Glazko Galina, Makarenkov Vladimir, Liu Jing, Mushegian Arcady
Stowers Institute for Medical Research, 1000 E 50th St,, Kansas City, MO 64110, USA.
Biol Direct. 2007 Dec 6;2:36. doi: 10.1186/1745-6150-2-36.
Reconstruction of evolutionary history of bacteriophages is a difficult problem because of fast sequence drift and lack of omnipresent genes in phage genomes. Moreover, losses and recombinational exchanges of genes are so pervasive in phages that the plausibility of phylogenetic inference in phage kingdom has been questioned.
We compiled the profiles of presence and absence of 803 orthologous genes in 158 completely sequenced phages with double-stranded DNA genomes and used these gene content vectors to infer the evolutionary history of phages. There were 18 well-supported clades, mostly corresponding to accepted genera, but in some cases appearing to define new taxonomic groups. Conflicts between this phylogeny and trees constructed from sequence alignments of phage proteins were exploited to infer 294 specific acts of intergenome gene transfer.
A notoriously reticulate evolutionary history of fast-evolving phages can be reconstructed in considerable detail by quantitative comparative genomics.
由于噬菌体基因组中序列快速漂移以及缺乏普遍存在的基因，重建噬菌体的进化历史是一个难题。此外，基因的丢失和重组交换在噬菌体中非常普遍，以至于噬菌体王国中系统发育推断的合理性受到质疑。
我们汇编了158个具有双链DNA基因组的完全测序噬菌体中803个直系同源基因的有无情况，并使用这些基因含量向量来推断噬菌体的进化历史。共有18个得到充分支持的进化枝，大多对应于已被认可的属，但在某些情况下似乎定义了新的分类群。利用这种系统发育与由噬菌体蛋白质序列比对构建的树之间的冲突来推断294次基因组间基因转移的具体事件。
通过定量比较基因组学，可以相当详细地重建快速进化的噬菌体那众所周知的网状进化历史。
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