Horizontal gene transfer and the evolution of microvirid coliphage genomes
Horizontal gene transfer and the evolution of microvirid coliphage genomes
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DOI：
10.1128/jb.188.3.1134-1142.2006
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发表时间：
2006-02-01
影响因子：
3.2
通讯作者：
Wichman, HA
中科院分区：
文献类型：
--
作者：
Rokyta, DR;Burch, CL;Wichman, HA
噬菌体基因组进化的主要特征是涉及同源和非同源源 DNA 的猖獗、混杂的水平基因转移。这种模式是通过对有尾双链 DNA (dsDNA) 噬菌体的研究而出现的，并且基于对这些噬菌体的巨大多样性的稀疏采样。微病毒科的单链 DNA 噬菌体，包括 phi X174，似乎通过性质不同的机制进化，可能是由于它们严格的裂解生活方式和较小的基因组大小。然而，这种明显的差异可能仅仅反映了相关数据的缺乏。我们试图描述促进微病毒科分子进化的力量，并通过对单个细菌宿主上分离的微病毒噬菌体的基因组进行测序来检查这个噬菌体单一家族的遗传结构。在我们的环境样本中，微病毒占可检测噬菌体的 3.5%，测序产生了 42 个新的微病毒基因组。对这些噬菌体和之前描述的五种微病毒噬菌体中包含的基因进行系统发育分析，鉴定出三个不同的进化枝，并揭示了进化枝之间至少两个水平转移事件。一个进化枝的所有成员都具有由五个推定基因组成的块，这些基因在其他两个进化枝的任何成员中都不存在。我们的数据表明，水平转移确实有助于微病毒的进化，但在数量和质量上都与在 dsDNA 噬菌体中观察到的不同。
Bacteriophage genomic evolution has been largely characterized by rampant, promiscuous horizontal gene transfer involving both homologous and nonhomologous source DNA. This pattern has emerged through study of the tailed double-stranded DNA (dsDNA) phages and is based upon a sparse sampling of the enormous diversity of these phages. The single-stranded DNA phages of the family Microviridae, including phi X174, appear to evolve through qualitatively different mechanisms, possibly as result of their strictly lytic lifestyle and small genome size. However, this apparent difference could reflect merely a dearth of relevant data. We sought to characterize the forces that contributed to the molecular evolution of the Microviridae and to examine the genetic structure of this single family of bacteriophage by sequencing the genomes of microvirid phage isolated on a single bacterial host. Microvirids comprised 3.5% of the detectable phage in our environmental samples, and sequencing yielded 42 new microvirid genomes. Phylogenetic analysis of the genes contained in these and five previously described microvirid phages identified three distinct clades and revealed at least two horizontal transfer events between clades. All members of one clade have a block of five putative genes that are not present in any member of the other two clades. Our data indicate that horizontal transfer does contribute to the evolution of the microvirids but is both quantitatively and qualitatively different from what has been observed for the dsDNA phages.