Inferring genomic flux in bacteria
Inferring genomic flux in bacteria
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DOI：
10.1101/gr.082263.108
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发表时间：
2009-02-01
期刊：
影响因子：
7
通讯作者：
Falush, Daniel
中科院分区：
文献类型：
--
作者：
Didelot, Xavier;Darling, Aaron;Falush, Daniel
遗传物质的获得和丢失是细菌微进化的基本力量。它们一再与谱系适应新的生活方式，特别是致病性有关。比较基因组学有可能阐明这种遗传通量，但从基因组序列的集合中推断进化事件涉及许多方法上的挑战。在这里，我们描述了一个基于模型的方法，使用全基因组序列来推断基因组内容的演变模式。我们的模型的一个基本属性是，它允许遗传元素获得或丢失的速率随时间和血统而变化。我们的方法是纯粹基于序列的，不依赖于基因鉴定。我们展示了如何在我们的模型下进行推理，并说明了它在土拉弗朗西斯菌，化脓性链球菌和大肠杆菌的三个数据集上的使用。在这三个例子中，我们发现了遗传物质获得和损失率的有趣变化，这与他们的生活方式密切相关。我们描述的算法是在一个名为GenoPlast的计算机软件中实现的。
Acquisition and loss of genetic material are essential forces in bacterial microevolution. They have been repeatedly linked with adaptation of lineages to new lifestyles, and in particular, pathogenicity. Comparative genomics has the potential to elucidate this genetic flux, but there are many methodological challenges involved in inferring evolutionary events from collections of genome sequences. Here we describe a model-based method for using whole-genome sequences to infer the patterns of genome content evolution. A fundamental property of our model is that it allows the rates at which genetic elements are gained or lost to vary in time and from one lineage to another. Our approach is purely sequence based, and does not rely on gene identification. We show how inference can be performed under our model and illustrate its use on three datasets from Francisella tularensis, Streptococcus pyogenes, and Escherichia coli. In all three examples, we found interesting variations in the rates of genetic material gain and loss, which strongly correlate with their lifestyle. The algorithms we describe are implemented in a computer software named GenoPlast.