Rokyta D R, Burch C L, Caudle S B, Wichman H A
Department of Biological Sciences, University of Idaho, Moscow, ID 83844-3051, USA.
J Bacteriol. 2006 Feb;188(3):1134-42. doi: 10.1128/JB.188.3.1134-1142.2006.
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 phiX174, 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.
噬菌体基因组进化在很大程度上以涉及同源和非同源来源DNA的猖獗、混杂的水平基因转移为特征。这种模式是通过对有尾双链DNA（dsDNA）噬菌体的研究得出的，并且基于对这些噬菌体巨大多样性的稀疏采样。微小病毒科的单链DNA噬菌体，包括φX174，似乎通过性质不同的机制进化，这可能是由于它们严格的裂解生活方式和小基因组大小。然而，这种明显的差异可能仅仅反映了相关数据的缺乏。我们试图描述促成微小病毒科分子进化的力量，并通过对在单个细菌宿主上分离的微小病毒噬菌体的基因组进行测序，来研究这个单一噬菌体家族的遗传结构。微小病毒在我们环境样本中可检测到的噬菌体中占3.5%，测序产生了42个新的微小病毒基因组。对这些以及五个先前描述的微小病毒噬菌体中所含基因的系统发育分析确定了三个不同的进化枝，并揭示了进化枝之间至少有两次水平转移事件。一个进化枝的所有成员都有一组五个推定基因，而其他两个进化枝的任何成员都没有。我们的数据表明水平转移确实促成了微小病毒的进化，但在数量和质量上都与dsDNA噬菌体所观察到的情况不同。
