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Advanced Genetic Technologies, KY
Department of Plant Pathology
Agricultural productivity depends heavily on the genetic potential and general health of crops and livestock. The project aims are to enhance techniques of genetic analysis, and through such techniques, to increase understanding of plant and animal genomics, the genomics of microbial pathogens and symbionts of plants and animals. The project will integrate the modern laboratory methods of large-scale DNA sequencing with computational methods to interpret DNA sequences and identify genes and key features of genomes. Personnel will be hired in both the life science and computer science areas to work together on enhancing the data flow and processing of all data generated in the Advanced Genetic Technologies Center at the University of Kentucky. Pilot studies will be conducted to obtain sequences from an important symbiont of tall fescue, the most widely planted forage grass in the U.S.A., and also from an important horse parasite. Other pilot studies will be invited, and undergraduate interns will be trained in genomics techniques and concepts.
2010 Project Description
The Advanced Genetic Technologies Center at the University of Kentucky College of Agriculture conducted deep-sequence analysis of the transcriptomes of the woody plants, magnolia and acacia, the transcriptome of the oil-producing alga, Botryococcus braunii, and the transcriptomes of two insect species, Cimex lectularius (bedbug) and Leptinotarsa decemlineata (Colorado potato beetle). In addition, the genome was sequenced for the fungus Claviceps purpurea, the ergot pathogen of rye (Secale cereale). Bioinformatic analysis was conducted on the transcriptome and genome sequences. Sequencing was also conducted on thousands of individual cloned or amplified DNA molecules for 13 research groups in the college. Results contributed to 50 published research papers.
DNA and RNA sequencing, and bioinformatic analysis supported on this project contributed to new knowledge of plant, insect, and fungal biology. For example, genes were identified for protective metabolites in magnolia and Claviceps, and the genetic basis for insecticide resistance was elucidated in several insect pests.
de Sa PB, Havens WM, Ghabrial SA (2010) Characterization of a novel broad-spectrum antifungal protein from virus-infected Helminthosporium (Cochliobolus) victoriae. Phytopathology 100: 880-889.
de Sa PB, Li H, Havens WM, Farman ML, Ghabrial SA (2010) Overexpression of the victoriocin gene in Helminthosporium (Cochliobolus) victoriae enhances the antifungal activity of culture filtrates. Phytopathology 100: 890-896.
Denlinger DL, Palli SR (2010) A tribute to Judy Willis insect molecular physiology: Basic science to applications. Journal of Insect Physiology 56: 1363-1365.
Faraldos JA, Wu SQ, Chappell J, Coates RM (2010) Doubly deuterium-labeled patchouli alcohol from cyclization of singly labeled 2-H-2(1) farnesyl diphosphate catalyzed by recombinant patchoulol synthase. Journal of the American Chemical Society 132: 2998-3008.
Ghabrial SA, Suzuki N (2009) Viruses of plant pathogenic fungi. Annual Review of Phytopathology 47: 353-384.
Huang B, Troese MJ, Howe D, Ye SJ, Sims JT, Heinzen RA, Borjesson DL, Carlyon JA (2010) Anaplasma phagocytophilum APH 0032 is expressed late during infection and localizes to the pathogen-occupied vacuolar membrane. Microbial Pathogenesis 49: 273-284.
Jeong RD, Chandra-Shekara AC, Barman SR, Navarre D, Klessig DF, Kachroo A, Kachroo P (2010) Cryptochrome 2 and phototropin 2 regulate resistance protein-mediated viral defense by negatively regulating an E3 ubiquitin ligase. Proceedings of the National Academy of Sciences of the United States of America 107: 13538-13543.
Johansen KJ, Sharkey MJ, Fisher JR (2010) Molecular evidence from a parasitoid wasp, Schlettererius cinctipes (Hymenoptera: Stephanidae), for a North American west-to-east transcontinental conduit for wood-boring insects. Annals of the Entomological Society of America 103: 548-554.
Kachroo A, Kachroo P (2009) Fatty acid-derived signals in plant defense. Annual Review of Phytopathology 47: 153-176.
