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

Autores
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.; Priya Rajarapu, Swapna; 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 Esteban; 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 Georg; Chao, Hsu; Dinh, Huyen; Vardhan Doddapaneni, Harsha; 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.; Waterhouse, Robert M.; Weirauch, Matthew T.; Werren, John H.; Whitfield, Anna E.; Zdobnov, Evgeny M.; Gibbs, Richard A.; Richards, Stephen
Año de publicación
2020
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
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 Vegetal
Fil: Rotenberg, Dorith. North Carolina State University. Department of Entomology and Plant Pathology; Estados Unidos
Fil: Baumann, Aaron A. University of Tennessee. Virology Section, College of Veterinary Medicine; Estados Unidos
Fil: Ben-Mahmoud, Sulley. University of California Davis. Department of Entomology and Nematology; Estados Unidos
Fil: Christiaens, Olivier. Ghent University. Department of Plants and Crops. Laboratory of Agrozoology; Bélgica
Fil: Dermauw, Wannes.Ghent University. Department of Plants and Crops. Laboratory of Agrozoology; Bélgica
Fil: 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; Suiza
Fil: Jacobs, Chris G. C. Leiden University. Institute of Biology; Países Bajos
Fil: Vargas Jentzsch, Iris M. University of Cologne. Institute for Zoology: Developmental Biology; Alemania
Fil: Oliver, Jonathan E. University of Georgia - Tifton Campus. Department of Plant Pathology; Estados Unidos
Fil: Poelchau, Monica F. National Agricultural Library. USDA-ARS; Estados Unidos
Fil: Priya Rajarapu, Swapna. North Carolina State University. Department of Entomology and Plant Pathology; Estados Unidos
Fil: Schneweis, Derek J. Kansas State University. Department of Plant Pathology; Estados Unidos
Fil: Snoeck, Simon. University of Washington. Department of Biology; Estados Unidos. Ghent University. Department of Plants and Crops. Laboratory of Agrozoology; Bélgica
Fil: Taning, Clauvis N. T. Ghent University. Department of Plants and Crops. Laboratory of Agrozoology; Bélgica
Fil: 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; Bélgica
Fil: Widana Gamage, Shirani M. K. University of Ruhuna. Department of Botany; Sri Lanka
Fil: Hughes, Daniel S. T. Baylor College of Medicine. Department of Human and Molecular Genetics. Human Genome Sequencing Center; Estados Unidos
Fil: Murali, Shwetha C. Baylor College of Medicine. Department of Human and Molecular Genetics. Human Genome Sequencing Center; Estados Unidos
Fil: Bailey, Samuel T. University of Cincinnati. Department of Biological Sciences; Estados Unidos
Fil: 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 Unidos
Fil: Jennings, Emily C. University of Cincinnati. Department of Biological Sciences; Estados Unidos
Fil: Rosendale, Andrew J. University of Cincinnati. Department of Biological Sciences; Estados Unidos. Mount St. Joseph University.Department of Biology; Estados Unidos
Fil: Rosselot, Andrew. University of Cincinnati. Department of Biological Sciences; Estados Unidos
Fil: Hervey, Kaylee. Kansas State University. Department of Plant Pathology; Estados Unidos
Fil: Schneweis, Brandi A. Kansas State University. Department of Plant Pathology; Estados Unidos
Fil: Cheng, Sammy. University of Rochester. Department of Biology; Estados Unidos
Fil: Childers, Christopher. National Agricultural Library. USDA-ARS; Estados Unidos
Fil: Simão, Felipe A. University of Geneva Medical School. Swiss Institute of Bioinformatics. Department of Genetic Medicine and Development: Suiza
Fil: Dietzgen, Ralf G. University of Queensland. Queensland Alliance for Agriculture and Food Innovation; Australia
Fil: Chao, Hsu. Baylor College of Medicine. Department of Human and Molecular Genetics. Human Genome Sequencing Center; Estados Unidos
Fil: Dinh, Huyen. Baylor College of Medicine. Department of Human and Molecular Genetics. Human Genome Sequencing Center; Estados Unidos
