Transcriptomic insights into genetic diversity of protein-coding genes in X. laevis

We characterize the genetic diversity of Xenopus laevis strains using RNA-seq data and allele-specific analysis.
This data provides 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
four crosses: inbred genomic (J)-strain, outbred albino (B)-strain, and two hybrid crosses of J and B strains. We
identify a subset of mutations specific to the B strain, which allows us to investigate the selection pressures
affecting duplicated genes in this allotetraploid. From these crosses we find the ratio of non-synonymous to
synonymous mutations is lower in duplicated genes, which suggests that they are 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 suggests a role for subfunctionalization in coding variation
affecting duplicated genes.