUCACAA + + 225/226/227
    inwardly AAGTGAAC AUAAGUGA GCACUG
    rectifier . . .
    0145 AAGTTAATGGTGAC GUUAAUGGUGA GAGGGCAGUCACC + 228/229/230
    TGCCCTCGA CUGCCCUC AUUAAC
    0146 AATAAAGCGATGAC UAAAGCGAUGA CUAUGGGGUCAUC NT 231/232/233
    CCCATAGGA CCCCAUAG GCUUUA
    0147 ise2c.pk005.l20 amino acid AAACGGTACTGCAG ACGGUACUGCA CUUUUUGCUGCAG + 234/235/236
    transporter CAAAAAGAC GCAAAAAG UACCGU
    0148 AAGCTGCATACTTCT GCUGCAUACUU GAGCCAAGAAGU 237/238/239
    TGGCTCTC CUUGGCUC AUGCAGC
    0149 AAATGTTTACAGAG AUGUUUACAGA AUCGCGUCUCUGU + 240/241/242
    ACGCGATGA GACGCGAU AAACAU
    0150 ise2c.pk001.d1 tubulin AACGTCGATCTTACC CGUCGAUCUUA GAACUCGGUAAG + + 243/244/245
    GAGTTCCA CCGAGUUC AUCGACG
    0151 ise2c.pk001.k6 tubulin AATTCAAAATGCGT UUCAAAAUGCG UGCACUCACGCAU + 246/247/248
    GAGTGCATC UGAGUGCA UUUGAA
    0152 AAATCGTAGACCTA AUCGUAGACCU CGAGGACUAGGUC + + 249/250/251
    GTCCTCGAC AGUCCUCG UACGAU
    0153 ise2c.pk001.l2 tubulin AAACTCAATTCAAA ACUCAAUUCAA CACGCAUUUUGAA + + 252/253/254
    ATGCGTGAG AAUGCGUG UUGAGU
    0154 AACTTATCACTGGTA CUUAUCACUGG CUUCCUUACCAGU NT 255/256/257
    AGGAAGAT UAAGGAAG GAUAAG
    0155 ise2c.pk002.b4 ubiquitin AAGAGTTACGAACC GAGUUACGAAC UGGUGACGGUUC + 258/259/260
    GTCACCATA CGUCACCA GUAACUC
    0156 AAACTTAGTCCGGA ACUUAGUCCGG UUCAUUAUCCGGA + + 261/262/263
    TAATGAACC AUAAUGAA CUAAGU
    0157 AAGGCGATGTACGA GGCGAUGUACG CAGGUUCUCGUAC + 264/265/266
    GAACCTGTT AGAACCUG AUCGCC
    0158 ise2c.pk001.J16 small nuclear AACGACAAGATGCT CGACAAGAUGC CUCCUUCAGCAUC + 267/268/269
    ribonucleo- GAAGGAGAC UGAAGGAG UUGUCG
    protein
    0159 ise2c.pk006.h23 small nuclear AAGATAAAGGTCGC GAUAAAGGUCG UCCACACGCGACC + 270/271/272
    ribonucleo- GTGTGGACC CGUGUGGA UUUAUC
    protein
    0160 AATGTCAAGACTGA UGUCAAGACUG GUUUGGAUCAGU + 273/274/275
    TCCAAACAC AUCCAAAC CUUGACA
    0161 AACATTCGAGTCTG CAUUCGAGUCU ACCUGUUCAGACU + + 276/277/278
    AACAGGTGG GAACAGGU CGAAUG
    (Note: the sense RNA primer sequence and the antisense RNA primer sequences shown in table 9 were generated with 2 thymine residues at the 3′ end.)
  • TABLE 10
    Injection Droplet Topical Topical Topical Topical Topical Topical
    Mortality Feeding assay 1 Assay 2 Assay 3 Assay 4 Assay 4 Assay 4 Top. 5 Top. 5
    well seq i.d. midgut gene id (%) Result 30 ppm 30 ppm 30 ppm 30 ppm 15 ppm 8 ppm 15 ppm 8 ppm
    77 ise1c.pk002.m13 no Juvenile NT NT NT − − + +
    hormone
    query
    81 ise1c.pk005.a15 no Juvenile NT NT NT − − + + +
    hormone
    query
    114 ise2c.pk001.i23 no translation NT NT NT + + + +
    initiation
    factor
    122 ise2c.pk005.b9 Yes translation NT NT NT + + + + + + +
    initiation
    factor
    143 ise2c.pk001.b14 no potassium NT NT NT − + +
    channel ami-
    acid
    transporter
    145 ise2c.pk003.f2 Yes potassium NT NT NT + + + + +
    inwardly
    rectifier . . .
    146 ise2c.pk003.f2 Yes potassium NT NT NT + + + +
    inwardly
    rectifier . . .
