Dorith Rotenberg1, Aaron A Baumann2, Sulley Ben-Mahmoud3, Olivier Christiaens4, Wannes Dermauw4, Panagiotis Ioannidis5,6, Chris G C Jacobs7, Iris M Vargas Jentzsch8, Jonathan E Oliver9, Monica F Poelchau10, Swapna Priya Rajarapu11, Derek J Schneweis12, Simon Snoeck4,13, Clauvis N T Taning4, Dong Wei4,14,15, Shirani M K Widana Gamage16, Daniel S T Hughes17, Shwetha C Murali17, Samuel T Bailey18, Nicolas E Bejerman19, Christopher J Holmes18, Emily C Jennings18, Andrew J Rosendale18,20, Andrew Rosselot18, Kaylee Hervey12, Brandi A Schneweis12, Sammy Cheng21, Christopher Childers10, Felipe A Simão6, Ralf G Dietzgen22, Hsu Chao17, Huyen Dinh17, Harsha Vardhan Doddapaneni17, Shannon Dugan17, Yi Han17, Sandra L Lee17, Donna M Muzny17, Jiaxin Qu17, Kim C Worley17, Joshua B Benoit18, Markus Friedrich23, Jeffery W Jones23, Kristen A Panfilio8,24, Yoonseong Park25, Hugh M Robertson26, Guy Smagghe4,14,15, Diane E Ullman3, Maurijn van der Zee7, Thomas Van Leeuwen4, Jan A Veenstra27, Robert M Waterhouse28, Matthew T Weirauch29,30, John H Werren21, Anna E Whitfield11, Evgeny M Zdobnov6, Richard A Gibbs17, Stephen Richards17. 1. Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA. drotenb@ncsu.edu. 2. Virology Section, College of Veterinary Medicine, University of Tennessee, A239 VTH, 2407 River Drive, Knoxville, TN, 37996, USA. 3. Department of Entomology and Nematology, University of California Davis, Davis, CA, 95616, USA. 4. Laboratory of Agrozoology, Department of Plants and Crops, Ghent University, Coupure Links 653, 9000, Ghent, Belgium. 5. Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Vassilika Vouton, 70013, Heraklion, Greece. 6. Department of Genetic Medicine and Development, University of Geneva Medical School, and Swiss Institute of Bioinformatics, Geneva, Switzerland. 7. Institute of Biology, Leiden University, 2333 BE, Leiden, The Netherlands. 8. Institute for Zoology: Developmental Biology, University of Cologne, 50674, Cologne, Germany. 9. Department of Plant Pathology, University of Georgia - Tifton Campus, Tifton, GA, 31793-5737, USA. 10. National Agricultural Library, USDA-ARS, Beltsville, MD, 20705, USA. 11. Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA. 12. Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA. 13. Department of Biology, University of Washington, Seattle, WA, 98105, USA. 14. Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China. 15. International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, Academy of Agricultural Sciences, Southwest University, Chongqing, China and Ghent University, Ghent, Belgium. 16. Department of Botany, University of Ruhuna, Matara, Sri Lanka. 17. Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA. 18. Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA. 19. IPAVE-CIAP-INTA, 5020, Cordoba, Argentina. 20. Department of Biology, Mount St. Joseph University, Cincinnati, OH, 45233, USA. 21. Department of Biology, University of Rochester, Rochester, NY, 14627, USA. 22. Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, 4072, Australia. 23. Department of Biological Sciences, Wayne State University, Detroit, MI, 48202, USA. 24. School of Life Sciences, University of Warwick, Gibbet Hill Campus, Coventry, CV4 7AL, UK. 25. Department of Entomology, Kansas State University, Manhattan, KS, 66506, USA. 26. Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. 27. INCIA UMR 5287 CNRS, University of Bordeaux, Pessac, France. 28. Department of Ecology and Evolution, Swiss Institute of Bioinformatics, University of Lausanne, 1015, Lausanne, Switzerland. 29. Center for Autoimmune Genomics and Etiology, Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA. 30. Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, 45229, USA.
Abstract
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.
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.
Authors: J S Ramsey; D S Rider; T K Walsh; M De Vos; K H J Gordon; L Ponnala; S L Macmil; B A Roe; G Jander Journal: Insect Mol Biol Date: 2010-03 Impact factor: 3.585
Authors: Christine Missbach; Hany Km Dweck; Heiko Vogel; Andreas Vilcinskas; Marcus C Stensmyr; Bill S Hansson; Ewald Grosse-Wilde Journal: Elife Date: 2014-03-26 Impact factor: 8.140
Authors: J Joe Hull; Kendrick Chaney; Scott M Geib; Jeffrey A Fabrick; Colin S Brent; Douglas Walsh; Laura Corley Lavine Journal: PLoS One Date: 2014-11-17 Impact factor: 3.240
Authors: Dorith Rotenberg; Aaron A Baumann; Sulley Ben-Mahmoud; Olivier Christiaens; Wannes Dermauw; Panagiotis Ioannidis; Chris G C Jacobs; Iris M Vargas Jentzsch; Jonathan E Oliver; Monica F Poelchau; Swapna Priya Rajarapu; Derek J Schneweis; Simon Snoeck; Clauvis N T Taning; Dong Wei; Shirani M K Widana Gamage; Daniel S T Hughes; Shwetha C Murali; Samuel T Bailey; Nicolas E Bejerman; Christopher J Holmes; Emily C Jennings; Andrew J Rosendale; Andrew Rosselot; Kaylee Hervey; Brandi A Schneweis; Sammy Cheng; Christopher Childers; Felipe A Simão; Ralf G Dietzgen; Hsu Chao; Huyen Dinh; Harsha Vardhan Doddapaneni; Shannon Dugan; Yi Han; Sandra L Lee; Donna M Muzny; Jiaxin Qu; Kim C Worley; Joshua B Benoit; Markus Friedrich; Jeffery W Jones; Kristen A Panfilio; Yoonseong Park; Hugh M Robertson; Guy Smagghe; Diane E Ullman; Maurijn van der Zee; Thomas Van Leeuwen; Jan A Veenstra; Robert M Waterhouse; Matthew T Weirauch; John H Werren; Anna E Whitfield; Evgeny M Zdobnov; Richard A Gibbs; Stephen Richards Journal: BMC Biol Date: 2020-11-16 Impact factor: 7.431
Authors: Emma Bailey; Linda Field; Christopher Rawlings; Rob King; Fady Mohareb; Keywan-Hassani Pak; David Hughes; Martin Williamson; Eric Ganko; Benjamin Buer; Ralf Nauen Journal: BMC Genomics Date: 2022-01-11 Impact factor: 3.969
Authors: Emma Bailey; Linda Field; Christopher Rawlings; Rob King; Fady Mohareb; Keywan-Hassani Pak; David Hughes; Martin Williamson; Eric Ganko; Benjamin Buer; Ralf Nauen Journal: BMC Genomics Date: 2022-03-12 Impact factor: 3.969