Transcriptomic insights into genetic diversity of protein-coding genes in X. laevis.
Transcriptomic insights into genetic diversity of protein-coding genes in X. laevis.
复制标题
对非洲虎蛋白质编码基因遗传多样性的转录组学见解。
DOI：
10.1016/j.ydbio.2017.02.019
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发表时间：
2017
影响因子：
2.7
通讯作者：
Peshkin,Leonid
中科院分区：
文献类型：
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作者：
Savova,Virginia;Pearl,EstherJ;Boke,Elvan;Nag,Anwesha;Adzhubei,Ivan;Horb,MarkoE;Peshkin,Leonid
我们使用RNA-seq数据和等位基因特异性分析来表征非洲爪蟾品系的遗传多样性。该数据提供了编码变异的目录，其可用于改进基因组序列，以及用于更好的序列比对、探针设计和蛋白质组学分析。此外，我们描绘了一个广泛的图片的物种的遗传景观功能注释不同类别的突变与一个完善的预测工具（PolyPhen-2）。此外，我们特别比较了四个杂交后代的变异：近交基因组（J）株，远交白化病（B）株，和两个杂交的J和B株。我们确定了一个特定的突变子集的B菌株，这使我们能够调查选择压力影响重复基因在这个异源四倍体。从这些杂交中，我们发现在重复基因中非同义突变与同义突变的比例较低，这表明它们处于更大的纯化选择之下。令人惊讶的是，我们还发现，功能改变（“破坏性”）突变构成了该组中的非同义变体的更大比例，这表明亚功能化在影响重复基因的编码变异中的作用。
We characterize the genetic diversity ofXenopus laevisstrains 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.