    149 ise2c.pk005.l20 Yes hypothetical NT NT NT + + +
    sodium
    dependent
    transport
    151 ise2c.pk001.d1 No alpha tubulin NT NT NT + + + + +
    154 ise2c.pk001.l2 No alpha tubulin NT NT NT + + + + +
    157 ise2c.pk002.b4 Yes Probable NT NT NT + + + + +
    ubiquitin-
    protein
    ligase
    158 ise2c.pk002.b4 Yes Probable NT NT NT + + − +
    ubiquitin-
    protein
    ligase
    162 ise2c.pk006.h23 Yes RNA- NT NT NT + + + + +
    binding
    protein squid
  • TABLE 11
    DsRNA
    # gene id seqID Comment 8 ppm 4 ppm 2 ppm
    0163 pre-mRNA-binding protein ise2c.pk006.m8 Plate 2 A1
    0164 pre-mRNA-binding protein ise2c.pk006.m8 Plate 2 B1
    0165 pre-mRNA-binding protein ise2c.pk006.m8 Plate 2 C1
    0166 pre-mRNA-binding protein ise2c.pk006.m8 Plate 2 D1 S
    0167 pre-mRNA-binding protein ise2c.pk006.m8 Plate 2 E1 S
    0168 chymotrypsin-like; protease ise2c.pk001.a23 Plate 2 F1 S
    0169 chymotrypsin-like; protease ise2c.pk001.a23 Plate 2 G1
    0170 chymotrypsin-like; protease ise2c.pk001.a23 Plate 2 H1
    0171 chymotrypsin-like; protease ise2c.pk001.a23 Plate 2 A2 S
    0172 chymotrypsin-like; protease ise2c.pk001.a23 Plate 2 B2 S
    0173 chymotrypsinogen; protease ise2c.pk001.a7 Plate 2 C2 S
    0174 chymotrypsinogen; protease ise2c.pk001.a7 Plate 2 D2
    0175 chymotrypsinogen; protease ise2c.pk001.a7 Plate 2 E2
    0176 chymotrypsinogen; protease ise2c.pk001.a7 Plate 2 F2
    0177 chymotrypsinogen; protease ise2c.pk001.a7 Plate 2 G2
    0178 actin-depolymerizing ise2c.pk004.c4 Plate 2 H2
    0179 actin-depolymerizing ise2c.pk004.c4 Plate 2 A3
    0180 actin-depolymerizing ise2c.pk004.c4 Plate 2 B3
    0181 actin-depolymerizing ise2c.pk004.c4 Plate 2 C3
    0182 actin-depolymerizing ise2c.pk004.c4 Plate 2 D3
    0183 actin depolymerizing factor ise2c.pk004.l4 Plate 2 E3
    0184 actin depolymerizing factor ise2c.pk004.l4 Plate 2 F3
    0185 actin depolymerizing factor ise2c.pk004.l4 Plate 2 G3
    0186 actin depolymerizing factor ise2c.pk004.l4 Plate 2 H3
    0187 actin depolymerizing factor ise2c.pk004.l4 Plate 2 A4
    0188 dismutase; superoxide ise2c.pk004.n19 Plate 2 B4
    0189 dismutase; superoxide ise2c.pk004.n19 Plate 2 C4
    0190 dismutase; superoxide ise2c.pk004.n19 Plate 2 D4
    0191 dismutase; superoxide ise2c.pk004.n19 Plate 2 E4
    0192 dismutase; superoxide ise2c.pk004.n19 Plate 2 F4
    0193 superoxide dismutase ise2c.pk005.f21 Plate 2 G4
    0194 superoxide dismutase ise2c.pk005.f21 Plate 2 H4
    0195 superoxide dismutase ise2c.pk005.f21 Plate 2 A5
    0196 adenylate kinase isozyme 3 ise2c.pk010.h5 Plate 2 B5
    0197 adenylate kinase isozyme 3 ise2c.pk010.h5 Plate 2 C5
    0198 adenylate kinase isozyme 3 ise2c.pk010.h5 Plate 2 D5
    0199 adenylate kinase isozyme 3 ise2c.pk010.h5 Plate 2 E5
    0200 adenylate kinase isozyme 3 ise2c.pk010.h5 Plate 2 F5
    0201 ecdysone oxidase ise2c.pk001.c18 Plate 2 G5
    0202 ecdysone oxidase ise2c.pk001.c18 Plate 2 H5
    0203 ecdysone oxidase ise2c.pk001.c18 Plate 2 A6
    0204 innexin-2 ise2c.pk004.p1 Plate 2 B6
    0205 innexin-2 ise2c.pk004.p1 Plate 2 C6
    0206 innexin-2 ise2c.pk004.p1 Plate 2 D6
    0207 innexin-2 ise2c.pk004.p1 Plate 2 E6
    0208 innexin-2 ise2c.pk004.p1 Plate 2 F6
  • TABLE 12
    DsRNA
    # gene id seqID Comment 16 ppm 8 ppm 4 ppm
    0163 pre-mRNA-binding protein ise2c.pk006.m8 Plate 2 A1 S
    0164 pre-mRNA-binding protein ise2c.pk006.m8 Plate 2 B1 S
    0165 pre-mRNA-binding protein ise2c.pk006.m8 Plate 2 C1 S
    0166 pre-mRNA-binding protein ise2c.pk006.m8 Plate 2 D1 S
    0167 pre-mRNA-binding protein ise2c.pk006.m8 Plate 2 E1 S
    0168 chymotrypsin-like; protease ise2c.pk001.a23 Plate 2 F1 ss S
    0169 chymotrypsin-like; protease ise2c.pk001.a23 Plate 2 G1 ss
    0170 chymotrypsin-like; protease ise2c.pk001.a23 Plate 2 H1
    0171 chymotrypsin-like; protease ise2c.pk001.a23 Plate 2 A2
    0172 chymotrypsin-like; protease ise2c.pk001.a23 Plate 2 B2
    0173 chymotrypsinogen; protease ise2c.pk001.a7 Plate 2 C2 ss
    0174 chymotrypsinogen; protease ise2c.pk001.a7 Plate 2 D2 S
    0175 chymotrypsinogen; protease ise2c.pk001.a7 Plate 2 E2 S
    0176 chymotrypsinogen; protease ise2c.pk001.a7 Plate 2 F2 S
    0177 chymotrypsinogen; protease ise2c.pk001.a7 Plate 2 G2 S
    0178 actin-depolymerizing ise2c.pk004.c4 Plate 2 H2
    0179 actin-depolymerizing ise2c.pk004.c4 Plate 2 A3 ss
    0180 actin-depolymerizing ise2c.pk004.c4 Plate 2 B3 s
    0181 actin-depolymerizing ise2c.pk004.c4 Plate 2 C3
    0182 actin-depolymerizing ise2c.pk004.c4 Plate 2 D3
    0183 actin depolymerizing factor ise2c.pk004.l4 Plate 2 E3
    0184 actin depolymerizing factor ise2c.pk004.l4 Plate 2 F3
    0185 actin depolymerizing factor ise2c.pk004.l4 Plate 2 G3
    0186 actin depolymerizing factor ise2c.pk004.l4 Plate 2 H3
    0187 actin depolymerizing factor ise2c.pk004.l4 Plate 2 A4
    0188 dismutase; superoxide ise2c.pk004.n19 Plate 2 B4
    0189 dismutase; superoxide ise2c.pk004.n19 Plate 2 C4 s
    0190 dismutase; superoxide ise2c.pk004.n19 Plate 2 D4
    0191 dismutase; superoxide ise2c.pk004.n19 Plate 2 E4
    0192 dismutase; superoxide ise2c.pk004.n19 Plate 2 F4 s
    0193 superoxide dismutase ise2c.pk005.f21 Plate 2 G4
    0194 superoxide dismutase ise2c.pk005.f21 Plate 2 H4
    0195 superoxide dismutase ise2c.pk005.f21 Plate 2 A5
    0196 adenylate kinase isozyme 3 ise2c.pk010.h5 Plate 2 B5
    0197 adenylate kinase isozyme 3 ise2c.pk010.h5 Plate 2 C5
    0198 adenylate kinase isozyme 3 ise2c.pk010.h5 Plate 2 D5
