Data from: Comparative ecological transcriptomics and the contribution of gene expression to the evolutionary potential of a threatened fish
Brauer, Chris J., Flinders University
Unmack, Peter J., University of Canberra
Beheregaray, Luciano B., Flinders University
Published Nov 08, 2017 on Dryad.
Cite this dataset
Brauer, Chris J.; Unmack, Peter J.; Beheregaray, Luciano B. (2017). Data from: Comparative ecological transcriptomics and the contribution of gene expression to the evolutionary potential of a threatened fish [Dataset]. Dryad. https://doi.org/10.5061/dryad.6gh7b
Understanding whether small populations with low genetic diversity can respond to rapid environmental change via phenotypic plasticity is an outstanding research question in biology. RNA sequencing (RNA-seq) has recently provided the opportunity to examine variation in gene expression, a surrogate for phenotypic variation, in non-model species. We used a comparative RNA-seq approach to assess expression variation within and among adaptively divergent populations of a threatened freshwater fish, Nannoperca australis, found across a steep hydroclimatic gradient in the Murray-Darling Basin, Australia. These populations evolved under contrasting selective environments (e.g. dry/hot lowland; wet/cold upland) and represent opposite ends of the species’ spectrum of genetic diversity and population size. We tested the hypothesis that environmental variation among isolated populations has driven the evolution of divergent expression at ecologically important genes using differential expression (DE) analysis and an ANOVA-based comparative phylogenetic expression variance and evolution model framework based on 27,425 de novo assembled transcripts. Additionally, we tested whether gene expression variance within-populations was correlated with levels of standing genetic diversity. We identified 290 DE candidate transcripts, 33 transcripts with evidence for high expression plasticity, and 50 candidates for divergent selection on gene expression after accounting for phylogenetic structure. Variance in gene expression appeared unrelated to levels of genetic diversity. Functional annotation of the candidate transcripts revealed variation in water quality is an important factor influencing expression variation for N. australis. Our findings suggest that gene expression variation can contribute to the evolutionary potential of small populations.
Nannoperca australis liver transcriptome
Nannoperca australis liver transcriptome assembled using Trinity based on RNAseq data from five individuals. Assembly contains 201,037 Trinity transcripts clustered into 96,717 Trinity "genes".
Raw counts data for 27,425 longest open reading frames