Efficient Inference of Recent and Ancestral Recombination within Bacterial Populations.
Efficient Inference of Recent and Ancestral Recombination within Bacterial Populations.
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DOI：
10.1093/molbev/msx066
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发表时间：
2017-05-01
影响因子：
10.7
通讯作者：
Marttinen P
中科院分区：
文献类型：
--
作者：
Mostowy R;Croucher NJ;Andam CP;Corander J;Hanage WP;Marttinen P
原核生物的进化受到遗传物质通过重组进行水平转移的影响。因此，细菌进化树的推断依赖于对种群遗传结构的准确识别和重组衍生的嵌合体。快速增长的数据库对检测细菌基因组中重组的计算方法提出了挑战。我们介绍了一种名为FastGEAR的新算法，它可以识别不同微生物序列中的谱系，以及它们之间的重组和来自外部来源的重组。该算法同时检测最近的重组(影响少数分离株)和检测到的谱系之间的祖先重组(影响整个谱系)，从而提供对影响系统发育树深层分支的重组的洞察。在模拟中，与最先进的方法相比，FastGEAR检测最近重组的能力相当，检测祖先重组的能力突出，计算成本往往只有一小部分。我们通过分析重组病原体肺炎链球菌的616个全基因组集合来证明该方法的实用性，该方法提供了跨基因组重组的高分辨率视图。我们详细研究了整个链球菌属的青霉素结合基因，证明了这三个基因座上不同物种之间以前未检测到的遗传交换。因此，FastGEAR可以很容易地应用于研究跨物种细菌基因的嵌合体。最后，FastGear正确地识别了许多已知的重组热点，并指出了潜在的新热点。MatLab代码和linux/windows可执行文件可以在https://users.ics.aalto.fi/~pemartti/fastGEAR/上找到(最后一次访问是在2017年2月6日)。
Prokaryotic evolution is affected by horizontal transfer of genetic material through recombination. Inference of an evolutionary tree of bacteria thus relies on accurate identification of the population genetic structure and recombination-derived mosaicism. Rapidly growing databases represent a challenge for computational methods to detect recombinations in bacterial genomes. We introduce a novel algorithm called fastGEAR which identifies lineages in diverse microbial alignments, and recombinations between them and from external origins. The algorithm detects both recent recombinations (affecting a few isolates) and ancestral recombinations between detected lineages (affecting entire lineages), thus providing insight into recombinations affecting deep branches of the phylogenetic tree. In simulations, fastGEAR had comparable power to detect recent recombinations and outstanding power to detect the ancestral ones, compared with state-of-the-art methods, often with a fraction of computational cost. We demonstrate the utility of the method by analyzing a collection of 616 whole-genomes of a recombinogenic pathogen Streptococcus pneumoniae, for which the method provided a high-resolution view of recombination across the genome. We examined in detail the penicillin-binding genes across the Streptococcus genus, demonstrating previously undetected genetic exchanges between different species at these three loci. Hence, fastGEAR can be readily applied to investigate mosaicism in bacterial genes across multiple species. Finally, fastGEAR correctly identified many known recombination hotspots and pointed to potential new ones. Matlab code and Linux/Windows executables are available at https://users.ics.aalto.fi/~pemartti/fastGEAR/ (last accessed February 6, 2017).
影响因子：
5.8
作者：
Webb, Alex;Hancock, John M.;Holmes, Chris C.
通讯作者：
Holmes, Chris C.