Kang HG, Oh CS, Sato M, Katagiri F, Glazebrook J, Takahashi H, Kachroo P, Martin GB, Klessig DF (2010) Endosome-associated CRT1 functions early in resistance gene-mediated defense signaling in Arabidopsis and tobacco. Plant Cell 22: 918-936.
Li RZ, Yu KS, Hatanaka T, Hildebrand DF (2010) Vernonia DGATs increase accumulation of epoxy fatty acids in oil. Plant Biotechnology Journal 8: 184-195.
Li RZ, Yu KS, Hildebrand DF (2010) DGAT1, DGAT2 and PDAT expression in seeds and other tissues of epoxy and hydroxy fatty acid accumulating plants. Lipids 45: 145-157.
Liu HQ, Fu YP, Jiang DH, Li GQ, Xie JT, Cheng JS, Peng YL, Ghabrial SA, Yi XH (2010) Widespread horizontal gene transfer from double-stranded RNA viruses to eukaryotic nuclear genomes. Journal of Virology 84: 11876-11887.
Luque D, Gonzalez JM, Garriga D, Ghabrial SA, Havens WM, Trus B, Verdaguer N, Carrascosa JL, Caston JR (2010) The T=1 capsid protein of Penicillium chrysogenum virus Is formed by a repeated helix-rich core indicative of gene duplication. Journal of Virology 84: 7256-7266.
McDonald M, Kendall A, Bian W, McCullough I, Lio E, Havens WM, Ghabrial SA, Stubbs G (2010) Architecture of the potyviruses. Virology 405: 309-313.
Nibert ML, Woods KM, Upton SJ, Ghabrial SA (2009) Cryspovirus: a new genus of protozoan viruses in the family Partitiviridae. Archives of Virology 154: 1959-1965.
Parthasarathy R, Sheng ZT, Sun ZY, Palli SR (2010) Ecdysteroid regulation of ovarian growth and oocyte maturation in the red flour beetle, Tribolium castaneum. Insect Biochemistry and Molecular Biology 40: 429-439.
Parthasarathy R, Sun ZY, Bai H, Palli SR (2010) Juvenile hormone regulation of vitellogenin synthesis in the red flour beetle, Tribolium castaneum. Insect Biochemistry and Molecular Biology 40: 405-414.
Rao SS, Hildebrand D (2009) Changes in oil content of transgenic soybeans expressing the yeast SLC1 gene. Lipids 44: 945-951.
Rao SS, Mamadou L, McConnell M, Polisetty R, Kwanyuen P, Hildebrand D (2009) Non-antibiotic selection systems for soybean somatic embryos: the lysine analog aminoethyl-cysteine as a selection agent. BMC Biotechnology 9: 1186.
Schwartz SL, Farman ML (2010) Systematic overrepresentation of DNA termini and underrepresentation of subterminal regions among sequencing templates prepared from hydrodynamically sheared linear DNA molecules. BMC Genomics 11: 87.
Selote D, Kachroo A (2010) RPG1-B-derived resistance to AvrB-expressing Pseudomonas syringae requires RIN4-like proteins in soybean. Plant Physiology 153: 1199-1211.
Soria-Guerra RE, Rosales-Mendoza S, Chang S, Haudenshield JS, Zheng DM, Rao SS, Hartman GL, Ghabrial SA, Korban SS (2010) Identifying differentially expressed genes in leaves of Glycine tomentella in the presence of the fungal pathogen Phakopsora pachyrhizi. Planta 232: 1181-1189.
Soria-Guerra RE, Rosales-Mendoza S, Chang SY, Haudenshield JS, Padmanaban A, Rodriguez-Zas S, Hartman GL, Ghabrial SA, Korban SS (2010) Transcriptome analysis of resistant and susceptible genotypes of Glycine tomentella during Phakopsora pachyrhizi infection reveals novel rust resistance genes. Theoretical and Applied Genetics 120: 1315-1333.
