Genome-enabled insights into the biology of thrips as crop pests

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. While there are numerous studies centered on thrips pest and vector biology, feeding behaviors, ecology, and insecticide resistance, the underlying genetic mechanisms of the processes governing these areas of research 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: 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-associated 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 compared to complete metamorphosis in the Holometabola.Instituto de Patología VegetalFil: Rotenberg, Dorith. North Carolina State University. Department of Entomology and Plant Pathology; Estados UnidosFil: Baumann, Aaron A. University of Tennessee. Virology Section, College of Veterinary Medicine; Estados UnidosFil: Ben-Mahmoud, Sulley. University of California Davis. Department of Entomology and Nematology; Estados UnidosFil: Christiaens, Olivier. Ghent University. Department of Plants and Crops. Laboratory of Agrozoology; BélgicaFil: Dermauw, Wannes.Ghent University. Department of Plants and Crops. Laboratory of Agrozoology; BélgicaFil: Ioannidis, Panagiotis. Foundation for Research and Technology-Hellas. Institute of Molecular Biology and Biotechnology; Grecia. University of Geneva Medical School. Swiss Institute of Bioinformatics. Department of Genetic Medicine and Development; SuizaFil: Jacobs, Chris G. C. Leiden University. Institute of Biology; Países BajosFil: Vargas Jentzsch, Iris M. University of Cologne. Institute for Zoology: Developmental Biology; AlemaniaFil: Oliver, Jonathan E. University of Georgia - Tifton Campus. Department of Plant Pathology; Estados UnidosFil: Poelchau, Monica F. National Agricultural Library. USDA-ARS; Estados UnidosFil: Priya Rajarapu, Swapna. North Carolina State University. Department of Entomology and Plant Pathology; Estados UnidosFil: Schneweis, Derek J. Kansas State University. Department of Plant Pathology; Estados UnidosFil: Snoeck, Simon. University of Washington. Department of Biology; Estados Unidos. Ghent University. Department of Plants and Crops. Laboratory of Agrozoology; BélgicaFil: Taning, Clauvis N. T. Ghent University. Department of Plants and Crops. Laboratory of Agrozoology; BélgicaFil: Wei, Dong. Ghent University. Department of Plants and Crops. Laboratory of Agrozoology; Bélgica. Southwest University. College of Plant Protection. Chongqing Key Laboratory of Entomology and Pest Control Engineering; China. Ghent University. Southwest University, Chongqing. Academy of Agricultural Sciences. International Joint Laboratory of China-Belgium on Sustainable Crop Pest; BélgicaFil: Widana Gamage, Shirani M. K. University of Ruhuna. Department of Botany; Sri LankaFil: Hughes, Daniel S. T. Baylor College of Medicine. Department of Human and Molecular Genetics. Human Genome Sequencing Center; Estados UnidosFil: Murali, Shwetha C. Baylor College of Medicine. Department of Human and Molecular Genetics. Human Genome Sequencing Center; Estados UnidosFil: Bailey, Samuel T. University of Cincinnati. Department of Biological Sciences; Estados UnidosFil: Bejerman, Nicolas Esteban. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; Argentina.Fil: Holmes, Christopher J. University of Cincinnati. Department of Biological Sciences; Estados UnidosFil: Jennings, Emily C. University of Cincinnati. Department of Biological Sciences; Estados UnidosFil: Rosendale, Andrew J. University of Cincinnati. Department of Biological Sciences; Estados Unidos. Mount St. Joseph University.Department of Biology; Estados UnidosFil: Rosselot, Andrew. University of Cincinnati. Department of Biological Sciences; Estados UnidosFil: Hervey, Kaylee. Kansas State University. Department of Plant Pathology; Estados UnidosFil: Schneweis, Brandi A. Kansas State University. Department of Plant Pathology; Estados UnidosFil: Cheng, Sammy. University of Rochester. Department of Biology; Estados UnidosFil: Childers, Christopher. National