Ribosomal DNA sequence heterogeneity reflects intraspecies phylogenies and predicts genome structure in two contrasting yeast species.
Ribosomal DNA sequence heterogeneity reflects intraspecies phylogenies and predicts genome structure in two contrasting yeast species.
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DOI：
10.1093/sysbio/syu019
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发表时间：
2014-07
影响因子：
6.5
通讯作者：
Roberts IN
中科院分区：
文献类型：
--
作者：
West C;James SA;Davey RP;Dicks J;Roberts IN
核糖体RNA封装了丰富的进化信息，包括遗传变异，可用于在广泛的分类水平上区分生物体。例如，原核生物的16S rDNA序列在系统发育研究和宏基因组调查中都被广泛使用，而植物系统发育中经常使用的内部转录间隔区现在被认为是真菌DNA条形码。然而，这种广泛的使用并没有逃脱批评，主要是由于诸如同源与同源rDNA单位的分类困难和基因组内变异等问题，这两者都可能是准确的系统发育推断的重大障碍。我们最近分析了来自Saccharomyces Genome Resequencing Project的数据集，以前所未有的细节描述了多种烘焙酵母（Saccharomyces cerevisiae）及其最近的野生亲戚Saccharomyces paradoxus的rDNA序列变化。值得注意的是，这两个物种都具有单位点rDNA系统。在这里，我们使用这些新的变异数据集来评估更详细的rDNA位点特征是否可以缓解第二个系统发育问题，序列异质性，同时控制第一个问题。我们证明了在这两个数据集中存在一个强大的系统发育信号，并说明了如何使用现有的方法来估计与全基因组方法一致的酵母菌株的种内系统发育。我们还描述了部分单核苷酸多态性的使用，这是一种仅在重复基因组区域中发现的序列变异，用于识别基因组杂交事件等关键进化特征，并显示其与全基因组结构分析的一致性。我们得出的结论是，我们的方法可以将rDNA序列异质性从一个问题转化为一个有用的进化信息来源，从而能够高度准确地估计密切相关生物的系统发育，并讨论如何将其扩展到未来的多位点rDNA系统研究中。[协同进化;基因组hydridisation;系统发育分析;核糖体DNA;全基因组测序；酵母)
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 internal transcribed spacer region, frequently used in plant phylogenetics, is now recognized 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 analyzed data sets from the Saccharomyces Genome Resequencing Project, characterizing 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 characterization 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 intraspecies 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 hybridization 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 multilocus rDNA systems. [concerted evolution; genome hydridisation; phylogenetic analysis; ribosomal DNA; whole genome sequencing; yeast]
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DOI：
10.1099/00207713-50-3-1351
发表时间：
2000-05-01
影响因子：
2.8
作者：
Fell, JW;Boekhout, T;Statzell-Tallman, A
通讯作者：
Statzell-Tallman, A
影响因子：
10.7
作者：
Bryant, D;Moulton, V
通讯作者：
Moulton, V
影响因子：
10.7
作者：
SAITOU, N;NEI, M
通讯作者：
NEI, M
影响因子：
5.8
作者：
Stamatakis, Alexandros
通讯作者：
Stamatakis, Alexandros
影响因子：
1.9
作者：
BALDWIN, BG;SANDERSON, MJ;DONOGHUE, MJ
通讯作者：
DONOGHUE, MJ