酿酒酵母转座因子的进化基因组学研究
Evolutionary genomics of transposable elements in Saccharomyces cerevisiae
摘要：
酿酒酵母是研究转座因子基因组学和进化的主要模型系统之一。S.酿酒酵母基因组的研究在完成后不久的几年内导致了对其五个已知转座因子家族（Ty 1-Ty 5）的许多见解。然而，随后的进展，生物信息学工具分析转座因子和基因组序列的多个菌株和酵母物种的最近可用性激发新的调查泰进化的S。啤酒。在这里，我们提供了S中Ty家族的全面系统发育和群体遗传分析。基于S288 c参考基因组中的Ty元件的重新注释，我们发现，以前的注释工作低估了所有已知的家庭泰元素的总拷贝数。此外，我们还鉴定了一个新的Ty 3样元件家族。paradoxus Ty 3 p，其完全由简并的solo LTR组成。LTR序列的系统发育分析鉴定了三个具有短分支、最近活跃的进化枝嵌套在长分支、非活性插入中的家族（Ty 1、Ty 3、Ty 4），一个具有基本上所有最近活跃的元件的家族（Ty 2）和两个仅具有非活性元件的家族（Ty 3 p和Ty 5）。来自另外38株S.酿酒酵母表明，存在于活性进化枝中的元素主要是多态性的，而大多数非活性元素是固定的。最后，我们使用比较基因组数据提供证据，Ty 2和Ty 3 p家族已经出现在S。酿酒酵母基因组水平转移。我们的研究结果表明，一个单一的个人的基因组包含重要的信息TE种群动力学的状态在一个物种，并建议水平转移可能发挥重要作用，在单细胞真核生物中的转座因子的多样性的塑造。
英文摘要：
Saccharomyces cerevisiae is one of the premier model systems for studying the genomics and evolution of transposable elements. The availability of the S. cerevisiae genome led to many insights into its five known transposable element families (Ty1-Ty5) in the years shortly after its completion. However, subsequent advances in bioinformatics tools for analysing transposable elements and the recent availability of genome sequences for multiple strains and species of yeast motivates new investigations into Ty evolution in S. cerevisiae. Here we provide a comprehensive phylogenetic and population genetic analysis of Ty families in S. cerevisiae based on a reannotation of Ty elements in the S288c reference genome. We show that previous annotation efforts have underestimated the total copy number of Ty elements for all known families. In addition, we identify a new family of Ty3-like elements related to the S. paradoxus Ty3p which is composed entirely of degenerate solo LTRs. Phylogenetic analyses of LTR sequences identified three families with short-branch, recently active clades nested among long branch, inactive insertions (Ty1, Ty3, Ty4), one family with essentially all recently active elements (Ty2) and two families with only inactive elements (Ty3p and Ty5). Population genomic data from 38 additional strains of S. cerevisiae show that elements present in active clades are predominantly polymorphic, whereas most of the inactive elements are fixed. Finally, we use comparative genomic data to provide evidence that the Ty2 and Ty3p families have arisen in the S. cerevisiae genome by horizontal transfer. Our results demonstrate that the genome of a single individual contains important information about the state of TE population dynamics within a species and suggest that horizontal transfer may play an important role in shaping the diversity of transposable elements in unicellular eukaryotes.
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