Fil: Vardhan Doddapaneni, Harsha. Baylor College of Medicine. Department of Human and Molecular Genetics. Human Genome Sequencing Center; Estados Unidos
Fil: Dugan, Shannon. Baylor College of Medicine. Department of Human and Molecular Genetics. Human Genome Sequencing Center; Estados Unidos
Fil: Han, Yi. Baylor College of Medicine. Department of Human and Molecular Genetics. Human Genome Sequencing Center; Estados Unidos
Fil: Lee, Sandra L. Baylor College of Medicine. Department of Human and Molecular Genetics. Human Genome Sequencing Center; Estados Unidos
Fil: Muzny, Donna M. Baylor College of Medicine. Department of Human and Molecular Genetics. Human Genome Sequencing Center; Estados Unidos
Fil: Qu, Jiaxin. Baylor College of Medicine. Department of Human and Molecular Genetics. Human Genome Sequencing Center; Estados Unidos
Fil: Worley, Kim C. Baylor College of Medicine. Department of Human and Molecular Genetics. Human Genome Sequencing Center; Estados Unidos
Fil: Benoit, Joshua B. University of Cincinnati. Department of Biological Sciences; Estados Unidos
Fil: Friedrich, Markus. Wayne State University. Department of Biological Sciences; Estados Unidos
Fil: Jones, Jeffery W. Wayne State University. Department of Biological Sciences; Estados Unidos
Fil: Panfilio, Kristen A. University of Cologne. Institute for Zoology: Developmental Biology; Alemania. University of Warwick. Gibbet Hill Campus. School of Life Sciences; Reino Unido
Fil: Park, Yoonseong. Kansas State University. Department of Entomology; Estados Unidos
Fil: Robertson, Hugh M. University of Illinois at Urbana-Champaign. Department of Entomology; Estados Unidos
Fil: 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; Bélgica
Fil: Ullman, Diane E. University of California Davis. Department of Entomology and Nematology; Estados Unidos
Fil: Van der Zee, Maurijn. Leiden University. Institute of Biology. Leiden; Países Bajos
Fil: Van Leeuwen, Thomas. Ghent University. Department of Plants and Crops. Laboratory of Agrozoology; Bélgica
Fil: Veenstra, Jan A. University of Bordeaux; Francia
Fil: Waterhouse, Robert M. University of Lausanne. Swiss Institute of Bioinformatics. Department of Ecology and Evolution; Suiza
Fil: 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 Unidos
Fil: Werren, John H. University of Rochester. Department of Biology; Estados Unidos
Fil: Whitfield, Anna E. North Carolina State University. Department of Entomology and Plant Pathology; Estados Unidos
Fil: Zdobnov, Evgeny M. University of Geneva Medical School. Swiss Institute of Bioinformatics. Department of Genetic Medicine and Development; Suiza
Fil: Gibbs, Richard A. Baylor College of Medicine. Human Genome Sequencing Center. Department of Human and Molecular Genetics; Estados Unidos
Fil: Richards, Stephen. Baylor College of Medicine. Human Genome Sequencing Center. Department of Human and Molecular Genetics; Estados Unidos
Fuente
BMC Biology 18 (1): 142 (2020)
Materia
Thysanoptera
Salivary Glands
Detoxification
Glándulas Salivales
Desintoxicación
Western Flower Thrips
Hemipteroid Assemblage
Insect Genomics
Chemosensory Receptors
Opsins
Innate Immunity
Tospovirus
Nivel de accesibilidad
acceso abierto
Condiciones de uso
http://creativecommons.org/licenses/by-nc-sa/4.0/
Repositorio
INTA Digital (INTA)
Institución
Instituto Nacional de Tecnología Agropecuaria
OAI Identificador