    0199 adenylate kinase isozyme 3 ise2c.pk010.h5 Plate 2 E5
    0200 adenylate kinase isozyme 3 ise2c.pk010.h5 Plate 2 F5
    0201 ecdysone oxidase ise2c.pk001.c18 Plate 2 G5
    0202 ecdysone oxidase ise2c.pk001.c18 Plate 2 H5
    0203 ecdysone oxidase ise2c.pk001.c18 Plate 2 A6
    0204 innexin-2 ise2c.pk004.p1 Plate 2 B6
    0205 innexin-2 ise2c.pk004.p1 Plate 2 C6
    0206 innexin-2 ise2c.pk004.p1 Plate 2 D6
    0207 innexin-2 ise2c.pk004.p1 Plate 2 E6
    0208 innexin-2 ise2c.pk004.p1 Plate 2 F6
  • TABLE 13
    Summary of FAW droplet feeding data for the first set of synthetic dsRNA primers
    Assay #1 Assay #2 Assay #3 Assay #4
    (table 6) (table 7) (table 8) (table 8)
    30 ppm 30 ppm 30 ppm 30 ppm 15 ppm 8 ppm
    0075 ise1c.pk002.m13 Juvenile hormone query − − − NT − −
    0076 NT − − − − −
    0077 NT − − + − −
    0078 ise1c.pk003.f7 Juvenile hormone query NT − − − − −
    0079 NT − − − − −
    0080 NT − + − − −
    0081 ise1c.pk005.a15 Juvenile hormone query NT − − + + −
    0082 NT − − − − −
    0083 + + NT NT − −
    0084 ise1c.pk006.d24 Juvenile hormone query NT − + − − −
    0085 + − − + − −
    0086 ise2c.pk009.i4 Juvenile hormone query − − − − − −
    0087 NT − − − − −
    0088 + − − + − −
    0089 ise2c.pk001.d19 vacuolar query + − + + − −
    0090 NT − − − − −
    0091 + − + NT − −
    0092 ise2c.pk001.e14 vacuolar query NT − − − − −
    0093 NT − − + − −
    0094 ise2c.pk001.f20 vacuolar query + − − − − −
    0095 + − − − − −
    0096 NT − − − − −
    0097 ise2c.pk010.h3 cadherin query NT − − − − −
    0098 NT + − − − −
    0099 NT − − NT − −
    0100 ise2c.pk007.k24 cuticle protein NT − − − − −
    0101 NT − − − − −
    0102 NT − − − − −
    0103 ise2c.pk011.a10 cuticle protein NT + − − − −
    0104 NT + + + − −
    0105 ise2c.pk011.h12 cuticle protein NT − − − − −
    0106 NT + − + − −
    0107 + − − NT − −
    0108 ise2c.pk001.d22 translation initiation factor NT − + − − −
    0109 NT + + + − −
    0110 NT − + + − −
    0111 ise2c.pk001.d9 translation initiation factor NT − − − − −
    0112 NT + − − − −
    0113 NT − + + − −
    0114 ise2c.pk001.i23 translation initiation factor NT + + + − −
    0115 − − NT NT − −
    0116 NT − − + − −
    0117 ise2c.pk001.l24 translation initiation factor NT − + + − −
    0118 NT − + + − −
    0119 NT + − − − −
    0120 ise2c.pk005.b9 translation initiation factor NT − − − − −
    0121 NT + + + − −
    0122 NT + + + + +
    0123 ise2c.pk002.m10 SAR1 − − + NT − −
    0124 NT − + + − −
    0125 NT + + + − −
    0126 ise2c.pk001.c14 Elongation factor NT + + + − −
    0127 NT + + + − −
    0128 NT − + + − −
    0129 ise2c.pk001.d16 Elongation factor NT + + + − −
    0130 NT − + − − −
    0131 ise2c.pk005.h3 phosphooligosaccharide . . . − − − NT − −
    0132 NT − − − − −
    0133 NT − − − − −
    0134 ise2c.pk001.d21 myosin NT − − − − −
    0135 NT − − − − −
    0136 NT − − − − −
    0137 ise2c.pk001.j9 myosin NT − − − − −
    0138 NT + − − − −
    0139 − − − NT − −
    0140 ise2c.pk002.f12 myosin NT − − − − −
    0141 NT − − − − −
    0142 ise2c.pk001.b14 potassium channel amino acid NT − − − − −
    transporter
    0143 NT − + − − −
    0144 NT − + + − −
    0145 ise2c.pk003.f2 potassium inwardly rectifier . . . NT + + + + −
    0146 NT + + + − −
    0147 + + + NT − −
    0148 ise2c.pk005.l20 amino acid transporter NT + + + − −
    0149 NT + + − − −
    0150 NT − + + − −
    0151 ise2c.pk001.d1 tubulin NT + + + + −
    0152 ise2c.pk001.k6 tubulin NT − − + − −
    0153 NT + + + + −
    0154 ise2c.pk001.l2 tubulin NT + + + + −
    0155 − − − NT − −
    0156 ise2c.pk002.b4 ubiquitin NT − + + − −
    0157 NT + + + + −
    0158 NT + + + − −
    0159 ise2c.pk001.j16 small nuclear ribonucleoprotein NT + + + − −
    0160 ise2c.pk006.h23 small nuclear ribonucleoprotein NT − + + − −
    0161 NT − + + − −
    0162 NT + + + + −
    • Example 2. Transformation of Maize
  • Immature maize embryos from greenhouse donor plants are bombarded with a plasmid containing the silencing element of the invention operably linked to either a tissue specific, tissue selective, or constitutive promoter and the selectable marker gene PAT (Wohlleben et al. (1988) Gene 70:25-37), which confers resistance to the herbicide Bialaphos. In one embodiment, the constructs will have 2 identical 2-300 bp segments of the target gene in opposite orientations with an “intron” segment between them acting as a hairpin loop. Such a construct can be linked to the dMMB promoter. Alternatively, the selectable marker gene is provided on a separate plasmid. Transformation is performed as follows. Media recipes follow below.
    • Preparation of Target Tissue
  • The ears are husked and surface sterilized in 30% Clorox bleach plus 0.5% Micro detergent for 20 minutes, and rinsed two times with sterile water. The immature embryos are excised and placed embryo axis side down (scutellum side up), 25 embryos per plate, on 560Y medium for 4 hours and then aligned within the 2.5 cm target zone in preparation for bombardment.
  • A plasmid vector comprising the silencing element of interest operably linked to either the tissue specific, tissue selective, or constitutive promoter is made. This plasmid DNA plus plasmid DNA containing a PAT selectable marker is precipitated onto 1.1 μm (average diameter) tungsten pellets using a CaCl2 precipitation procedure as follows: 100 μl prepared tungsten particles in water; 10 μl (1 μg) DNA in Tris EDTA buffer (1 μg total DNA); 100 μl 2.5 M CaCl2; and, 10 μl 0.1 M spermidine.
