The genome of the water strider<i>Gerris buenoi</i>reveals expansions of gene repertoires associated with adaptations to life on the water

Armisén, David; Rajakumar, Rajendhran; Friedrich, Markus; Benoit, Joshua B.; Robertson, Hugh M.; Panfilio, Kristen A.; Ahn, Seung‐Joon; Poelchau, Monica F.; Chao, Hsu; Dinh, Huyen; Doddapaneni, Harshavardhan; Dugan-Perez, Shannon; Gibbs, Richard A.; Hughes, Daniel; Han, Yi; Lee, Sandra L.; Murali, Shwetha C.; Qu, Jiaxin; Worley, Kim C.; Muñoz-Torres, Monica; Abouheif, Ehab; Bonneton, François; Chen, Travis; Chiang, Li-Mei; Childers, Christopher P.; Cridge, Andrew G.; Crumiere, Antonin Jj; Decaras, Amélie; Didion, Elise M.; Duncan, Elizabeth J.; Elpidina, Elena N.; Favé, Marie-Julie; Finet, Cédric; Jacobs, Chris G.C.; Jarvela, Alys M. Cheatle; Jennings, Emily J; Jones, Jeffery W.; Lesoway, Maryna P.; Lovegrove, Mackenzie; Martynov, Alexander; Oppert, Brenda; Lilico-Ouachour, Angelica; Rajakumar, Arjuna; Refki, Peter Nagui; Rosendale, Andrew J.; Santos, Maria Emília Madeira; Toubiana, William; Zee, Maurijn van der; Jentzsch, Iris M. Vargas; Lowman, Aidamalia Vargas; Viala, Séverine; Richards, Stephen; Khila, Abderrahman

doi:10.1101/242230

Cited by 15 publications

(14 citation statements)

References 102 publications

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“…At the same time, the considerable protein sequence divergence of the three paralogs, which differ at over 140 amino acid sites in each pairwise comparison, indicated a more ancient origin of the cluster, potentially associated with elevated adaptive sequence change. Comparative searches for possible wavelength-sensitivity shifting/tuning substitutions paralleling those identified in the water strider LW opsin paralogs did not produce compelling evidence of candidate changes (not shown) [66]. Understanding the functional significance of the F. occidentalis LW opsin gene cluster thus requires future study.…”

Section: Vision Genesmentioning

confidence: 98%

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

et al. 2020

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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.

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Section: Vision Genesmentioning

confidence: 98%

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

et al. 2020

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“…The C. dipterum genome was assembled in 1395 scaffolds, with an N50 of 0.461 Mb. The total genome assembly length of C. dipterum is 180 Mb, which in comparison to other pterygote species [11][12][13][14] , constitutes a relatively compact genome, probably due to the low fraction of transposable elements (TEs) (5%, in contrast to the median of 24% ± 12% found in other insects 15 , Supplementary Fig. 1).…”

Section: Resultsmentioning

confidence: 99%

Genomic adaptations to aquatic and aerial life in mayflies and the origin of insect wings

et al. 2020

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The evolution of winged insects revolutionized terrestrial ecosystems and led to the largest animal radiation on Earth. However, we still have an incomplete picture of the genomic changes that underlay this diversification. Mayflies, as one of the sister groups of all other winged insects, are key to understanding this radiation. Here, we describe the genome of the mayfly Cloeon dipterum and its gene expression throughout its aquatic and aerial life cycle and specific organs. We discover an expansion of odorant-binding-protein genes, some expressed specifically in breathing gills of aquatic nymphs, suggesting a novel sensory role for this organ. In contrast, flying adults use an enlarged opsin set in a sexually dimorphic manner, with some expressed only in males. Finally, we identify a set of wing-associated genes deeply conserved in the pterygote insects and find transcriptomic similarities between gills and wings, suggesting a common genetic program. Globally, this comprehensive genomic and transcriptomic study uncovers the genetic basis of key evolutionary adaptations in mayflies and winged insects.

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“…The i5K pilot initiative has assembled an unparalleled genomic dataset for arthropod research and conducted a detailed phylogenetic analysis of evolutionary changes at the genomic level within this diverse and fascinating phylum. The combined research output of species-level i5K work has been substantial and wide-ranging, addressing pests of agricultural crops [33,34] and animals [35], urban [20,36] and forest [37] pests, biocontrol species [38], along with developmental models [18,39,40], indicators of water quality and models for toxicology [15,41] (Additional file 1: Table S1).…”

Section: Discussionmentioning

confidence: 99%

Gene content evolution in the arthropods

et al. 2020

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Background: Arthropods comprise the largest and most diverse phylum on Earth and play vital roles in nearly every ecosystem. Their diversity stems in part from variations on a conserved body plan, resulting from and recorded in adaptive changes in the genome. Dissection of the genomic record of sequence change enables broad questions regarding genome evolution to be addressed, even across hyper-diverse taxa within arthropods. Results: Using 76 whole genome sequences representing 21 orders spanning more than 500 million years of arthropod evolution, we document changes in gene and protein domain content and provide temporal and phylogenetic context for interpreting these innovations. We identify many novel gene families that arose early in the evolution of arthropods and during the diversification of insects into modern orders. We reveal unexpected variation in patterns of DNA methylation across arthropods and examples of gene family and protein domain evolution coincident with the appearance of notable phenotypic and physiological adaptations such as flight, metamorphosis, sociality, and chemoperception. Conclusions: These analyses demonstrate how large-scale comparative genomics can provide broad new insights into the genotype to phenotype map and generate testable hypotheses about the evolution of animal diversity.

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The genome of the water striderGerris buenoireveals expansions of gene repertoires associated with adaptations to life on the water

Abstract: The semi-aquatic bugs conquered water surfaces worldwide and occupy ponds, streams, lakes,

Cited by 15 publications

References 102 publications

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

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

Genomic adaptations to aquatic and aerial life in mayflies and the origin of insect wings

Gene content evolution in the arthropods

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