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Genome-enabled insights into the biology of thrips as crop pests.
Rotenberg, Dorith; Baumann, Aaron A; Ben-Mahmoud, Sulley; Christiaens, Olivier; Dermauw, Wannes; Ioannidis, Panagiotis; Jacobs, Chris G C; Vargas Jentzsch, Iris M; Oliver, Jonathan E; Poelchau, Monica F; Rajarapu, Swapna Priya; Schneweis, Derek J; Snoeck, Simon; Taning, Clauvis N T; Wei, Dong; Widana Gamage, Shirani M K; Hughes, Daniel S T; Murali, Shwetha C; Bailey, Samuel T; Bejerman, Nicolas E; Holmes, Christopher J; Jennings, Emily C; Rosendale, Andrew J; Rosselot, Andrew; Hervey, Kaylee; Schneweis, Brandi A; Cheng, Sammy; Childers, Christopher; Simão, Felipe A; Dietzgen, Ralf G; Chao, Hsu; Dinh, Huyen; Doddapaneni, Harsha Vardhan; Dugan, Shannon; Han, Yi; Lee, Sandra L; Muzny, Donna M; Qu, Jiaxin; Worley, Kim C; Benoit, Joshua B; Friedrich, Markus; Jones, Jeffery W; Panfilio, Kristen A; Park, Yoonseong; Robertson, Hugh M; Smagghe, Guy; Ullman, Diane E; van der Zee, Maurijn; Van Leeuwen, Thomas; Veenstra, Jan A.
Afiliación
  • Rotenberg D; Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA. drotenb@ncsu.edu.
  • Baumann AA; Virology Section, College of Veterinary Medicine, University of Tennessee, A239 VTH, 2407 River Drive, Knoxville, TN, 37996, USA.
  • Ben-Mahmoud S; Department of Entomology and Nematology, University of California Davis, Davis, CA, 95616, USA.
  • Christiaens O; Laboratory of Agrozoology, Department of Plants and Crops, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.
  • Dermauw W; Laboratory of Agrozoology, Department of Plants and Crops, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.
  • Ioannidis P; Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Vassilika Vouton, 70013, Heraklion, Greece.
  • Jacobs CGC; Department of Genetic Medicine and Development, University of Geneva Medical School, and Swiss Institute of Bioinformatics, Geneva, Switzerland.
  • Vargas Jentzsch IM; Institute of Biology, Leiden University, 2333 BE, Leiden, The Netherlands.
  • Oliver JE; Institute for Zoology: Developmental Biology, University of Cologne, 50674, Cologne, Germany.
  • Poelchau MF; Department of Plant Pathology, University of Georgia - Tifton Campus, Tifton, GA, 31793-5737, USA.
  • Rajarapu SP; National Agricultural Library, USDA-ARS, Beltsville, MD, 20705, USA.
  • Schneweis DJ; Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA.
  • Snoeck S; Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.
  • Taning CNT; Laboratory of Agrozoology, Department of Plants and Crops, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.
  • Wei D; Department of Biology, University of Washington, Seattle, WA, 98105, USA.
  • Widana Gamage SMK; Laboratory of Agrozoology, Department of Plants and Crops, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.
  • Hughes DST; Laboratory of Agrozoology, Department of Plants and Crops, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.
  • Murali SC; Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China.
  • Bailey ST; International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, Academy of Agricultural Sciences, Southwest University, Chongqing, China and Ghent University, Ghent, Belgium.
  • Bejerman NE; Department of Botany, University of Ruhuna, Matara, Sri Lanka.
  • Holmes CJ; Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
  • Jennings EC; Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
  • Rosendale AJ; Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA.
  • Rosselot A; IPAVE-CIAP-INTA, 5020, Cordoba, Argentina.
  • Hervey K; Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA.
  • Schneweis BA; Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA.
  • Cheng S; Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA.
  • Childers C; Department of Biology, Mount St. Joseph University, Cincinnati, OH, 45233, USA.
  • Simão FA; Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA.
  • Dietzgen RG; Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.
  • Chao H; Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.
  • Dinh H; Department of Biology, University of Rochester, Rochester, NY, 14627, USA.