  • Each reagent is added sequentially to the tungsten particle suspension, while maintained on the multitube vortexer. The final mixture is sonicated briefly and allowed to incubate under constant vortexing for 10 minutes. After the precipitation period, the tubes are centrifuged briefly, liquid removed, washed with 500 ml 100% ethanol, and centrifuged for 30 seconds. Again the liquid is removed, and 105 μl 100% ethanol is added to the final tungsten particle pellet. For particle gun bombardment, the tungsten/DNA particles are briefly sonicated and 10 μl spotted onto the center of each macrocarrier and allowed to dry about 2 minutes before bombardment.
  • The sample plates are bombarded at level #4 in a particle gun. All samples receive a single shot at 650 PSI, with a total of ten aliquots taken from each tube of prepared particles/DNA.
  • Following bombardment, the embryos are kept on 560Y medium for 2 days, then transferred to 560R selection medium containing 3 mg/liter Bialaphos, and subcultured every 2 weeks. After approximately 10 weeks of selection, selection-resistant callus clones are transferred to 288 J medium to initiate plant regeneration. Following somatic embryo maturation (2-4 weeks), well-developed somatic embryos are transferred to medium for germination and transferred to the lighted culture room. Approximately 7-10 days later, developing plantlets are transferred to 272V hormone-free medium in tubes for 7-10 days until plantlets are well established. Plants are then transferred to inserts in flats (equivalent to 2.5″ pot) containing potting soil and grown for 1 week in a growth chamber, subsequently grown an additional 1-2 weeks in the greenhouse, then transferred to classic 600 pots (1.6 gallon) and grown to maturity.
  • Plants are monitored and scored for the appropriate marker, such as the control of Lepidoptera and have insecticidal activity. For example, a FAW feeding assay could be preformed. In such assays, leaf discs from the transgenic plant are excised using a 1 cm cork borer or leaf punch. Six leaf discs are prepared for each plant. The leaves are placed in a 24 well microtiter plate on top of 500 ul of 0.8% agar. Each leaf disc is infested with 2 neonate Fall armyworm and the plate is then sealed with mylar. A small ventilation hole is made for each well and the plates are then stored in a 28 C growth chamber. The assay is scored for mortality, stunting, and leaf consumption at 96 hours.
  • Bombardment medium (560Y) comprises 4.0 g/l N6 basal salts (SIGMA C-1416), 1.0 ml/l Eriksson's Vitamin Mix (1000× SIGMA-1511), 0.5 mg/l thiamine HCl, 120.0 g/l sucrose, 1.0 mg/l 2,4-D, and 2.88 g/l L-proline (brought to volume with D-I H2O following adjustment to pH 5.8 with KOH); 2.0 g/l Gelrite (added after bringing to volume with D-I H2O); and 8.5 mg/l silver nitrate (added after sterilizing the medium and cooling to room temperature). Selection medium (560R) comprises 4.0 g/l N6 basal salts (SIGMA C-1416), 1.0 ml/l Eriksson's Vitamin Mix (1000× SIGMA-1511), 0.5 mg/l thiamine HCl, 30.0 g/l sucrose, and 2.0 mg/l 2,4-D (brought to volume with D-I H2O following adjustment to pH 5.8 with KOH); 3.0 g/l Gelrite (added after bringing to volume with D-I H2O); and 0.85 mg/l silver nitrate and 3.0 mg/l bialaphos (both added after sterilizing the medium and cooling to room temperature).
  • Plant regeneration medium (288 J) comprises 4.3 g/l MS salts (GIBCO 11117-074), 5.0 ml/l MS vitamins stock solution (0.100 g nicotinic acid, 0.02 g/l thiamine HCl, 0.10 g/l pyridoxine HCl, and 0.40 g/l glycine brought to volume with polished D-I H2O) (Murashige and Skoog (1962) Physiol. Plant. 15:473), 100 mg/l myo-inositol, 0.5 mg/l zeatin, 60 g/l sucrose, and 1.0 ml/l of 0.1 mM abscisic acid (brought to volume with polished D-I H2O after adjusting to pH 5.6); 3.0 g/l Gelrite (added after bringing to volume with D-I H2O); and 1.0 mg/l indoleacetic acid and 3.0 mg/l bialaphos (added after sterilizing the medium and cooling to 60° C.). Hormone-free medium (272V) comprises 4.3 g/l MS salts (GIBCO 11117-074), 5.0 ml/l MS vitamins stock solution (0.100 g/l nicotinic acid, 0.02 g/l thiamine HCl, 0.10 g/l pyridoxine HCl, and 0.40 g/l glycine brought to volume with polished D-I H2O), 0.1 g/l myo-inositol, and 40.0 g/l sucrose (brought to volume with polished D-I H2O after adjusting pH to 5.6); and 6 g/l bacto-agar (added after bringing to volume with polished D-I H2O), sterilized and cooled to 60° C.
    • Example 3. Agrobacterium-Mediated Transformation of Maize
  • For Agrobacterium-mediated transformation of maize with a silencing element of the invention, the method of Zhao is employed (U.S. Pat. No. 5,981,840, and PCT patent publication WO98/32326; the contents of which are hereby incorporated by reference). Such as a construct can comprise 2 identical 2-300 bp segments of the target gene in opposite orientations with an “intron” segment between them acting as a hairpin loop. Such a construct can be linked to the dMMB promoter. Briefly, immature embryos are isolated from maize and the embryos contacted with a suspension of Agrobacterium, where the bacteria are capable of transferring the polynucleotide comprising the silencing element to at least one cell of at least one of the immature embryos (step 1: the infection step). In this step the immature embryos are immersed in an Agrobacterium suspension for the initiation of inoculation. The embryos are co-cultured for a time with the Agrobacterium (step 2: the co-cultivation step). The immature embryos are cultured on solid medium following the infection step. Following this co-cultivation period an optional “resting” step is contemplated. In this resting step, the embryos are incubated in the presence of at least one antibiotic known to inhibit the growth of Agrobacterium without the addition of a selective agent for plant transformants (step 3: resting step). The immature embryos are cultured on solid medium with antibiotic, but without a selecting agent, for elimination of Agrobacterium and for a resting phase for the infected cells. Next, inoculated embryos are cultured on medium containing a selective agent and growing transformed callus is recovered (step 4: the selection step). The immature embryos are cultured on solid medium with a selective agent resulting in the selective growth of transformed cells. The callus is then regenerated into plants (step 5: the regeneration step), and calli grown on selective medium are cultured on solid medium to regenerate the plants.
