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Dev Biol 2017 Apr 15;4242:181-188. doi: 10.1016/j.ydbio.2017.02.019.
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Transcriptomic insights into genetic diversity of protein-coding genes in X. laevis.

Savova V , Pearl EJ , Boke E , Nag A , Adzhubei I , Horb ME , Peshkin L .

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.

PubMed ID: 28283406
PMC ID: PMC5405699
Article link: Dev Biol
Grant support: [+]

GEO Series: GSE74470: Xenbase,  NCBI

Article Images: [+] show captions
References [+] :
Abecasis, An integrated map of genetic variation from 1,092 human genomes. 2012, Pubmed