  • Doddapaneni HV; National Agricultural Library, USDA-ARS, Beltsville, MD, 20705, USA.
  • Dugan S; Department of Genetic Medicine and Development, University of Geneva Medical School, and Swiss Institute of Bioinformatics, Geneva, Switzerland.
  • Han Y; Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, 4072, Australia.
  • Lee SL; Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
  • Muzny DM; Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
  • Qu J; Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
  • Worley KC; Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
  • Benoit JB; Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
  • Friedrich M; Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
  • Jones JW; Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
  • Panfilio KA; Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
  • Park Y; Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
  • Robertson HM; Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA.
  • Smagghe G; Department of Biological Sciences, Wayne State University, Detroit, MI, 48202, USA.
  • Ullman DE; Department of Biological Sciences, Wayne State University, Detroit, MI, 48202, USA.
  • van der Zee M; Institute for Zoology: Developmental Biology, University of Cologne, 50674, Cologne, Germany.
  • Van Leeuwen T; School of Life Sciences, University of Warwick, Gibbet Hill Campus, Coventry, CV4 7AL, UK.
  • Veenstra JA; Department of Entomology, Kansas State University, Manhattan, KS, 66506, USA.
BMC Biol ; 18(1): 142, 2020 10 19.
Article en En | MEDLINE | ID: mdl-33070780
BACKGROUND: The western flower thrips, Frankliniella occidentalis (Pergande), is a globally invasive pest and plant virus vector on a wide array of food, fiber, and ornamental crops. The underlying genetic mechanisms of the processes governing thrips pest and vector biology, feeding behaviors, ecology, and insecticide resistance are largely unknown. To address this gap, we present the F. occidentalis draft genome assembly and official gene set. RESULTS: We report on the first genome sequence for any member of the insect order Thysanoptera. Benchmarking Universal Single-Copy Ortholog (BUSCO) assessments of the genome assembly (size = 415.8 Mb, scaffold N50 = 948.9 kb) revealed a relatively complete and well-annotated assembly in comparison to other insect genomes. The genome is unusually GC-rich (50%) compared to other insect genomes to date. The official gene set (OGS v1.0) contains 16,859 genes, of which ~ 10% were manually verified and corrected by our consortium. We focused on manual annotation, phylogenetic, and expression evidence analyses for gene sets centered on primary themes in the life histories and activities of plant-colonizing insects. Highlights include the following: (1) divergent clades and large expansions in genes associated with environmental sensing (chemosensory receptors) and detoxification (CYP4, CYP6, and CCE enzymes) of substances encountered in agricultural environments; (2) a comprehensive set of salivary gland genes supported by enriched expression; (3) apparent absence of members of the IMD innate immune defense pathway; and (4) developmental- and sex-specific expression analyses of genes associated with progression from larvae to adulthood through neometaboly, a distinct form of maturation differing from either incomplete or complete metamorphosis in the Insecta. CONCLUSIONS: Analysis of the F. occidentalis genome offers insights into the polyphagous behavior of this insect pest that finds, colonizes, and survives on a widely diverse array of plants. The genomic resources presented here enable a more complete analysis of insect evolution and biology, providing a missing taxon for contemporary insect genomics-based analyses. Our study also offers a genomic benchmark for molecular and evolutionary investigations of other Thysanoptera species.
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Texto completo: 1 Banco de datos: MEDLINE Asunto principal: Genoma de los Insectos / Thysanoptera / Transcriptoma / Rasgos de la Historia de Vida Tipo de estudio: Prognostic_studies Límite: Animals Idioma: En Revista: BMC Biol Asunto de la revista: BIOLOGIA Año: 2020 Tipo del documento: Article País de afiliación: Estados Unidos
Texto completo
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Texto completo: 1 Banco de datos: MEDLINE Asunto principal: Genoma de los Insectos / Thysanoptera / Transcriptoma / Rasgos de la Historia de Vida Tipo de estudio: Prognostic_studies Límite: Animals Idioma: En Revista: BMC Biol Asunto de la revista: BIOLOGIA Año: 2020 Tipo del documento: Article País de afiliación: Estados Unidos