    • Example 4: Soybean Embryo Transformation Culture Conditions
  • Soybean embryogenic suspension cultures (cv. Jack) are maintained in 35 ml liquid medium SB196 (see recipes below) on rotary shaker, 150 rpm, 26° C. with cool white fluorescent lights on 16:8 hr day/night photoperiod at light intensity of 60-85 μE/m2/s. Cultures are subcultured every 7 days to two weeks by inoculating approximately 35 mg of tissue into 35 ml of fresh liquid SB196 (the preferred subculture interval is every 7 days).
  • Soybean embryogenic suspension cultures are transformed with the plasmids and DNA fragments described in the examples above by the method of particle gun bombardment (Klein et al. (1987) Nature, 327:70).
    • Soybean Embryogenic Suspension Culture Initiation
  • Soybean cultures are initiated twice each month with 5-7 days between each initiation.
  • Pods with immature seeds from available soybean plants 45-55 days after planting are picked, removed from their shells and placed into a sterilized magenta box. The soybean seeds are sterilized by shaking them for 15 minutes in a 5% Clorox solution with 1 drop of ivory soap (95 ml of autoclaved distilled water plus 5 ml Clorox and 1 drop of soap). Mix well. Seeds are rinsed using 2 1-liter bottles of sterile distilled water and those less than 4 mm are placed on individual microscope slides. The small end of the seed are cut and the cotyledons pressed out of the seed coat. Cotyledons are transferred to plates containing SB1 medium (25-30 cotyledons per plate). Plates are wrapped with fiber tape and stored for 8 weeks. After this time secondary embryos are cut and placed into SB196 liquid media for 7 days.
    • Preparation of DNA for Bombardment
  • Either an intact plasmid or a DNA plasmid fragment containing the genes of interest and the selectable marker gene are used for bombardment. Plasmid DNA for bombardment are routinely prepared and purified using the method described in the Promega™ Protocols and Applications Guide, Second Edition (page 106). Fragments of the plasmids carrying the silencing element of interest are obtained by gel isolation of double digested plasmids. In each case, 100 ug of plasmid DNA is digested in 0.5 ml of the specific enzyme mix that is appropriate for the plasmid of interest. The resulting DNA fragments are separated by gel electrophoresis on 1% SeaPlaque GTG agarose (BioWhitaker Molecular Applications) and the DNA fragments containing silencing element of interest are cut from the agarose gel. DNA is purified from the agarose using the GELase digesting enzyme following the manufacturer's protocol.
  • A 50 μl aliquot of sterile distilled water containing 3 mg of gold particles (3 mg gold) is added to 5 μl of a 1 μg/μl DNA solution (either intact plasmid or DNA fragment prepared as described above), 50 μl 2.5M CaCl2 and 20 μl of 0.1 M spermidine. The mixture is shaken 3 min on level 3 of a vortex shaker and spun for 10 sec in a bench microfuge. After a wash with 400 μl 100% ethanol the pellet is suspended by sonication in 40 μl of 100% ethanol. Five μl of DNA suspension is dispensed to each flying disk of the Biolistic PDS1000/HE instrument disk. Each 5 μl aliquot contains approximately 0.375 mg gold per bombardment (i.e. per disk).
  • Tissue Preparation and Bombardment with DNA
  • Approximately 150-200 mg of 7 day old embryonic suspension cultures are placed in an empty, sterile 60×15 mm petri dish and the dish covered with plastic mesh. Tissue is bombarded 1 or 2 shots per plate with membrane rupture pressure set at 1100 PSI and the chamber evacuated to a vacuum of 27-28 inches of mercury. Tissue is placed approximately 3.5 inches from the retaining/stopping screen.
    • Selection of Transformed Embryos
  • Transformed embryos were selected either using hygromycin (when the hygromycin phosphotransferase, HPT, gene was used as the selectable marker) or chlorsulfuron (when the acetolactate synthase, ALS, gene was used as the selectable marker).
    • Hygromycin (HPT) Selection
  • Following bombardment, the tissue is placed into fresh SB196 media and cultured as described above. Six days post-bombardment, the SB196 is exchanged with fresh SB196 containing a selection agent of 30 mg/L hygromycin. The selection media is refreshed weekly. Four to six weeks post selection, green, transformed tissue may be observed growing from untransformed, necrotic embryogenic clusters. Isolated, green tissue is removed and inoculated into multiwell plates to generate new, clonally propagated, transformed embryogenic suspension cultures.
    • Chlorsulfuron (ALS) Selection
  • Following bombardment, the tissue is divided between 2 flasks with fresh SB196 media and cultured as described above. Six to seven days post-bombardment, the SB196 is exchanged with fresh SB196 containing selection agent of 100 ng/ml Chlorsulfuron. The selection media is refreshed weekly. Four to six weeks post selection, green, transformed tissue may be observed growing from untransformed, necrotic embryogenic clusters. Isolated, green tissue is removed and inoculated into multiwell plates containing SB196 to generate new, clonally propagated, transformed embryogenic suspension cultures.
  • Regeneration of Soybean Somatic Embryos into Plants
  • In order to obtain whole plants from embryogenic suspension cultures, the tissue must be regenerated.
    • Embryo Maturation
  • Embryos are cultured for 4-6 weeks at 26° C. in SB196 under cool white fluorescent (Phillips cool white Econowatt F40/CW/RS/EW) and Agro (Phillips F40 Agro) bulbs (40 watt) on a 16:8 hr photoperiod with light intensity of 90-120 uE/m2s. After this time embryo clusters are removed to a solid agar media, SB166, for 1-2 weeks. Clusters are then subcultured to medium SB103 for 3 weeks. During this period, individual embryos can be removed from the clusters and screened for the appropriate marker or the ability of the plant, when injected with the silencing elements, to contol the Lepidoptera.
    • Embryo Desiccation and Germination
  • Matured individual embryos are desiccated by placing them into an empty, small petri dish (35×10 mm) for approximately 4-7 days. The plates are sealed with fiber tape (creating a small humidity chamber). Desiccated embryos are planted into SB71-4 medium where they were left to germinate under the same culture conditions described above. Germinated plantlets are removed from germination medium and rinsed thoroughly with water and then planted in Redi-Earth in 24-cell pack tray, covered with clear plastic dome. After 2 weeks the dome is removed and plants hardened off for a further week. If plantlets looked hardy they are transplanted to 10″ pot of Redi-Earth with up to 3 plantlets per pot.
