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

TitleGenome-enabled insights into the biology of thrips as crop pests.
Publication TypeJournal Article
Year of Publication2020
AuthorsRotenberg, D, Baumann, AA, Ben-Mahmoud, S, Christiaens, O, Dermauw, W, Ioannidis, P, Jacobs, CGC, Jentzsch, IMVargas, Oliver, JE, Poelchau, MF, Rajarapu, SPriya, Schneweis, DJ, Snoeck, S, Taning, CNT, Wei, D, Gamage, SMKWidana, Hughes, DST, Murali, SC, Bailey, ST, Bejerman, NE, Holmes, CJ, Jennings, EC, Rosendale, AJ, Rosselot, A, Hervey, K, Schneweis, BA, Cheng, S, Childers, C, Simão, FA, Dietzgen, RG, Chao, H, Dinh, H, Doddapaneni, H, Dugan, S, Han, Y, Lee, SL, Muzny, DM, Qu, J, Worley, KC, Benoit, JB, Friedrich, M, Jones, JW, Panfilio, KA, Park, Y, Robertson, HM, Smagghe, G, Ullman, DE, Van der Zee, M, Van Leeuwen, T, Veenstra, JA, Waterhouse, RM, Weirauch, MT, Werren, JH, Whitfield, AE, Zdobnov, EM, Gibbs, RA, Richards, S
JournalBMC Biol
Volume18
Issue1
Pagination142
Date Published2020 Oct 19
ISSN1741-7007
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.

DOI10.1186/s12915-020-00862-9
Alternate JournalBMC Biol
PubMed ID33070780
PubMed Central IDPMC7570057
Grant ListU54 HG003273 / HG / NHGRI NIH HHS / United States
DEB1257053 / / National Science Foundation /
IOS1456233 / / National Science Foundation /
DEB1654417 / / National Science Foundation /
31003A-125350 / / Swiss NSF /
31003A-143936 / / Swiss NSF /
PP00P3_170664 / / Swiss NSF /
G053815N / / Research Foundation Flanders /
2012-68004-20166 / / National Institute of Food and Agriculture /
2018-67013-28495 / / National Institute of Food and Agriculture /