Data from: Ribosomal DNA sequence heterogeneity reflects intra-species phylogenies and predicts genome structure in two contrasting yeast species

The ribosomal RNA encapsulates a wealth of evolutionary information, including genetic variation that can be used to discriminate between organisms at a wide range of taxonomic levels. For example, the prokaryotic 16S rDNA sequence is very widely used both in phylogenetic studies and as a marker in metagenomic surveys and the ITS region, frequently used in plant phylogenetics, is now recognised as a fungal DNA barcode. However, this widespread use does not escape criticism, principally due to issues such as difficulties in classification of paralogous versus orthologous rDNA units and intragenomic variation, both of which may be significant barriers to accurate phylogenetic inference. We recently analysed datasets from the Saccharomyces Genome Resequencing Project, characterising rDNA sequence variation within multiple strains of the baker's yeast Saccharomyces cerevisiae and its nearest wild relative Saccharomyces paradoxus in unprecedented detail. Notably, both species possess single locus rDNA systems. Here, we use these new variation datasets to assess whether a more detailed characterisation of the rDNA locus can alleviate the second of these phylogenetic issues, sequence heterogeneity, while controlling for the first. We demonstrate that a strong phylogenetic signal exists within both datasets and illustrate how they can be used, with existing methodology, to estimate intra-species phylogenies of yeast strains consistent with those derived from whole-genome approaches. We also describe the use of partial Single Nucleotide Polymorphisms, a type of sequence variation found only in repetitive genomic regions, in identifying key evolutionary features such as genome hybridisation events and show their consistency with whole-genome Structure analyses. We conclude that our approach can transform rDNA sequence heterogeneity from a problem to a useful source of evolutionary information, enabling the estimation of highly accurate phylogenies of closely related organisms, and discuss how it could be extended to future studies of multi-locus rDNA systems.

核糖体RNA（ribosomal RNA）蕴含着丰富的进化信息，其中包含可用于区分不同分类层级生物的遗传变异。例如，原核生物的16S核糖体DNA（16S rDNA）序列被广泛应用于系统发育研究，同时也作为宏基因组研究的分子标记；而常用于植物系统发育研究的内部转录间隔区（ITS region），如今已被认定为真菌DNA条形码。然而，这种广泛应用并未免于批评，其核心问题在于旁系同源与直系同源核糖体DNA单元的分类困难，以及基因组内变异，这二者均可能成为准确系统发育推断的重大障碍。我们近期对酿酒酵母基因组重测序项目（Saccharomyces Genome Resequencing Project）的数据集展开分析，以前所未有的精细程度刻画了酿酒酵母（Saccharomyces cerevisiae，即面包酵母）及其近缘野生种奇异酿酒酵母（Saccharomyces paradoxus）多个菌株内的核糖体DNA序列变异。值得注意的是，这两个物种均拥有单座位核糖体DNA系统（single locus rDNA systems）。本研究借助这些全新的变异数据集，旨在评估：在控制旁系同源/直系同源分类问题的前提下，对核糖体DNA座位的更精细刻画能否缓解上述第二类系统发育问题——序列异质性（sequence heterogeneity）。我们证实两类数据集内部均存在强烈的系统发育信号，并展示了如何结合现有方法，利用这些数据估算出与全基因组分析结果一致的酵母菌株种内系统发育关系。我们还描述了仅在重复基因组区域中存在的序列变异类型——部分单核苷酸多态性（Single Nucleotide Polymorphisms, SNPs）的应用，其可用于识别基因组杂交事件等关键进化特征，且该结果与全基因组Structure分析结果一致。我们得出结论：本研究方法可将核糖体DNA序列异质性从一个问题转化为极具价值的进化信息来源，从而实现对近缘生物高精度系统发育关系的估算，并讨论了该方法如何拓展至多座位核糖体DNA系统（multi-locus rDNA systems）的未来研究。