Comparative genomics of the miniature wasp and pest control agent Trichogramma pretiosum

Lindsey, Amelia R.I.; Kelkar, Yogeshwar D.; Wu, Xin; Sun, Dan; Martinson, Ellen O.; Yan, Zhichao; Rugman‐Jones, Paul F.; Hughes, Daniel; Murali, Shwetha C.; Qu, Jiaxin; Dugan, Shannon; Lee, Sandra L.; Chao, Hsu; Dinh, Huyen; Han, Yi; Doddapaneni, Harshavardhan; Worley, Kim C.; Muzny, Donna M.; Yè, Gōngyín; Gibbs, Richard A.; Richards, Stephen; Yi, Soojin V.; Stouthamer, Richard; Werren, John H.

doi:10.1186/s12915-018-0520-9

Cited by 56 publications

(76 citation statements)

References 122 publications

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“…The i5K pilot initiative has assembled an unparalleled genomic dataset for arthropods 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 32,33 and animals 34 , urban 20,35 and forest 36 pests, biocontrol species 37 , along with developmental models 18,38,39 , indicators of water quality and models for toxicology 15,40 (Table S1).…”

Section: Concluding Remarks and Future Directionsmentioning

confidence: 99%

Gene Content Evolution in the Arthropods

Thomas

Dohmen

Hughes

et al. 2018

Preprint

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110

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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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Section: Concluding Remarks and Future Directionsmentioning

confidence: 99%

Gene Content Evolution in the Arthropods

Thomas

Dohmen

Hughes

et al. 2018

Preprint

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110

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“…To more precisely characterize the age of the young regulators in sex-biased clusters, we integrated phylostratigraphic assignments from additional parasitoid wasp species (Lindsey et al 2018) in the superfamily Chalcidoidea. In addition to Nasonia (family Pteromalidae), the chalcids used here are those with published genome assemblies, and belong to different chalcid families, Ceratosolen solmsi (Agaonidae fig wasps), Copidosoma floridanum (Encyrtidae), and Trichogramma pretiosum, in the more basal family Trichogrammatidae.…”

Section: Sex-biased Clusters Integrate New Genes In Regulatory Positionsmentioning

confidence: 99%

“…We performed a second identical set of analyses using the subset of genes included in the hymenopteran and chalcid strata, and adding more species to increase the phylogenetic resolution within hymenoptera. We used data from Lindsey et al (2018) for homology assignments to the chalcid species Ceratosolen solmsi, Copidosoma floridanum, and Trichogramma pretiosum, as well as the additional hymenopterans Athalia rosae, Orussus abietinus, and Microplitis demolitor. These additional data allowed separating genes that are found within chalcidoid wasps (matching with Ceratosolen, Copidosoma or Trichogramma), but not in the other Hymenoptera.…”

Section: Phylostratigraphic Analyses On Network Parametersmentioning

confidence: 99%

“…Genes were assigned to the Chalcid stratum when an ortholog was found in one or more of the other chalcidoids, and to the Nasonia stratum when the Nasonia gene did not have any ortholog. Orthologs for this set were assigned using OrthoMCL with an e-value cutoff of 10e-10, percent match cutoff of 70 and inflation of 2.5 (Lindsey et al 2018, Supplementary Information, section S2.2).…”

Section: Phylostratigraphic Analyses On Network Parametersmentioning

confidence: 99%

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Sex biased expression and co-expression networks in development, using the hymenopteran Nasonia vitripennis