Agricultural Library. USDA-ARS; Estados UnidosFil: Simão, Felipe A. University of Geneva Medical School. Swiss Institute of Bioinformatics. Department of Genetic Medicine and Development: SuizaFil: Dietzgen, Ralf G. University of Queensland. Queensland Alliance for Agriculture and Food Innovation; AustraliaFil: Chao, Hsu. Baylor College of Medicine. Department of Human and Molecular Genetics. Human Genome Sequencing Center; Estados UnidosFil: Dinh, Huyen. Baylor College of Medicine. Department of Human and Molecular Genetics. Human Genome Sequencing Center; Estados UnidosFil: Vardhan Doddapaneni, Harsha. Baylor College of Medicine. Department of Human and Molecular Genetics. Human Genome Sequencing Center; Estados UnidosFil: Dugan, Shannon. Baylor College of Medicine. Department of Human and Molecular Genetics. Human Genome Sequencing Center; Estados UnidosFil: Han, Yi. Baylor College of Medicine. Department of Human and Molecular Genetics. Human Genome Sequencing Center; Estados UnidosFil: Lee, Sandra L. Baylor College of Medicine. Department of Human and Molecular Genetics. Human Genome Sequencing Center; Estados UnidosFil: Muzny, Donna M. Baylor College of Medicine. Department of Human and Molecular Genetics. Human Genome Sequencing Center; Estados UnidosFil: Qu, Jiaxin. Baylor College of Medicine. Department of Human and Molecular Genetics. Human Genome Sequencing Center; Estados UnidosFil: Worley, Kim C. Baylor College of Medicine. Department of Human and Molecular Genetics. Human Genome Sequencing Center; Estados UnidosFil: Benoit, Joshua B. University of Cincinnati. Department of Biological Sciences; Estados UnidosFil: Friedrich, Markus. Wayne State University. Department of Biological Sciences; Estados UnidosFil: Jones, Jeffery W. Wayne State University. Department of Biological Sciences; Estados UnidosFil: Panfilio, Kristen A. University of Cologne. Institute for Zoology: Developmental Biology; Alemania. University of Warwick. Gibbet Hill Campus. School of Life Sciences; Reino UnidoFil: Park, Yoonseong. Kansas State University. Department of Entomology; Estados UnidosFil: Robertson, Hugh M. University of Illinois at Urbana-Champaign. Department of Entomology; Estados UnidosFil: Smagghe, Guy. Ghent University. Department of Plants and Crops. Laboratory of Agrozoology; Bélgica. Southwest University. College of Plant Protection. Chongqing Key Laboratory of Entomology and Pest Control Engineering; China. Chongqing, China and Ghent University. Southwest University. Academy of Agricultural Sciences. International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control; BélgicaFil: Ullman, Diane E. University of California Davis. Department of Entomology and Nematology; Estados UnidosFil: Van der Zee, Maurijn. Leiden University. Institute of Biology. Leiden; Países BajosFil: Van Leeuwen, Thomas. Ghent University. Department of Plants and Crops. Laboratory of Agrozoology; BélgicaFil: Veenstra, Jan A. University of Bordeaux; FranciaFil: Waterhouse, Robert M. University of Lausanne. Swiss Institute of Bioinformatics. Department of Ecology and Evolution; SuizaFil: Weirauch, Matthew T. Cincinnati Children’s Hospital Medical Center. Center for Autoimmune Genomics and Etiology. Divisions of Biomedical Informatics and Developmental Biology; Estados Unidos. University of Cincinnati. College of Medicine. Department of Pediatrics; Estados UnidosFil: Werren, John H. University of Rochester. Department of Biology; Estados UnidosFil: Whitfield, Anna E. North Carolina State University. Department of Entomology and Plant Pathology; Estados UnidosFil: Zdobnov, Evgeny M. University of Geneva Medical School. Swiss Institute of Bioinformatics. Department of Genetic Medicine and Development; SuizaFil: Gibbs, Richard A. Baylor College of Medicine. Human Genome Sequencing Center. Department of Human and Molecular Genetics; Estados UnidosFil: Richards, Stephen. Baylor College of Medicine. Human Genome Sequencing Center. Department of Human and Molecular Genetics; Estados Unido