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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
.
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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.
Fig. 1. Three groups are considered independently for discovery and validation of
genomic variants in X. laevis: a straight J, a straight B and an F1 cross.
Fig. 2. Assessment of diversity in Xenopus laevis by RNA-seq of clutches of inbred (J), and occasionally outbred (B) lines, and F1 crosses. A-B. Number of SNPs (A) and INDELs (B) as
a function of bcftools call quality. Call quality corresponds to −10log10 probability that call is wrong). C. Ratio of transitions to transversions as a function of call quality (see A-B). D.
Number of calls as a function of coverage depth.
Fig. 3. A comparison between Dn/Ds distribution for paired and singleton genes,
illustrating a shift between two groups of genes. X-axis: log2 Dn/Ds.
V. Savova et al. Developmental Biology 424 (2017) 181–188
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