Evolutionary genomics of transposable elements in Saccharomyces cerevisiae.
Evolutionary genomics of transposable elements in Saccharomyces cerevisiae.
复制标题
酿酒酵母转座元件的进化基因组学。
DOI：
10.1371/journal.pone.0050978
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Bergman CM
中科院分区：
文献类型：
--
作者：
Carr M;Bensasson D;Bergman CM
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。酿酒酵母基因组的可用性使得在完成后不久，人们对其五个已知的转座元件家族（LTR反转录转座子Ty1-Ty5）有了前所未有的了解。然而，用于分析转座因子的生物信息学工具的后续进展，以及最近酵母多菌株和多种基因组序列的可用性，促使人们对酿酒酵母的Ty进化进行新的研究。在此，我们基于S288c参考基因组中Ty元素的系统重新注释，对酿酒酵母所有Ty家族进行了全面的系统发育和群体遗传分析。我们表明，以前的注释工作低估了所有已知族的Ty元素的总拷贝数。此外，我们还发现了一个与S. paradoxus Ty3p有关的ty3样元素的新家族，它完全由简并的单ltr组成。LTR序列的系统发育分析发现，有3个家族（Ty1、Ty3、Ty4）具有短分支、最近活跃的分支嵌套在长分支、不活跃的插入中，一个家族（Ty2）具有几乎所有最近活跃的元件，两个家族（Ty3p和Ty5）只有不活跃的元件。来自另外38个酿酒酵母菌株的群体基因组数据表明，S288c参考基因组中的大部分Ty插入在该物种中是固定的，在活跃枝上的插入主要是多态性的，而在不活跃枝上的插入主要是固定的。最后，我们利用比较基因组数据提供了证据，证明酿酒葡萄球菌基因组中的Ty2和Ty3p家族是通过水平转移产生的。我们的研究结果表明，单个个体的基因组包含有关物种内TE种群动态状态的重要信息，并表明水平转移可能在单细胞真核生物中形成转座因子的基因组多样性中起重要作用。
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 unprecedented insights into its five known transposable element families (the LTR retrotransposons 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 all Ty families in S. cerevisiae based on a systematic re-annotation 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 the majority of Ty insertions in the S288c reference genome are fixed in the species, with insertions in active clades being predominantly polymorphic and insertions in inactive clades being predominantly 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 genomic diversity of transposable elements in unicellular eukaryotes.
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影响因子：
64.8
作者：
Dymond, Jessica S.;Richardson, Sarah M.;Coombes, Candice E.;Babatz, Timothy;Muller, Heloise;Annaluru, Narayana;Blake, William J.;Schwerzmann, Joy W.;Dai, Junbiao;Lindstrom, Derek L.;Boeke, Annabel C.;Gottschling, Daniel E.;Chandrasegaran, Srinivasan;Bader, Joel S.;Boeke, Jef D.
通讯作者：
Boeke, Jef D.
影响因子：
3.4
作者：
Bensasson D
通讯作者：
Bensasson D
DOI：
10.1073/pnas.0702552104
发表时间：
2007-07-03
影响因子：
11.1
作者：
Bergman, Casey M.;Bensasson, Douda
通讯作者：
Bensasson, Douda
DOI：
10.1073/pnas.1103665108
发表时间：
2011-12-20
影响因子：
11.1
作者：
Baller, Joshua A.;Gao, Jiquan;Voytas, Daniel F.
通讯作者：
Voytas, Daniel F.
影响因子：
12.3
作者：
Bartolomé C;Bello X;Maside X
通讯作者：
Maside X