    • Media Recipes
  • SB 196 - FN Lite liquid proliferation medium (per liter) -
    MS FeEDTA - 100x Stock 1 10 ml
    MS Sulfate - 100x Stock 2 10 ml
    FN Lite Halides - 100x Stock 3 10 ml
    FN Lite P, B, Mo - 100x Stock 4 10 ml
    B5 vitamins (1 ml/L) 1.0 ml
    2,4-D (10 mg/L final concentration) 1.0 ml
    KNO3 2.83 gm
    (NH4)2 SO4 0.463 gm
    Asparagine 1.0 gm
    Sucrose (1%) 10 gm
    pH 5.8
    • FN Lite Stock Solutions
  • Stock # 1000 ml 500 ml
    1 MS Fe EDTA 100x Stock
    Na2 EDTA* 3.724 g 1.862 g
    FeSO4—7H2O 2.784 g 1.392 g
    2 MS Sulfate 100x stock
    MgSO4—7H2O  37.0 g  18.5 g
    MnSO4—H2O  1.69 g 0.845 g
    ZnSO4—7H2O  0.86 g  0.43 g
    CuSO4—5H2O 0.0025 g  0.00125 g 
    3 FN Lite Halides 100x Stock
    CaCl2—2H2O  30.0 g  15.0 g
    KI 0.083 g 0.0715 g 
    CoCl2—6H2O 0.0025 g  0.00125 g 
    4 FN Lite P,B,Mo 100x Stock
    KH2PO4  18.5 g  9.25 g
    H3BO3  0.62 g  0.31 g
    Na2MoO4—2H2O 0.025 g 0.0125 g 
    *Add first, dissolve in dark bottle while stirring
  • SB1 solid medium (per liter) comprises: 1 pkg. MS salts (Gibco/BRL—Cat#11117-066); 1 ml B5 vitamins 1000× stock; 31.5 g sucrose; 2 ml 2,4-D (20 mg/L final concentration); pH 5.7; and, 8 g TC agar.
  • SB 166 solid medium (per liter) comprises: 1 pkg. MS salts (Gibco/BRL—Cat#11117-066); 1 ml B5 vitamins 1000× stock; 60 g maltose; 750 mg MgCl2 hexahydrate; 5 g activated charcoal; pH 5.7; and, 2 g gelrite.
  • SB 103 solid medium (per liter) comprises: 1 pkg. MS salts (Gibco/BRL—Cat#11117-066); 1 ml B5 vitamins 1000× stock; 60 g maltose; 750 mg MgCl2 hexahydrate; pH 5.7; and, 2 g gelrite.
  • SB 71-4 solid medium (per liter) comprises: 1 bottle Gamborg's B5 salts w/sucrose (Gibco/BRL—Cat#21153-036); pH 5.7; and, 5 g TC agar.
  • 2,4-D stock is obtained premade from Phytotech cat# D 295—concentration is 1 mg/ml.
  • B5 Vitamins Stock (per 100 ml) which is stored in aliquots at −20 C comprises: 10 g myo-inositol; 100 mg nicotinic acid; 100 mg pyridoxine HCl; and, 1 g thiamine. If the solution does not dissolve quickly enough, apply a low level of heat via the hot stir plate. Chlorsulfuron Stock comprises 1 mg/ml in 0.01 N Ammonium Hydroxide
  • The article “a” and “an” are used herein to refer to one or more than one (i.e., to at least one) of the grammatical object of the article. By way of example, “an element” means one or more element.
  • All publications and patent applications mentioned in the specification are indicative of the level of those skilled in the art to which this invention pertains. All publications and patent applications are herein incorporated by reference to the same extent as if each individual publication or patent application was specifically and individually indicated to be incorporated by reference.
  • Although the foregoing invention has been described in some detail by way of illustration and example for purposes of clarity of understanding, it will be obvious that certain changes and modifications may be practiced within the scope of the appended claims.

Claims (26)

That which is claimed:
1. A plant cell having stably incorporated into its genome a heterologous polynucleotide comprising a silencing, wherein said silencing element comprises a fragment of at least 20 consecutive nucleotides of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50,
wherein said silencing element, when ingested by a pest from the Lepidoptera order, reduces the level of a target sequence in said pest and thereby controls the pest from the Lepidoptera order.
2. The plant cell of claim 1, wherein said pest comprises Spodoptera frugiperda.
3. The plant cell of claim 1, wherein said silencing element comprises
a) a polynucleotide comprising the sense or antisense sequence of the sequence set forth in SEQ ID NO: 51, 54, 57, 60, 63, 66, 69, 72, 75, 78, 81, 84, 87, 90, 93, 96, 99, 102, 105, 108, 111, 114, 117, 120, 123, 126, 129, 132, 135, 138, 141, 144, 147, 150, 153, 156, 159, 162, 165, 168, 171, 174, 177, 180, 183, 186, 189, 192, 195, 198, 201, 204, 207, 210, 213, 216, 219, 222, 225, 228, 231, 234, 237, 240, 243, 246, 249, 252, 255, 258, 261, 264, 267, 270, 273, 276, 279, 282, 285, 288, 291, 294, 297, 300, 303, 306, 309, 312, 315, 318, 321, 324, 327, 330, 333, 336, 339, 342, 345, 348, 351, 354, 357, 360, 363, 366, 369, 372, 375, 378, 381, 384, 387, 390, 393, 396, 399, 402, 405, 408, 411, 415, or 418;
b) a polynucleotide comprising the sense or antisense sequence of a sequence having at least 95% sequence identity to the sequence set forth in SEQ ID NO: 51, 54, 57, 60, 63, 66, 69, 72, 75, 78, 81, 84, 87, 90, 93, 96, 99, 102, 105, 108, 111, 114, 117, 120, 123, 126, 129, 132, 135, 138, 141, 144, 147, 150, 153, 156, 159, 162, 165, 168, 171, 174, 177, 180, 183, 186, 189, 192, 195, 198, 201, 204, 207, 210, 213, 216, 219, 222, 225, 228, 231, 234, 237, 240, 243, 246, 249, 252, 255, 258, 261, 264, 267, 270, 273, 276, 279, 282, 285, 288, 291, 294, 297, 300, 303, 306, 309, 312, 315, 318, 321, 324, 327, 330, 333, 336, 339, 342, 345, 348, 351, 354, 357, 360, 363, 366, 369, 372, 375, 378, 381, 384, 387, 390, 393, 396, 399, 402, 405, 408, 411, 415, or 418;