Stajich JE, Wilke SK, Ahren D, Au CH, Birren BW, Borodovsky M, Burns C, Canback B, Casselton LA, Cheng CK, Deng JX, Dietrich FS, Fargo DC, Farman ML, Gathman AC, Goldberg J, Guigo R, Hoegger PJ, Hooker JB, Huggins A, James TY, Kamada T, Kilaru S, Kodira C, Kues U, Kupfert D, Kwan HS, Lomsadze A, Li WX, Lilly WW, Ma LJ, Mackey AJ, Manning G, Martin F, Muraguchi H, Natvig DO, Palmerini H, Ramesh MA, Rehmeyer CJ, Roe BA, Shenoy N, Stanke M, Ter-Hovhannisyan V, Tunlid A, Velagapudi R, Vision TJ, Zeng QD, Zolan ME, Pukkila PJ (2010) Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus). Proceedings of the National Academy of Sciences of the United States of America 107: 11889-11894.
Tang JH, Ochoa WF, Li H, Havens WM, Nibert ML, Ghabrial SA, Baker TS (2010) Structure of Fusarium poae virus 1 shows conserved and variable elements of partitivirus capsids and evolutionary relationships to picobirnavirus. Journal of Structural Biology 172: 363-371.
Tang JH, Pan JH, Havens WM, Ochoa WF, Guu TSY, Ghabrial SA, Nibert ML, Tao YZJ, Baker TS (2010) Backbone trace of Partitivirus capsid protein from electron cryomicroscopy and homology modeling. Biophysical Journal 99: 685-694.
Tzertzinis G, Egana AL, Palli SR, Robinson-Rechavi M, Gissendanner CR, Liu CH, Unnasch TR, Maina CV (2010) Molecular evidence for a functional ecdysone signaling system in Brugia malayi. PLoS Neglected Tropical Diseases 4: e625.
Wei SJ, Shi M, Chen XX, Sharkey MJ, van Achterberg C, Ye GY, He JH (2010) New views on strand asymmetry in insect mitochondrial genomes. PLoS One 5: e12708.
Wei SJ, Shi M, He JH, Sharkey M, Chen XX (2009) The complete mitochondrial genome of Diadegma semiclausum (Hymenoptera: Ichneumonidae) indicates extensive independent evolutionary events. Genome 52: 308-319.
Wei SJ, Shi M, Sharkey MJ, van Achterberg C, Chen XX (2010) Comparative mitogenomics of Braconidae (Insecta: Hymenoptera) and the phylogenetic utility of mitochondrial genomes with special reference to Holometabolous insects. BMC Genomics 11: 37.
Weiss TL, Johnston JS, Fujisawa K, Sumimoto K, Okada S, Chappell J, Devarenne TP (2010) Phylogenetic placement, genome size, and GC content of the liquid-hydrocarbon-producing green microalga Botryococcus braunii strain Berkeley (showa) (Chlorophyta). Journal of Phycology 46: 534-540.
Wu MD, Zhang L, Li GQ, Jiang DH, Ghabrial SA (2010) Genome characterization of a debilitation-associated mitovirus infecting the phytopathogenic fungus Botrytis cinerea. Virology 406: 117-126.
Xia Y, Yu KS, Navarre D, Seebold K, Kachroo A, Kachroo P (2010) The glabra1 mutation affects cuticle formation and plant responses to microbes. Plant Physiology 154: 833-846.
Sharanowski BJ, Robbertse B, Walker J, Voss SR, Yoder R, Spatafora J, Sharkey MJ (2010) Expressed sequence tags reveal Proctotrupomorpha (minus Chalcidoidea) as sister to Aculeata (Hymenoptera: Insecta). Molecular Phylogenetics and Evolution 57: 101-112.
Singh AK, Tavva VS, Collins GB, Palli SR (2010) Improvement of ecdysone receptor gene switch for applications in plants: Locusta migratoria retinoid X receptor (LmRXR) mutagenesis and optimization of translation start site. Febs Journal 277: 4640-4650.
Xu JJ, Tan AJ, Palli SR (2010) The function of nuclear receptors in regulation of female reproduction and embryogenesis in the red flour beetle, Tribolium castaneum. Journal of Insect Physiology 56: 1471-1480.
