Journal article

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

  • 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 Institute of Biology, Leiden University, 2333 BE, Leiden, The Netherlands.
  • Vargas Jentzsch IM Institute for Zoology: Developmental Biology, University of Cologne, 50674, Cologne, Germany.
  • Oliver JE Department of Plant Pathology, University of Georgia - Tifton Campus, Tifton, GA, 31793-5737, USA.
  • Poelchau MF National Agricultural Library, USDA-ARS, Beltsville, MD, 20705, USA.
  • Rajarapu SP Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA.
  • Schneweis DJ Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.
  • Snoeck S Laboratory of Agrozoology, Department of Plants and Crops, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.
  • Taning CNT Laboratory of Agrozoology, Department of Plants and Crops, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.
  • Wei D Laboratory of Agrozoology, Department of Plants and Crops, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.
  • Widana Gamage SMK Department of Botany, University of Ruhuna, Matara, Sri Lanka.
  • Hughes DST Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
  • Murali SC Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
  • Bailey ST Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA.
  • Bejerman NE IPAVE-CIAP-INTA, 5020, Cordoba, Argentina.
  • Holmes CJ Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA.
  • Jennings EC Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA.
  • Rosendale AJ Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA.
  • Rosselot A Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA.
  • Hervey K Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.
  • Schneweis BA Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.
  • Cheng S Department of Biology, University of Rochester, Rochester, NY, 14627, USA.
  • Childers C National Agricultural Library, USDA-ARS, Beltsville, MD, 20705, USA.
  • Simão FA Department of Genetic Medicine and Development, University of Geneva Medical School, and Swiss Institute of Bioinformatics, Geneva, Switzerland.
  • Dietzgen RG Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, 4072, Australia.
  • Chao H Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
  • Dinh H Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
  • Doddapaneni HV Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
  • Dugan S Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
  • Han Y Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
  • 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 Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA.
  • Friedrich M Department of Biological Sciences, Wayne State University, Detroit, MI, 48202, USA.
  • Jones JW Department of Biological Sciences, Wayne State University, Detroit, MI, 48202, USA.
  • Panfilio KA Institute for Zoology: Developmental Biology, University of Cologne, 50674, Cologne, Germany.
  • Park Y Department of Entomology, Kansas State University, Manhattan, KS, 66506, USA.
  • Robertson HM Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
  • Smagghe G Laboratory of Agrozoology, Department of Plants and Crops, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.
  • Ullman DE Department of Entomology and Nematology, University of California Davis, Davis, CA, 95616, USA.
  • van der Zee M Institute of Biology, Leiden University, 2333 BE, Leiden, The Netherlands.
  • Van Leeuwen T Laboratory of Agrozoology, Department of Plants and Crops, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.
  • Veenstra JA INCIA UMR 5287 CNRS, University of Bordeaux, Pessac, France.
  • Waterhouse RM Department of Ecology and Evolution, Swiss Institute of Bioinformatics, University of Lausanne, 1015, Lausanne, Switzerland.
  • Weirauch MT Center for Autoimmune Genomics and Etiology, Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.
  • Werren JH Department of Biology, University of Rochester, Rochester, NY, 14627, USA.
  • Whitfield AE Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA.
  • Zdobnov EM Department of Genetic Medicine and Development, University of Geneva Medical School, and Swiss Institute of Bioinformatics, Geneva, Switzerland.
  • Gibbs RA Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
  • Richards S Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
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  • 2020-10-19
Published in:
  • BMC biology. - 2020
English 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.
Language
  • English
Open access status
gold
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Persistent URL
https://sonar.ch/global/documents/242980
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