Genomes of the Hymenoptera

Branstetter, Michael G.; Childers, Anna K.; Cox-Foster, Diana; Hopper, Keith R.; Kapheim, Karen M.; Toth, Amy L.; Worley, Kim C.

doi:10.1016/j.cois.2017.11.008

Cited by 66 publications

(71 citation statements)

References 116 publications

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“…Here, paternally inherited genomes of diploid males are inactivated during embryogenesis (Normark, ). The phenomenon of haplodiploidy is known from Hymenoptera (Branstetter et al, ; Hansson & Schmidt, ) another group known to be rate accelerated, but it is largely unstudied throughout Diptera. Despite the need for more study, we conclude the true diversity of Diptera in Germany, Europe and the world has been seriously underestimated, a conclusion reached in several other studies (Erwin, ; Hebert et al, ; May, ; Ødegaard, ).…”

Section: Discussionmentioning

confidence: 99%

A DNA barcode library for 5,200 German flies and midges (Insecta: Diptera) and its implications for metabarcoding‐based biomonitoring

Morinière

Balke

Doczkal

et al. 2019

Molecular Ecology Resources

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This study summarizes results of a DNA barcoding campaign on German Diptera, involving analysis of 45,040 specimens. The resultant DNA barcode library includes records for 2,453 named species comprising a total of 5,200 barcode index numbers (BINs), including 2,700 COI haplotype clusters without species‐level assignment, so called “dark taxa.” Overall, 88 out of 117 families (75%) recorded from Germany were covered, representing more than 50% of the 9,544 known species of German Diptera. Until now, most of these families, especially the most diverse, have been taxonomically inaccessible. By contrast, within a few years this study provided an intermediate taxonomic system for half of the German Dipteran fauna, which will provide a useful foundation for subsequent detailed, integrative taxonomic studies. Using DNA extracts derived from bulk collections made by Malaise traps, we further demonstrate that species delineation using BINs and operational taxonomic units (OTUs) constitutes an effective method for biodiversity studies using DNA metabarcoding. As the reference libraries continue to grow, and gaps in the species catalogue are filled, BIN lists assembled by metabarcoding will provide greater taxonomic resolution. The present study has three main goals: (a) to provide a DNA barcode library for 5,200 BINs of Diptera; (b) to demonstrate, based on the example of bulk extractions from a Malaise trap experiment, that DNA barcode clusters, labelled with globally unique identifiers (such as OTUs and/or BINs), provide a pragmatic, accurate solution to the “taxonomic impediment”; and (c) to demonstrate that interim names based on BINs and OTUs obtained through metabarcoding provide an effective method for studies on species‐rich groups that are usually neglected in biodiversity research projects because of their unresolved taxonomy.

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Section: Discussionmentioning

confidence: 99%

A DNA barcode library for 5,200 German flies and midges (Insecta: Diptera) and its implications for metabarcoding‐based biomonitoring

Morinière

Balke

Doczkal

et al. 2019

Molecular Ecology Resources

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“…Here, we report the de novo genome assembly of the parasitoid wasp D. alloeum , adding to the genomic resources for parasitoid wasps, which are underrepresented among available hymenopteran genomes (Branstetter et al ., 2017). We performed a series of descriptive analyses to assess the overall quality and content of the D. alloeum genome, and then focused on annotation and evolutionary analyses of gene families with potential relevance to speciation and sex determination in Diachasma .…”

Section: Introductionmentioning

confidence: 99%

Genome of the parasitoid waspDiachasma alloeum, an emerging model for ecological speciation and transitions to asexual reproduction

Tvedte

Walden

McElroy

et al. 2019

Preprint

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Parasitoid wasps are among the most speciose animals, yet have relatively few available genomic resources. We report a draft genome assembly of the wasp Diachasma alloeum (Hymenoptera: Braconidae), a host-specific parasitoid of the apple maggot fly Rhagoletis pomonella (Diptera: Tephritidae) and a developing model for understanding how ecological speciation can “cascade” across trophic levels. Identification of gene content confirmed the overall quality of the draft genome, and we manually annotated ∼400 genes as part of this study, including those involved in oxidative phosphorylation, chemosensation, and reproduction. Through comparisons to model hymenopterans such as the European honeybee Apis mellifera and parasitoid wasp Nasonia vitripennis, as well as a more closely related braconid parasitoid Microplitis demolitor, we identified a proliferation of transposable elements in the genome, an expansion of chemosensory genes in D. alloeum and other parasitoid wasps, and the maintenance of several key genes with known roles in sexual reproduction and sex determination. The D. alloeum genome will provide a valuable resource for comparative genomics studies in Hymenoptera as well as specific investigations into the genomic changes associated with ecological speciation and transitions to asexuality.

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“…It's genome was the first hymenopteran to be sequenced after that of the Honeybee (The Honeybee Genome Sequencing Consortium 2006). Several other hymenoptera genomes have been sequenced since (Branstetter et al 2018), enabling us to study their genomic features in a broader phylogenetic context.…”

Section: Introductionmentioning

confidence: 99%

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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Genomes of the Hymenoptera

Cited by 66 publications

References 116 publications

A DNA barcode library for 5,200 German flies and midges (Insecta: Diptera) and its implications for metabarcoding‐based biomonitoring

A DNA barcode library for 5,200 German flies and midges (Insecta: Diptera) and its implications for metabarcoding‐based biomonitoring

Genome of the parasitoid waspDiachasma alloeum, an emerging model for ecological speciation and transitions to asexual reproduction

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

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