Yu X, Li B, Fu YP, Jiang DH, Ghabrial SA, Li GQ, Peng YL, Xie JT, Cheng JS, Huang JB, Yi XH (2010) A geminivirus-related DNA mycovirus that confers hypovirulence to a plant pathogenic fungus. Proceedings of the National Academy of Sciences of the United States of America 107: 8387-8392.
Zhang Z, Palli SR (2009) Identification of a cis-regulatory element required for 20-hydroxyecdysone enhancement of antimicrobial peptide gene expression in Drosophila melanogaster. Insect Molecular Biology 18: 595-605.
Zhu F, Parthasarathy R, Bai H, Woithe K, Kaussmann M, Nauen R, Harrison DA, Palli SR (2010) A brain-specific cytochrome P450 responsible for the majority of deltamethrin resistance in the QTC279 strain of Tribolium castaneum. Proceedings of the National Academy of Sciences of the United States of America 107: 8557-8562.
Zhu F, Wigginton J, Romero A, Moore A, Ferguson K, Palli R, Potter MF, Haynes KF, Palli SR (2010) Widespread distribution of knockdown resistance mutations in the bed bug, Cimex lectularius (Hemiptera: Cimicidae), populations in the United States. Archives of Insect Biochemistry and Physiology 73: 245-257.
Addepalli B, Limbach PA, Hunt AG (2010) A disulfide linkage in a CCCH zinc finger motif of an Arabidopsis CPSF30 ortholog. FEBS Letters 584: 4408-4412.
Bai H, Gelman DB, Palli SR (2010) Mode of action of methoprene in affecting female reproduction in the African malaria mosquito, Anopheles gambiae. Pest Management Science 66: 936-943.
Bai H, Palli SR (2010) Functional characterization of bursicon receptor and genome-wide analysis for identification of genes affected by bursicon receptor RNAi. Developmental Biology 344: 248-258.
Bell SA, Hunt AG (2010) The Arabidopsis ortholog of the 77 kDa subunit of the cleavage stimulatory factor (AtCstF-77) involved in mRNA polyadenylation is an RNA-binding protein. FEBS Letters 584: 1449-1454.
Bitra K, Palli SR (2010) The members of bHLH transcription factor superfamily are required for female reproduction in the red flour beetle, Tribolium castaneum. Journal of Insect Physiology 56: 1481-1489.
Bitra K, Tan AJ, Dowling A, Palli SR (2009) Functional characterization of PAS and HES family bHLH transcription factors during the metamorphosis of the red flour beetle, Tribolium castaneum. Gene 448: 74-87.
Chanda B, Venugopal SC, Kulshrestha S, Navarre DA, Downie B, Vaillancourt L, Kachroo A, Kachroo P (2008) Glycerol-3-phosphate levels are associated with basal resistance to the hemibiotrophic fungus Colletotrichum higginsianum in Arabidopsis. Plant Physiology 147: 2017-2029.
Chen TS, Nayak N, Majee SM, Lowenson J, Schafermeyer KR, Eliopoulos AC, Lloyd TD, Dinkins R, Perry SE, Forsthoefel NR, Clarke SG, Vernon DM, Zhou ZS, Rejtar T, Downie AB (2010) Substrates of the Arabidopsis thaliana protein isoaspartyl methyltransferase 1 identified using phage display and biopanning. Journal of Biological Chemistry 285: 37281-37292.
Coleman JJ, Rounsley SD, Rodriguez-Carres M, Kuo A, Wasmann CC, Grimwood J, Schmutz J, Taga M, White GJ, Zhou SG, Schwartz DC, Freitag M, Ma LJ, Danchin EGJ, Henrissat B, Coutinho PM, Nelson DR, Straney D, Napoli CA, Barker BM, Gribskov M, Rep M, Kroken S, Molnar I, Rensing C, Kennell JC, Zamora J, Farman ML, Selker EU, Salamov A, Shapiro H, Pangilinan J, Lindquist E, Lamers C, Grigoriev IV, Geiser DM, Covert SF, Temporini E, VanEtten HD (2009) The genome of Nectria haematococca: Contribution of supernumerary chromosomes to gene expansion. PLoS Genetics 5: e1000618.