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Transcriptomic Insights into Genetic Diversity of Protein-Coding Genes in X. laevis

ABSTRACT: We characterize the genetic diversity of Xenopus laevis strains using allele-specific RNA-seq data analysis and provide a catalogue of coding variation which can be used for improving the genomic sequence, as well as for better sequence alignment, probe design, and proteomic analysis. In addition, we paint a broad picture of the genetic landscape of the species by functionally annotating different classes of mutations with a well-established prediction tool (PolyPhen-2). Further, we specifically compare the variation in the progeny of a cross from the inbred genomic (J)-strain, a cross from the popular occasionally outbred albino (B)-strain, and two hybrid crosses. We use the comparison to identify a subset of mutations specific to the B-strain, which allows us to investigate the specific selection pressures affecting duplicated genes in this pseudo-tetraploid. We find the ratio of non-synonymous to synonymous mutations is lower in duplicated genes, which therefore appear to be under greater purifying selection. Surprisingly, we also find that function-altering ("damaging") mutations constitute a greater fraction of the non-synonymous variants in this group, which may suggest a role for subfunctionalization in coding variation affecting duplicated genes.

ORGANISM(S): Xenopus laevis

PROVIDER: GSE74470 | GEO | 2017/03/15

SECONDARY ACCESSION(S): PRJNA300520

REPOSITORIES: GEO

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Project description:Transcript abundance was measured in whole-body virgin male Drosophila serrata from 41 inbred lines that had diverged through 27 generations of mutation accumulation that were sexually selected Sexual selection is predicted to have widespread effects on the genetic variation generated by new mutations as a consequence of the genic capture of condition by male sexual traits. We manipulated the opportunity for sexual selection on males during 27 generations of mutation accumulation in inbred lines of Drosophila serrata, and used a microarray platform to investigate the effect of sexual selection on the expression of 2685 genes, representing a broad coverage of biological function. Sexual selection had little effect on mean gene expression levels, with only 4 genes diverging significantly at a false discovery rate of 5% . In contrast, sexual selection impacted on both the magnitude and nature of mutational variance accumulating in these genes. The magnitude of mutational variance increased under sexual selection by an average of 29%. Mutational variance was less commonly generated by extreme phenotypes less commonly under sexual selection. Furthermore, analysis of random sets of five genes revealed that the mutational variance that accumulated under sexual selection was less pleiotropic in nature than that found in the absence of sexual selection. The generation of greater mutational variance without a general concomitant change in mean expression under sexual selection suggested that gene expression traits were be under apparent rather than direct sexual selection. We discuss two main explanations for the broad-based increase in mutational variance under sexual selection that both require extensive pleiotropy between traits affecting male mating success, standard metric traits represented here by gene expression traits, and general fitness. We measured gene expression of male Drosophila serrata from 41 mutation accumulation lines (whole-body) that were sexually selected. Data from two replicates for each line are presented.

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Transcriptomic Insights into Genetic Diversity of Protein-Coding Genes in X. laevis

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