Whole-genome phylogeny of Escherichia coli/Shigella group by feature frequency profiles (FFPs)
Whole-genome phylogeny of Escherichia coli/Shigella group by feature frequency profiles (FFPs)
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DOI：
10.1073/pnas.1105168108
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发表时间：
2011-05-17
影响因子：
11.1
通讯作者：
Kim, Sung-Hou
中科院分区：
文献类型：
--
作者：
Sims, Gregory E.;Kim, Sung-Hou
利用特征频率谱（FFP）方法构建了大肠杆菌/志贺菌群的全基因组同源基因。该方法使用全基因组的l-mer特征的频率来推断同源距离。我们提出了两个强调不同方面的E。大肠杆菌/志贺氏菌基因组进化：（i）一个基于长度l = 24的所有可能特征的组合物一种是基于低频率、低变异性的核心特征的组合，另一种是基于低频率、低变异性的核心特征的组合（相似的56万个特征），占所研究的38个分类群中所有共有特征的69%，可能具有全基因组的线性进化信号。志贺氏菌出现作为一个单一的分支时，所有可能的功能，没有过滤的非核心功能。然而，使用核心功能的结果表明，志贺菌至少有两个远亲的亚支，这意味着亚支进化成一个单一的分支，因为高度的收敛影响的移动的遗传因素和生态位适应。在两株FFP树中，E.大肠杆菌/志贺菌是B2群，主要由泌尿系致病菌组成，提示大肠杆菌/志贺菌是泌尿系致病菌。大肠杆菌/志贺氏菌祖先可能是兼性或机会致病菌。现存的真菌菌株分化相对较晚，似乎是基因组还原进化的结果。我们还确定了分支的区别特征和它们相关的基因组区域内的每一个基因组。这些特征可以提供有用的信息，用于理解组的演化和用于快速诊断识别每个组。
A whole-genome phylogeny of the Escherichia coli/Shigella group was constructed by using the feature frequency profile (FFP) method. This alignment-free approach uses the frequencies of l-mer features of whole genomes to infer phylogenic distances. We present two phylogenies that accentuate different aspects of E. coli/Shigella genomic evolution: (i) one based on the compositions of all possible features of length l = 24 (similar to 8.4 million features), which are likely to reveal the phenetic grouping and relationship among the organisms and (ii) the other based on the compositions of core features with low frequency and low variability (similar to 0.56 million features), which account for similar to 69% of all commonly shared features among 38 taxa examined and are likely to have genome-wide lineal evolutionary signal. Shigella appears as a single clade when all possible features are used without filtering of noncore features. However, results using core features show that Shigella consists of at least two distantly related subclades, implying that the subclades evolved into a single clade because of a high degree of convergence influenced by mobile genetic elements and niche adaptation. In both FFP trees, the basal group of the E. coli/Shigella phylogeny is the B2 phylogroup, which contains primarily uropathogenic strains, suggesting that the E. coli/Shigella ancestor was likely a facultative or opportunistic pathogen. The extant commensal strains diverged relatively late and appear to be the result of reductive evolution of genomes. We also identify clade distinguishing features and their associated genomic regions within each phylogroup. Such features may provide useful information for understanding evolution of the groups and for quick diagnostic identification of each phylogroup.