Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA.
Nat Microbiol. 2017 Jul 10;2:17112. doi: 10.1038/nmicrobiol.2017.112.
Bacteriophages play key roles in microbial evolution, marine nutrient cycling and human disease. Phages are genetically diverse, and their genome architectures are characteristically mosaic, driven by horizontal gene transfer with other phages and host genomes. As a consequence, phage evolution is complex and their genomes are composed of genes with distinct and varied evolutionary histories. However, there are conflicting perspectives on the roles of mosaicism and the extent to which it generates a spectrum of genome diversity or genetically discrete populations. Here, we show that bacteriophages evolve within two general evolutionary modes that differ in the extent of horizontal gene transfer by an order of magnitude. Temperate phages distribute into high and low gene flux modes, whereas lytic phages share only the lower gene flux mode. The evolutionary modes are also a function of the bacterial host and different proportions of temperate and lytic phages are distributed in either mode depending on the host phylum. Groups of genetically related phages fall into either the high or low gene flux modes, suggesting there are genetic as well as ecological drivers of horizontal gene transfer rates. Consequently, genome mosaicism varies depending on the host, lifestyle and genetic constitution of phages.
噬菌体在微生物进化、海洋营养循环和人类疾病中起着关键作用。噬菌体具有遗传多样性，其基因组结构具有明显的镶嵌性，这是由噬菌体与其他噬菌体和宿主基因组之间的水平基因转移驱动的。因此，噬菌体的进化是复杂的，它们的基因组由具有不同进化历史的基因组成。然而，对于镶嵌性的作用以及它在多大程度上产生了一系列的基因组多样性或遗传上离散的种群，存在着相互矛盾的观点。在这里，我们表明噬菌体在两种一般的进化模式中进化，这两种模式在水平基因转移的程度上有很大的不同。温和噬菌体分布在高和低基因通量模式中，而裂解噬菌体只共享低基因通量模式。进化模式也是细菌宿主的一个功能，根据宿主门，不同比例的温和和裂解噬菌体分布在任何一种模式中。遗传上相关的噬菌体群落入高或低基因通量模式，这表明水平基因转移率存在遗传和生态驱动因素。因此，基因组镶嵌性取决于噬菌体的宿主、生活方式和遗传组成。
