Evolution of Pan-Genomes of Escherichia coli, Shigella spp., and Salmonella enterica
Evolution of Pan-Genomes of Escherichia coli, Shigella spp., and Salmonella enterica
复制标题
DOI：
10.1128/jb.02285-12
复制
发表时间：
2013-06-01
影响因子：
3.2
通讯作者：
Gelfand, Mikhail S.
中科院分区：
文献类型：
--
作者：
Gordienko, Evgeny N.;Kazanov, Marat D.;Gelfand, Mikhail S.
对一个细菌物种的基因组进行多次测序，可以分析和比较物种基因互补的统计数据和动态，以及它们的泛基因组。在这里，我们分析了大肠杆菌、志贺氏菌和肠沙门氏菌的多个基因组。我们证明了包含一个基因的基因组数量的分布很好地近似于两个幂函数的和，描述频繁基因（存在于许多菌株中）和罕见基因（存在于少数菌株中）。大肠杆菌基因组中不存在志贺氏菌特异性基因，这证实了先前的观察，即志贺氏菌不是一个独立的属。虽然泛基因组的大小随着每个新菌株的增加而增加，但在固定比例的菌株中存在的基因数量很快稳定下来。例如，在任何一组大肠杆菌基因组中，至少有一半的基因少于4000个。肠道链球菌和大肠杆菌泛基因组的比较显示存在一个共同的外围，即基因存在于某些菌株中，但不是所有菌株中。系统发育树分析表明，来自边缘的罕见基因可能在水平转移下进化，而频繁的边缘基因可能从共同祖先的边缘基因组遗传而来。
Multiple sequencing of genomes belonging to a bacterial species allows one to analyze and compare statistics and dynamics of the gene complements of species, their pan-genomes. Here, we analyzed multiple genomes of Escherichia coli, Shigella spp., and Salmonella enterica. We demonstrate that the distribution of the number of genomes harboring a gene is well approximated by a sum of two power functions, describing frequent genes (present in many strains) and rare genes (present in few strains). The virtual absence of Shigella-specific genes not present in E. coli genomes confirms previous observations that Shigella is not an independent genus. While the pan-genome size is increasing with each new strain, the number of genes present in a fixed fraction of strains stabilizes quickly. For instance, slightly fewer than 4,000 genes are present in at least half of any group of E. coli genomes. Comparison of S. enterica and E. coli pan-genomes revealed the existence of a common periphery, that is, genes present in some but not all strains of both species. Analysis of phylogenetic trees demonstrates that rare genes from the periphery likely evolve under horizontal transfer, whereas frequent periphery genes may have been inherited from the periphery genome of the common ancestor.