Systematic inference of highways of horizontal gene transfer in prokaryotes
Systematic inference of highways of horizontal gene transfer in prokaryotes
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DOI：
10.1093/bioinformatics/btt021
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发表时间：
2013-03-01
期刊：
影响因子：
5.8
通讯作者：
Shamir, Ron
中科院分区：
文献类型：
--
作者：
Bansal, Mukul S.;Banay, Guy;Shamir, Ron
动机：水平基因转移（HGT）在原核生物物种的进化中起着至关重要的作用。通常，在任何两个物种之间水平转移的基因不超过几个。然而，有几项研究确定了物种（或谱系）对之间的许多不同的基因水平转移。这样的一对被认为是通过基因共享的高速公路联系在一起的。推断这样的公路是至关重要的了解原核生物的进化和推断过去的共生和生态协会之间的不同species.Results：我们提出了一个新的改进方法，系统地检测公路的基因共享。正如我们使用各种模拟数据集所证明的那样，我们的方法是高度准确和高效的，并且对噪声和高HGT率具有鲁棒性。我们进一步验证了我们的方法，将其应用于已发表的数据集> 22 000基因树从144个原核生物物种。我们的方法使得它实用，第一次，执行准确的高速公路分析快速，轻松地在大型数据集与高HGT率。
Motivation: Horizontal gene transfer (HGT) plays a crucial role in the evolution of prokaryotic species. Typically, no more than a few genes are horizontally transferred between any two species. However, several studies identified pairs of species (or linages) between which many different genes were horizontally transferred. Such a pair is said to be linked by a highway of gene sharing. Inferring such highways is crucial to understanding the evolution of prokaryotes and for inferring past symbiotic and ecological associations among different species.Results: We present a new improved method for systematically detecting highways of gene sharing. As we demonstrate using a variety of simulated datasets, our method is highly accurate and efficient, and robust to noise and high rates of HGT. We further validate our method by applying it to a published dataset of > 22 000 gene trees from 144 prokaryotic species. Our method makes it practical, for the first time, to perform accurate highway analysis quickly and easily even on large datasets with high rates of HGT.