c) a polynucleotide comprising the sequence set forth in SEQ ID NO: 52, 53, 55, 56, 58, 59, 61, 62, 64, 65, 67, 68, 70, 71, 73, 74, 76, 77, 79, 80, 82, 83, 85, 86, 88, 89, 91, 92, 94, 95, 97, 98, 100, 101, 103, 104, 106, 107, 109, 110, 112, 113, 115, 116, 118, 119, 121, 122, 124, 125, 127, 128, 130, 131, 133, 134, 136, 137, 139, 140, 142, 143, 145, 146, 148, 149, 151, 152, 154, 155, 157, 158, 160, 161, 163, 164, 166, 167, 169, 170, 172, 173, 175, 176, 178, 179, 181, 182, 184, 185, 187, 188, 190, 191, 193, 194, 196, 197, 199, 200, 202, 203, 205, 206, 208, 209, 211, 212, 214, 215, 217, 218, 220, 221, 223, 224, 226, 227, 229, 230, 232, 233, 235, 236, 238, 239, 241, 242, 244, 245, 247, 248, 250, 251, 253, 254, 256, 257, 259, 260, 262, 263, 265, 266, 268, 269, 271, 272, 274, 275, 277, 278, 280, 281, 283, 284, 286, 287, 289, 290, 292, 293, 295, 296, 298, 299, 301, 302, 304, 305, 307, 308, 310, 311, 313, 314, 316, 317, 319, 320, 322, 323, 325, 326, 328, 329, 331, 332, 334, 335, 337, 338, 340, 341, 343, 344, 346, 347, 349, 350, 352, 353, 355, 356, 358, 359, 361, 362, 364, 365, 367, 368, 370, 371, 373, 374, 376, 377, 379, 380, 382, 383, 385, 386, 388, 389, 391, 392, 394, 395, 397, 398, 400, 401, 403, 404, 406, 407, 409, 410, 412, 413, 416, 417, 419, or 420
d) a polynucleotide comprising a nucleotide sequence having at least 95% sequence identity to SEQ ID NO: 52, 53, 55, 56, 58, 59, 61, 62, 64, 65, 67, 68, 70, 71, 73, 74, 76, 77, 79, 80, 82, 83, 85, 86, 88, 89, 91, 92, 94, 95, 97, 98, 100, 101, 103, 104, 106, 107, 109, 110, 112, 113, 115, 116, 118, 119, 121, 122, 124, 125, 127, 128, 130, 131, 133, 134, 136, 137, 139, 140, 142, 143, 145, 146, 148, 149, 151, 152, 154, 155, 157, 158, 160, 161, 163, 164, 166, 167, 169, 170, 172, 173, 175, 176, 178, 179, 181, 182, 184, 185, 187, 188, 190, 191, 193, 194, 196, 197, 199, 200, 202, 203, 205, 206, 208, 209, 211, 212, 214, 215, 217, 218, 220, 221, 223, 224, 226, 227, 229, 230, 232, 233, 235, 236, 238, 239, 241, 242, 244, 245, 247, 248, 250, 251, 253, 254, 256, 257, 259, 260, 262, 263, 265, 266, 268, 269, 271, 272, 274, 275, 277, 278, 280, 281, 283, 284, 286, 287, 289, 290, 292, 293, 295, 296, 298, 299, 301, 302, 304, 305, 307, 308, 310, 311, 313, 314, 316, 317, 319, 320, 322, 323, 325, 326, 328, 329, 331, 332, 334, 335, 337, 338, 340, 341, 343, 344, 346, 347, 349, 350, 352, 353, 355, 356, 358, 359, 361, 362, 364, 365, 367, 368, 370, 371, 373, 374, 376, 377, 379, 380, 382, 383, 385, 386, 388, 389, 391, 392, 394, 395, 397, 398, 400, 401, 403, 404, 406, 407, 409, 410, 412, 413, 416, 417, 419, or 420.
4. The plant cell of claim 1, wherein said silencing element comprises a hairpin RNA.
5. The plant cell of claim 4, wherein said polynucleotide comprising the silencing element comprises, in the following order, a first segment, a second segment, and a third segment, wherein
a) said first segment comprises at least about 20 nucleotides having at least 90% sequence complementarity to a target sequence set forth in SEQ ID NOS: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50;
b) said second segment comprises a loop of sufficient length to allow the silencing element to be transcribed as a hairpin RNA; and,
c) said third segment comprises at least about 20 nucleotides having at least 85% complementarity to the first segment.
6. The plant cell of claim 1, wherein said silencing element is operably linked to a heterologous promoter.
7. The plant cell of claim 1, wherein said plant cell has stably incorporated into its genome a second polynucleotide comprising a suppressor enhancer element comprising the target pest sequence or an active variant or fragment thereof, wherein the combined expression of the silencing element and the suppressor enhancer element increases the concentration of an inhibitory RNAi specific for the pest target sequence in said plant cell.
8. The plant cell of claim 1, wherein said plant cell is from a monocot.
9. The plant cell of claim 8, wherein said monocot is maize, barley, millet, wheat or rice.
10. The plant cell of claim 1, wherein said plant cell is from a dicot.
11. The plant cell of claim 10, wherein said dicot is soybean, canola, alfalfa, sunflower, safflower, tobacco, Arabidopsis, or cotton.
12. A plant or plant part comprising a plant cell of claim 1.
13. The plant or plant part of claim 7, wherein the combined expression of said silencing element and the suppressor enhancer element increases the concentration of an inhibitory RNA specific for the pest target sequence in the phloem of said plant or plant part.
14. A transgenic seed from the plant of claim 12.
15. A method for controlling Lepidoptera comprising feeding to a Lepidoptera a composition comprising a silencing element, wherein said silencing element, when ingested by said Lepidoptera, reduces the level of a target Lepidoptera sequence and thereby controls the Lepidoptera and said silencing element comprises a fragment of at least 20 consecutive nucleotides of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50.
16. The method of claim 15, wherein said composition comprises a plant or plant part having stably incorporated into its genome a polynucleotide comprising said silencing element.
