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.
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2020-10-19
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Subjects: | Thysanoptera, Salivary Glands, Detoxification, Glándulas Salivales, Desintoxicación, Western Flower Thrips, Hemipteroid Assemblage, Insect Genomics, Chemosensory Receptors, Opsins, Innate Immunity, Tospovirus, |
Online Access: | 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 |
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Thysanoptera Salivary Glands Detoxification Glándulas Salivales Desintoxicación Western Flower Thrips Hemipteroid Assemblage Insect Genomics Chemosensory Receptors Opsins Innate Immunity Tospovirus Thysanoptera Salivary Glands Detoxification Glándulas Salivales Desintoxicación Western Flower Thrips Hemipteroid Assemblage Insect Genomics Chemosensory Receptors Opsins Innate Immunity Tospovirus |
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Thysanoptera Salivary Glands Detoxification Glándulas Salivales Desintoxicación Western Flower Thrips Hemipteroid Assemblage Insect Genomics Chemosensory Receptors Opsins Innate Immunity Tospovirus Thysanoptera Salivary Glands Detoxification Glándulas Salivales Desintoxicación Western Flower Thrips Hemipteroid Assemblage Insect Genomics Chemosensory Receptors Opsins Innate Immunity Tospovirus 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 G. 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 Genome-enabled insights into the biology of thrips as crop pests |
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. |
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Thysanoptera Salivary Glands Detoxification Glándulas Salivales Desintoxicación Western Flower Thrips Hemipteroid Assemblage Insect Genomics Chemosensory Receptors Opsins Innate Immunity Tospovirus |
author |
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 G. 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_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 G. 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_sort |
Rotenberg, Dorith |
title |
Genome-enabled insights into the biology of thrips as crop pests |
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 |
publisher |
BMC |
publishDate |
2020-10-19 |
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 |
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oai:localhost:20.500.12123-84982020-12-28T17:04:05Z 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. 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 G. 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 Thysanoptera Salivary Glands Detoxification Glándulas Salivales Desintoxicación Western Flower Thrips Hemipteroid Assemblage Insect Genomics Chemosensory Receptors Opsins Innate Immunity Tospovirus 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 2020-12-28T14:29:20Z 2020-12-28T14:29:20Z 2020-10-19 info:ar-repo/semantics/artículo info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion 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 eng info:eu-repo/semantics/openAccess application/pdf BMC BMC Biology 18 (1): 142 (2020) |