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spelling Genome-enabled insights into the biology of thrips as crop pestsRotenberg, DorithBaumann, Aaron A.Ben-Mahmoud, SulleyChristiaens, OlivierDermauw, WannesIoannidis, PanagiotisJacobs, Chris G. C.Vargas Jentzsch, Iris M.Oliver, Jonathan E.Poelchau, Monica F.Priya Rajarapu, SwapnaSchneweis, Derek J.Snoeck, SimonTaning, Clauvis N. T.Wei, DongWidana Gamage, Shirani M. K.Hughes, Daniel S. T.Murali, Shwetha C.Bailey, Samuel T.Bejerman, Nicolas EstebanHolmes, Christopher J.Jennings, Emily C.Rosendale, Andrew J.Rosselot, AndrewHervey, KayleeSchneweis, Brandi A.Cheng, SammyChilders, ChristopherSimão, Felipe A.Dietzgen, Ralf GeorgChao, HsuDinh, HuyenVardhan Doddapaneni, HarshaDugan, ShannonHan, YiLee, Sandra L.Muzny, Donna M.Qu, JiaxinWorley, Kim C.Benoit, Joshua B.Friedrich, MarkusJones, Jeffery W.Panfilio, Kristen A.Park, YoonseongRobertson, Hugh M.Smagghe, GuyUllman, Diane E.Van der Zee, MaurijnVan Leeuwen, ThomasVeenstra, Jan A.Waterhouse, Robert M.Weirauch, Matthew T.Werren, John H.Whitfield, Anna E.Zdobnov, Evgeny M.Gibbs, Richard A.Richards, StephenThysanopteraSalivary GlandsDetoxificationGlándulas SalivalesDesintoxicaciónWestern Flower ThripsHemipteroid AssemblageInsect GenomicsChemosensory ReceptorsOpsinsInnate ImmunityTospovirusBackground 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 UnidosBMC2020-12-28T14:29:20Z2020-12-28T14:29:20Z2020-10-19info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfhttp://hdl.handle.net/20.500.12123/8498https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-020-00862-91741-7007 (online)https://doi.org/10.1186/s12915-020-00862-9BMC Biology 18 (1): 142 (2020)reponame:INTA Digital (INTA)instname:Instituto Nacional de Tecnología Agropecuariaenginfo:eu-repo/semantics/openAccesshttp://creativecommons.org/licenses/by-nc-sa/4.0/Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)2025-09-29T13:45:06Zoai:localhost:20.500.12123/8498instacron:INTAInstitucionalhttp://repositorio.inta.gob.ar/Organismo científico-tecnológicoNo correspondehttp://repositorio.inta.gob.ar/oai/requesttripaldi.nicolas@inta.gob.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:l2025-09-29 13:45:06.777INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuariafalse
dc.title.none.fl_str_mv Genome-enabled insights into the biology of thrips as crop pests
title Genome-enabled insights into the biology of thrips as crop pests
spellingShingle Genome-enabled insights into the biology of thrips as crop pests
Rotenberg, Dorith
Thysanoptera
Salivary Glands
Detoxification
Glándulas Salivales
Desintoxicación
Western Flower Thrips
Hemipteroid Assemblage
Insect Genomics
Chemosensory Receptors
Opsins
Innate Immunity
Tospovirus
title_short Genome-enabled insights into the biology of thrips as crop pests
title_full Genome-enabled insights into the biology of thrips as crop pests
title_fullStr Genome-enabled insights into the biology of thrips as crop pests
title_full_unstemmed Genome-enabled insights into the biology of thrips as crop pests
title_sort Genome-enabled insights into the biology of thrips as crop pests
dc.creator.none.fl_str_mv 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.
Priya Rajarapu, Swapna
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 Esteban
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 Georg
Chao, Hsu
Dinh, Huyen
Vardhan Doddapaneni, Harsha
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.
Waterhouse, Robert M.
Weirauch, Matthew T.
Werren, John H.
Whitfield, Anna E.
Zdobnov, Evgeny M.
Gibbs, Richard A.
Richards, Stephen
author Rotenberg, Dorith
author_facet 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.
Priya Rajarapu, Swapna
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 Esteban
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 Georg
Chao, Hsu
Dinh, Huyen
Vardhan Doddapaneni, Harsha
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.
Waterhouse, Robert M.
Weirauch, Matthew T.
Werren, John H.
Whitfield, Anna E.
Zdobnov, Evgeny M.
Gibbs, Richard A.
Richards, Stephen
author_role author
author2 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.
Priya Rajarapu, Swapna
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 Esteban
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 Georg
Chao, Hsu
Dinh, Huyen
Vardhan Doddapaneni, Harsha
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.
Waterhouse, Robert M.
Weirauch, Matthew T.
Werren, John H.
Whitfield, Anna E.
Zdobnov, Evgeny M.
Gibbs, Richard A.
