Data from: Comparative transcriptomics support evolutionary convergence of diapause responses across Insecta
Ragland, Gregory J., Kansas State University
Keep, Evan, Kansas State University
Published Feb 20, 2018 on Dryad.
Cite this dataset
Ragland, Gregory J.; Keep, Evan (2018). Data from: Comparative transcriptomics support evolutionary convergence of diapause responses across Insecta [Dataset]. Dryad. https://doi.org/10.5061/dryad.rq3sp
Diapause is a common phenotype that is broadly phylogenetically dispersed across Insecta and appears to have multiple evolutionary origins. Nevertheless, there are clear commonalities in diapause regulation across insect taxa. In the present study, we report a meta-analysis of diapause whole transcriptomic data sets from 11 different insect species that addresses three questions: (i) how similar are whole-transcriptome diapause responses across species within and across different diapause life-cycle stages; (ii) do the most closely-related species demonstrate the most similar diapause responses within and across diapause life-cycle stages (the existence of phylogenetic signal); and (iii) is there a core set of regulatory genes that universally associate with insect diapause at the transcript level? The included species are mostly Dipterans (n = 9), plus one species each from Lepidoptera and Hymenoptera. The group includes multiple species that enter diapause as either larvae, pupae or adults. We establish a set of 4791 orthologous transcript sequences with expression data acquired from published studies of diapause transcriptomes. We find no support for phylogenetic signal. Transcriptomic responses of nondipterans clustered within rather than outside of Dipteran responses. However, expression profiles do tend to cluster with the diapause stage of developmental arrest, although this pattern is only moderately supported. We identify a statistically significant set of 542 orthologues (11% of all orthologues) that are commonly differentially regulated during diapause across all included species. From this core set, we identify candidate genes participating in circadian rhythmicity, insulin signalling and Wnt signalling, which are pathways previously associated with insect diapause development. Clustering relationships among species are most consistent with evolutionary convergence of the shared transcriptomic response, although we are unable to determine whether this reflects convergence of the diapause initiation, maintenance or termination phases.
Archive containing files for target species-to-Drosophila melanogaster pairwise ortholog models. Each file maps ids from a transcriptome assembly to D. melanogaster flyabase IDs. Methods for orthology assignment and references for each transcriptome assembly available in Ragland and Keep, and in the 'MetaData' data file also contained in this archive.
Meta data for transcriptomic data sets used in the comparative analysis to generate gene expression matrix 'UnFilteredExpressionAllOrthos' also included in this archive.
Matrix of diapause expression data across included insect species. Each row of expression data is associated with a single gene orthologous across all species, designated with the flyabase id for the gene in Drosophila melanogaster. Each data value is a log2 fold change: log2(diapause) - log2(non-diapause) for each included species. See Ragland and Keep for methods. Species codes are described in the first metadata line of the file.