Rago

Werren

Colbourne

2019

Preprint

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Sexual dimorphism requires gene expression regulation in developing organisms. Differential expression, alternative splicing and transcript-transcript interactions all contribute to developmental differences between the sexes. However, few studies have described how these processes change across developmental stages, or how they interact to form co-expression networks. We compare the dynamics of all three regulatory processes in the sexual development of the model parasitoid wasp Nasonia vitripennis, a system that permits genome wide analysis of sex bias from early embryos to adults. We find relatively little sex-bias in embryos and larvae at the whole-gene level, but several sub-networks show sex-biased transcript-transcript interactions in early developmental stages. These provide new candidates for hymenopteran sex determination, including histone modification genes. In contrast, sex-bias in pupae and adults is driven by wholegene differential expression. We observe sex-biased splicing consistently across development, but mostly in genes that are already biased at the whole-gene level. Finally, we discover that sex-biased networks are enriched by genes specific to the Nasonia clade, and that those genes possess the topological properties of key regulators. These findings suggest that regulators in sex-biased networks evolve more rapidly than regulators of other developmental networks.(Chang et al. 2011; Innocenti and Morrow 2010 but see Wang, Werren and Clark 2015). However, the focus on adult gene expression does not reveal sex differential processes during development, and several genes are sex-biased only during those early stages (Perry, Harrison, and Mank 2014;Mank et al. 2010;Zhao et al. 2011). Changes in sex-bias expression of the same gene across development are most likely to create conflict, since the same locus may be under selection for changes in female-specific and male-specific functions in different developmental stages -a scenario that we term 'developmental sexual conflict'. Several studies have also shown that alternative splicing can show sex-bias (Telonis-Scott et al. 2008;Hartmann et al. 2011; Brown et al. 2014), and that sex-biased splicing affects sex determination (Verhulst et al. 2013; Verhulst, Beukeboom, and van de Zande 2010) and sexual development (Chang et al. 2011).The co-expression of multiple genes can result in effects that are qualitatively and quantitatively different from the sum of the effects of each gene (Ament et al. 2012;Spitz and Furlong 2012;Boyle et al. 2014), and provides a largely unexplored mechanism for the regulation of sex-specific differences; the same group of genes can have identical expression levels in males and females, yet still cause a sex-specific effect if they are only co-expressed in one sex (Arnold, van Nas and Lusis 2009;). These interactions are therefore impossible to detect by independently testing transcripts, but can be identified via differential correlation analyses on transcriptional modules, or differential cluster correlations (Tesson...

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“…The distribution of venom protein Y ( VenY ) across the chalcid phylogeny. The presence of paralogues VenY A and VenY B placed on the species phylogeny (Lindsey et al, ); minus signs indicate that VenY was not found and ‘na’ is marked when resources were not available.…”

Section: Resultsmentioning

confidence: 99%

Evaluating the evolution and function of the dynamic Venom Y protein in ectoparasitoid wasps

Martinson

Siebert

et al. 2019

Insect Molecular Biology

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Venom of the parasitoid wasp Nasonia vitripennis changes the metabolism and gene expression in its fly host Sarcophaga bullata to induce developmental arrest, suppression of the immune response and various other venom effects. Yet, the venom of ectoparasitoid wasps has not been fully characterized. A major component of N. vitripennis venom is an uncharacterized, high‐expressing protein referred to as Venom Y. Here we describe the evolutionary history and possible functions of this venom protein. We found that Venom Y is a relatively young gene that has duplicated to form two distinct paralogue groups. A copy of Venom Y has been recruited as a venom protein in at least five wasp species. Functional analysis found that Venom Y affects detoxification and immunity genes in envenomated fly hosts. Many of these genes are fat‐body specific, suggesting that Venom Y may have a targeted effect on fat body tissue. We also show that Venom Y may mitigate negative effects of other venom proteins. Finally, protein sequencing indicates that Venom Y is post‐translationally modified. This study contributes to elucidating parasitoid venom by using RNA interference knockdown to investigate venom protein function in the context of the whole venom cocktail.

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Comparative genomics of the miniature wasp and pest control agent Trichogramma pretiosum

Cited by 56 publications

References 122 publications

Gene Content Evolution in the Arthropods

Gene Content Evolution in the Arthropods

Sex biased expression and co-expression networks in development, using the hymenopteran Nasonia vitripennis

Evaluating the evolution and function of the dynamic Venom Y protein in ectoparasitoid wasps

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