Considering transposable element diversification in de novo annotation approaches.
Considering transposable element diversification in de novo annotation approaches.
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DOI：
10.1371/journal.pone.0016526
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发表时间：
2011-01-31
期刊：
影响因子：
3.7
通讯作者：
Quesneville H
中科院分区：
文献类型：
--
作者：
Flutre T;Duprat E;Feuillet C;Quesneville H
转座因子是一种移动的重复DNA序列，在原核和真核生物基因组中普遍存在。它们对基因组结构、功能和进化有很大影响。随着近年来高通量测序方法的发展，许多基因组序列已变得可用，使得在前所未有的规模上进行TE动力学的比较研究成为可能。已经提出了几种方法用于在测序的基因组中重新鉴定TE。大多数开始与基因组重复的检测，但随后的步骤定义TE家庭不同。高质量的TE注释可用于果蝇和拟南芥基因组序列，为此类方法的基准测试提供了坚实的基础。我们比较了特定算法的性能，为散布的重复序列的聚类，发现只有一个特定的组合算法检测TE家庭与良好的恢复的参考序列。然后，我们采用了一种新的程序，用于协调不同的聚类结果和分类TE序列。整个方法是使用REPET包在管道中实现的。最后，我们表明，我们的组合方法突出了明确定义的TE家族的动态，使其有可能确定其副本之间的结构变异。这种方法使得有可能注释TE家庭和研究他们的多样化在一个单一的分析，提高我们的理解TE动态在全基因组规模和不同的物种。
Transposable elements (TEs) are mobile, repetitive DNA sequences that are almost ubiquitous in prokaryotic and eukaryotic genomes. They have a large impact on genome structure, function and evolution. With the recent development of high-throughput sequencing methods, many genome sequences have become available, making possible comparative studies of TE dynamics at an unprecedented scale. Several methods have been proposed for the de novo identification of TEs in sequenced genomes. Most begin with the detection of genomic repeats, but the subsequent steps for defining TE families differ. High-quality TE annotations are available for the Drosophila melanogaster and Arabidopsis thaliana genome sequences, providing a solid basis for the benchmarking of such methods. We compared the performance of specific algorithms for the clustering of interspersed repeats and found that only a particular combination of algorithms detected TE families with good recovery of the reference sequences. We then applied a new procedure for reconciling the different clustering results and classifying TE sequences. The whole approach was implemented in a pipeline using the REPET package. Finally, we show that our combined approach highlights the dynamics of well defined TE families by making it possible to identify structural variations among their copies. This approach makes it possible to annotate TE families and to study their diversification in a single analysis, improving our understanding of TE dynamics at the whole-genome scale and for diverse species.
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