Richards, Stephen
author2_role author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
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dc.subject.none.fl_str_mv Thysanoptera
Salivary Glands
Detoxification
Glándulas Salivales
Desintoxicación
Western Flower Thrips
Hemipteroid Assemblage
Insect Genomics
Chemosensory Receptors
Opsins
Innate Immunity
Tospovirus
topic Thysanoptera
Salivary Glands
Detoxification
Glándulas Salivales
Desintoxicación
Western Flower Thrips
Hemipteroid Assemblage
Insect Genomics
Chemosensory Receptors
Opsins
Innate Immunity
Tospovirus
dc.description.none.fl_txt_mv 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 Vegetal
Fil: Rotenberg, Dorith. North Carolina State University. Department of Entomology and Plant Pathology; Estados Unidos
Fil: Baumann, Aaron A. University of Tennessee. Virology Section, College of Veterinary Medicine; Estados Unidos
Fil: Ben-Mahmoud, Sulley. University of California Davis. Department of Entomology and Nematology; Estados Unidos
Fil: Christiaens, Olivier. Ghent University. Department of Plants and Crops. Laboratory of Agrozoology; Bélgica
Fil: Dermauw, Wannes.Ghent University. Department of Plants and Crops. Laboratory of Agrozoology; Bélgica
Fil: 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; Suiza
Fil: Jacobs, Chris G. C. Leiden University. Institute of Biology; Países Bajos
Fil: Vargas Jentzsch, Iris M. University of Cologne. Institute for Zoology: Developmental Biology; Alemania
Fil: Oliver, Jonathan E. University of Georgia - Tifton Campus. Department of Plant Pathology; Estados Unidos
Fil: Poelchau, Monica F. National Agricultural Library. USDA-ARS; Estados Unidos
Fil: Priya Rajarapu, Swapna. North Carolina State University. Department of Entomology and Plant Pathology; Estados Unidos
Fil: Schneweis, Derek J. Kansas State University. Department of Plant Pathology; Estados Unidos
Fil: Snoeck, Simon. University of Washington. Department of Biology; Estados Unidos. Ghent University. Department of Plants and Crops. Laboratory of Agrozoology; Bélgica
Fil: Taning, Clauvis N. T. Ghent University. Department of Plants and Crops. Laboratory of Agrozoology; Bélgica
Fil: 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; Bélgica
Fil: Widana Gamage, Shirani M. K. University of Ruhuna. Department of Botany; Sri Lanka
Fil: Hughes, Daniel S. T. Baylor College of Medicine. Department of Human and Molecular Genetics. Human Genome Sequencing Center; Estados Unidos
Fil: Murali, Shwetha C. Baylor College of Medicine. Department of Human and Molecular Genetics. Human Genome Sequencing Center; Estados Unidos
Fil: Bailey, Samuel T. University of Cincinnati. Department of Biological Sciences; Estados Unidos
Fil: 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 Unidos
Fil: Jennings, Emily C. University of Cincinnati. Department of Biological Sciences; Estados Unidos
Fil: Rosendale, Andrew J. University of Cincinnati. Department of Biological Sciences; Estados Unidos. Mount St. Joseph University.Department of Biology; Estados Unidos
Fil: Rosselot, Andrew. University of Cincinnati. Department of Biological Sciences; Estados Unidos
Fil: Hervey, Kaylee. Kansas State University. Department of Plant Pathology; Estados Unidos
Fil: Schneweis, Brandi A. Kansas State University. Department of Plant Pathology; Estados Unidos
Fil: Cheng, Sammy. University of Rochester. Department of Biology; Estados Unidos
Fil: Childers, Christopher. National Agricultural Library. USDA-ARS; Estados Unidos
Fil: Simão, Felipe A. University of Geneva Medical School. Swiss Institute of Bioinformatics. Department of Genetic Medicine and Development: Suiza
Fil: Dietzgen, Ralf G. University of Queensland. Queensland Alliance for Agriculture and Food Innovation; Australia
Fil: Chao, Hsu. Baylor College of Medicine. Department of Human and Molecular Genetics. Human Genome Sequencing Center; Estados Unidos
Fil: Dinh, Huyen. Baylor College of Medicine. Department of Human and Molecular Genetics. Human Genome Sequencing Center; Estados Unidos
Fil: Vardhan Doddapaneni, Harsha. Baylor College of Medicine. Department of Human and Molecular Genetics. Human Genome Sequencing Center; Estados Unidos
