PhyloMCL: Accurate clustering of hierarchical orthogroups guided by phylogenetic relationship and inference of polyploidy events
PhyloMCL: Accurate clustering of hierarchical orthogroups guided by phylogenetic relationship and inference of polyploidy events
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PhyloMCL：由系统发育关系和多倍体事件推断指导的分层直系群的准确聚类
DOI：
10.1111/2041-210x.13401
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发表时间：
2020-06
影响因子：
6.6
通讯作者：
Qi Ji
中科院分区：
文献类型：
--
作者：
Zhou Shengyu;Chen Yamao;Guo Chunce;Qi Ji
同源关系的鉴定对于推断基因功能、检测基因家族的系统发育、发现生命的进化史至关重要，通常是许多遗传和基因组研究的第一步。然而，基因重复的存在，同系物进化速率的变化，基因的融合和裂变，可能导致同系物之间进化关系的错误识别。本文提出了一种基于马尔可夫聚类的方法，称为PhyloMCL，通过考虑生物的系统发育关系和多倍体事件的影响，精确检测包括同源物和相似物在内的等级正类群（hog），这些正类群是由相关物种形成后的重复产生的。通过基准基因家族列表对其性能进行评估，将其应用于来自12个后生动物基因组的hog聚类，召回率和准确率分别达到87.8%和83.2%。进一步应用PhyloMCL对种子植物进化过程中多次多倍体事件产生的成千上万个类似性进行分类，成功地识别了大多数不同分类水平的同源性。利用Markov聚类策略和物种树的指导，PhyloMCL可以在可承受的时间内对数百万个同源基因进行准确分类，满足了测序基因组快速增加对系统基因组研究的挑战。
Identification of homology relationships is essential for inferring gene functions, detecting phylogeny of gene families, discovering evolutionary history of life, and usually, is the first step of many genetic and genomic studies. However, the presence of gene duplicates, variation on evolutionary rates of homologs, fusion and fission of genes, can lead to misidentification of evolutionary relationships among homologs. Here we provide a Markov clustering based method called PhyloMCL to accurately detect hierarchical orthogroups (HOGs) including orthologs and paralogs, which derived from duplications subsequent to speciation of involved species, by considering both phylogenetic relationship of organisms and effects of polyploidy events. Its performance, evaluated by a list of benchmark gene families, when applying to the clustering of HOGs from 12 Metazoan genomes, reaches up to 87.8% and 83.2% on recall and precision rates respectively. Further application of PhyloMCL on classification of tens of thousands of paralogs, yielded by multiple polyploidy events during evolution of seed plants, successfully identifies the majority of in‐/out‐paralogs at different taxonomic levels. Benefiting from the strategy of Markov clustering and guidance of species tree, PhyloMCL can accurately classify millions of homologous genes with affordable time, meeting the challenge of phylogenomic studies upon rapid increasing of sequenced genomes.
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发表时间：
2002-07
影响因子：
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作者：
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通讯作者：
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DOI：
10.1073/pnas.0908007107
发表时间：
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影响因子：
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