17. The method of claim 15, wherein said pest comprises Spodoptera frugiperda.
18. The method of claim 15, wherein said silencing element comprises
a) a polynucleotide comprising the sense or antisense sequence of the sequence set forth in SEQ ID NO: 51, 54, 57, 60, 63, 66, 69, 72, 75, 78, 81, 84, 87, 90, 93, 96, 99, 102, 105, 108, 111, 114, 117, 120, 123, 126, 129, 132, 135, 138, 141, 144, 147, 150, 153, 156, 159, 162, 165, 168, 171, 174, 177, 180, 183, 186, 189, 192, 195, 198, 201, 204, 207, 210, 213, 216, 219, 222, 225, 228, 231, 234, 237, 240, 243, 246, 249, 252, 255, 258, 261, 264, 267, 270, 273, 276, 279, 282, 285, 288, 291, 294, 297, 300, 303, 306, 309, 312, 315, 318, 321, 324, 327, 330, 333, 336, 339, 342, 345, 348, 351, 354, 357, 360, 363, 366, 369, 372, 375, 378, 381, 384, 387, 390, 393, 396, 399, 402, 405, 408, 411, 415, or 418;
b) a polynucleotide comprising the sense or antisense sequence of a sequence having at least 95% sequence identity to the sequence set forth in SEQ ID NO: 51, 54, 57, 60, 63, 66, 69, 72, 75, 78, 81, 84, 87, 90, 93, 96, 99, 102, 105, 108, 111, 114, 117, 120, 123, 126, 129, 132, 135, 138, 141, 144, 147, 150, 153, 156, 159, 162, 165, 168, 171, 174, 177, 180, 183, 186, 189, 192, 195, 198, 201, 204, 207, 210, 213, 216, 219, 222, 225, 228, 231, 234, 237, 240, 243, 246, 249, 252, 255, 258, 261, 264, 267, 270, 273, 276, 279, 282, 285, 288, 291, 294, 297, 300, 303, 306, 309, 312, 315, 318, 321, 324, 327, 330, 333, 336, 339, 342, 345, 348, 351, 354, 357, 360, 363, 366, 369, 372, 375, 378, 381, 384, 387, 390, 393, 396, 399, 402, 405, 408, 411, 415, or 418;
c) a polynucleotide comprising the sequence set forth in SEQ ID NO: 52, 53, 55, 56, 58, 59, 61, 62, 64, 65, 67, 68, 70, 71, 73, 74, 76, 77, 79, 80, 82, 83, 85, 86, 88, 89, 91, 92, 94, 95, 97, 98, 100, 101, 103, 104, 106, 107, 109, 110, 112, 113, 115, 116, 118, 119, 121, 122, 124, 125, 127, 128, 130, 131, 133, 134, 136, 137, 139, 140, 142, 143, 145, 146, 148, 149, 151, 152, 154, 155, 157, 158, 160, 161, 163, 164, 166, 167, 169, 170, 172, 173, 175, 176, 178, 179, 181, 182, 184, 185, 187, 188, 190, 191, 193, 194, 196, 197, 199, 200, 202, 203, 205, 206, 208, 209, 211, 212, 214, 215, 217, 218, 220, 221, 223, 224, 226, 227, 229, 230, 232, 233, 235, 236, 238, 239, 241, 242, 244, 245, 247, 248, 250, 251, 253, 254, 256, 257, 259, 260, 262, 263, 265, 266, 268, 269, 271, 272, 274, 275, 277, 278, 280, 281, 283, 284, 286, 287, 289, 290, 292, 293, 295, 296, 298, 299, 301, 302, 304, 305, 307, 308, 310, 311, 313, 314, 316, 317, 319, 320, 322, 323, 325, 326, 328, 329, 331, 332, 334, 335, 337, 338, 340, 341, 343, 344, 346, 347, 349, 350, 352, 353, 355, 356, 358, 359, 361, 362, 364, 365, 367, 368, 370, 371, 373, 374, 376, 377, 379, 380, 382, 383, 385, 386, 388, 389, 391, 392, 394, 395, 397, 398, 400, 401, 403, 404, 406, 407, 409, 410, 412, 413, 416, 417, 419, or 420;
d) a polynucleotide comprising the sequence set forth in SEQ ID NO: 52, 53, 55, 56, 58, 59, 61, 62, 64, 65, 67, 68, 70, 71, 73, 74, 76, 77, 79, 80, 82, 83, 85, 86, 88, 89, 91, 92, 94, 95, 97, 98, 100, 101, 103, 104, 106, 107, 109, 110, 112, 113, 115, 116, 118, 119, 121, 122, 124, 125, 127, 128, 130, 131, 133, 134, 136, 137, 139, 140, 142, 143, 145, 146, 148, 149, 151, 152, 154, 155, 157, 158, 160, 161, 163, 164, 166, 167, 169, 170, 172, 173, 175, 176, 178, 179, 181, 182, 184, 185, 187, 188, 190, 191, 193, 194, 196, 197, 199, 200, 202, 203, 205, 206, 208, 209, 211, 212, 214, 215, 217, 218, 220, 221, 223, 224, 226, 227, 229, 230, 232, 233, 235, 236, 238, 239, 241, 242, 244, 245, 247, 248, 250, 251, 253, 254, 256, 257, 259, 260, 262, 263, 265, 266, 268, 269, 271, 272, 274, 275, 277, 278, 280, 281, 283, 284, 286, 287, 289, 290, 292, 293, 295, 296, 298, 299, 301, 302, 304, 305, 307, 308, 310, 311, 313, 314, 316, 317, 319, 320, 322, 323, 325, 326, 328, 329, 331, 332, 334, 335, 337, 338, 340, 341, 343, 344, 346, 347, 349, 350, 352, 353, 355, 356, 358, 359, 361, 362, 364, 365, 367, 368, 370, 371, 373, 374, 376, 377, 379, 380, 382, 383, 385, 386, 388, 389, 391, 392, 394, 395, 397, 398, 400, 401, 403, 404, 406, 407, 409, 410, 412, 413, 416, 417, 419, or 420.
19. The method of claim 15, wherein said silencing element comprises a hairpin RNA.
20. The method of claim 19 wherein said polynucleotide comprising the silencing element comprises, in the following order, a first segment, a second segment, and a third segment, wherein
a) said first segment comprises at least about 20 nucleotides having at least 90% sequence complementarity to the target polynucleotide;
b) said second segment comprises a loop of sufficient length to allow the silencing element to be transcribed as a hairpin RNA; and,
c) said third segment comprises at least about 20 nucleotides having at least 85% complementarity to the first segment.
21. The method of claim 15, wherein said silencing element is operably linked to a heterologous promoter.
22. The method of claim 16, wherein said plant or plant part has stably incorporated into its genome a second polynucleotide comprising a suppressor enhancer element comprising the target pest sequence or an active variant or fragment thereof, wherein the combined expression of the silencing element and the suppressor enhancer element increases the concentration of an inhibitory RNAi specific for the pest target sequence in said plant cell.
23. The method of claim 15, wherein said plant is a monocot.
24. The method of claim 23, wherein said monocot is maize, barley, millet, wheat or rice.
25. The method of claim 15, wherein said plant is a dicot.
26. The method of claim 25, wherein said plant is soybean, canola, alfalfa, sunflower, safflower, tobacco, Arabidopsis, or cotton.
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