Prevalence and Dynamics of Ribosomal DNA Micro-heterogeneity Are Linked to Population History in Two Contrasting Yeast Species.
Prevalence and Dynamics of Ribosomal DNA Micro-heterogeneity Are Linked to Population History in Two Contrasting Yeast Species.
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DOI：
10.1038/srep28555
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发表时间：
2016-06-27
影响因子：
4.6
通讯作者：
Roberts IN
中科院分区：
文献类型：
--
作者：
James SA;West C;Davey RP;Dicks J;Roberts IN
尽管过去和现在的基因组测序项目有相当多的数量和分类范围，其中许多项目必然包括核糖体DNA，但关于这个无处不在的基因组区域中序列变异的流行率和进化意义的详细信息严重缺乏。在这里，我们试图在两个密切相关但截然不同的酵母品种中解决这个问题，面包酵母酿酒酵母和野生酵母矛盾酵母。通过利用酵母基因组重测序计划的现有数据集，我们确定了丰富的核糖体DNA序列变异的矿层，分别在34株酿酒酵母和26株反常葡萄球菌中表现出1068和970个多态。我们发现这两个物种集表现出截然不同的突变特征。此外，我们首次发现，由于核糖体DNA区域的不完全协同进化而导致的未解决的rDNA序列变异在每个物种中遵循U型等位基因频率分布，类似于在非协同机制下进化的座位，但通过相当不同的进化过程而产生。最后，我们将这些等位基因频率分布形状之间的差异与两个物种不同的种群历史联系起来。
Despite the considerable number and taxonomic breadth of past and current genome sequencing projects, many of which necessarily encompass the ribosomal DNA, detailed information on the prevalence and evolutionary significance of sequence variation in this ubiquitous genomic region are severely lacking. Here, we attempt to address this issue in two closely related yet contrasting yeast species, the baker’s yeast Saccharomyces cerevisiae and the wild yeast Saccharomyces paradoxus. By drawing on existing datasets from the Saccharomyces Genome Resequencing Project, we identify a rich seam of ribosomal DNA sequence variation, characterising 1,068 and 970 polymorphisms in 34 S. cerevisiae and 26 S. paradoxus strains respectively. We discover the two species sets exhibit distinct mutational profiles. Furthermore, we show for the first time that unresolved rDNA sequence variation resulting from imperfect concerted evolution of the ribosomal DNA region follows a U-shaped allele frequency distribution in each species, similar to loci that evolve under non-concerted mechanisms but arising through rather different evolutionary processes. Finally, we link differences between the shapes of these allele frequency distributions to the two species’ contrasting population histories.