Fil: Dugan, Shannon. Baylor College of Medicine. Department of Human and Molecular Genetics. Human Genome Sequencing Center; Estados Unidos
Fil: Han, Yi. Baylor College of Medicine. Department of Human and Molecular Genetics. Human Genome Sequencing Center; Estados Unidos
Fil: Lee, Sandra L. Baylor College of Medicine. Department of Human and Molecular Genetics. Human Genome Sequencing Center; Estados Unidos
Fil: Muzny, Donna M. Baylor College of Medicine. Department of Human and Molecular Genetics. Human Genome Sequencing Center; Estados Unidos
Fil: Qu, Jiaxin. Baylor College of Medicine. Department of Human and Molecular Genetics. Human Genome Sequencing Center; Estados Unidos
Fil: Worley, Kim C. Baylor College of Medicine. Department of Human and Molecular Genetics. Human Genome Sequencing Center; Estados Unidos
Fil: Benoit, Joshua B. University of Cincinnati. Department of Biological Sciences; Estados Unidos
Fil: Friedrich, Markus. Wayne State University. Department of Biological Sciences; Estados Unidos
Fil: Jones, Jeffery W. Wayne State University. Department of Biological Sciences; Estados Unidos
Fil: Panfilio, Kristen A. University of Cologne. Institute for Zoology: Developmental Biology; Alemania. University of Warwick. Gibbet Hill Campus. School of Life Sciences; Reino Unido
Fil: Park, Yoonseong. Kansas State University. Department of Entomology; Estados Unidos
Fil: Robertson, Hugh M. University of Illinois at Urbana-Champaign. Department of Entomology; Estados Unidos
Fil: 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; Bélgica
Fil: Ullman, Diane E. University of California Davis. Department of Entomology and Nematology; Estados Unidos
Fil: Van der Zee, Maurijn. Leiden University. Institute of Biology. Leiden; Países Bajos
Fil: Van Leeuwen, Thomas. Ghent University. Department of Plants and Crops. Laboratory of Agrozoology; Bélgica
Fil: Veenstra, Jan A. University of Bordeaux; Francia
Fil: Waterhouse, Robert M. University of Lausanne. Swiss Institute of Bioinformatics. Department of Ecology and Evolution; Suiza
Fil: 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 Unidos
Fil: Werren, John H. University of Rochester. Department of Biology; Estados Unidos
Fil: Whitfield, Anna E. North Carolina State University. Department of Entomology and Plant Pathology; Estados Unidos
Fil: Zdobnov, Evgeny M. University of Geneva Medical School. Swiss Institute of Bioinformatics. Department of Genetic Medicine and Development; Suiza
Fil: Gibbs, Richard A. Baylor College of Medicine. Human Genome Sequencing Center. Department of Human and Molecular Genetics; Estados Unidos
Fil: Richards, Stephen. Baylor College of Medicine. Human Genome Sequencing Center. Department of Human and Molecular Genetics; Estados Unidos
description 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.
publishDate 2020
dc.date.none.fl_str_mv 2020-12-28T14:29:20Z
2020-12-28T14:29:20Z
2020-10-19
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/20.500.12123/8498
https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-020-00862-9
1741-7007 (online)
https://doi.org/10.1186/s12915-020-00862-9
url http://hdl.handle.net/20.500.12123/8498
https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-020-00862-9
https://doi.org/10.1186/s12915-020-00862-9
identifier_str_mv 1741-7007 (online)
dc.language.none.fl_str_mv eng
language eng
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
http://creativecommons.org/licenses/by-nc-sa/4.0/
Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
eu_rights_str_mv openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by-nc-sa/4.0/
Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv BMC
publisher.none.fl_str_mv BMC
dc.source.none.fl_str_mv BMC Biology 18 (1): 142 (2020)
reponame:INTA Digital (INTA)
instname:Instituto Nacional de Tecnología Agropecuaria
reponame_str INTA Digital (INTA)
collection INTA Digital (INTA)
instname_str Instituto Nacional de Tecnología Agropecuaria
repository.name.fl_str_mv INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuaria
repository.mail.fl_str_mv tripaldi.nicolas@inta.gob.ar
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