Department of Biology, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China.
BMC Evol Biol. 2010 Jun 22;10:192. doi: 10.1186/1471-2148-10-192.
The vast sequence divergence among different virus groups has presented a great challenge to alignment-based analysis of virus phylogeny. Due to the problems caused by the uncertainty in alignment, existing tools for phylogenetic analysis based on multiple alignment could not be directly applied to the whole-genome comparison and phylogenomic studies of viruses. There has been a growing interest in alignment-free methods for phylogenetic analysis using complete genome data. Among the alignment-free methods, a dynamical language (DL) method proposed by our group has successfully been applied to the phylogenetic analysis of bacteria and chloroplast genomes.
In this paper, the DL method is used to analyze the whole-proteome phylogeny of 124 large dsDNA viruses and 30 parvoviruses, two data sets with large difference in genome size. The trees from our analyses are in good agreement to the latest classification of large dsDNA viruses and parvoviruses by the International Committee on Taxonomy of Viruses (ICTV).
The present method provides a new way for recovering the phylogeny of large dsDNA viruses and parvoviruses, and also some insights on the affiliation of a number of unclassified viruses. In comparison, some alignment-free methods such as the CV Tree method can be used for recovering the phylogeny of large dsDNA viruses, but they are not suitable for resolving the phylogeny of parvoviruses with a much smaller genome size.
不同病毒群之间巨大的序列差异给基于比对的病毒系统发育分析带来了巨大挑战。由于比对不确定性引起的问题，现有的基于多重比对的系统发育分析工具不能直接应用于病毒全基因组比较和基因组系统发育研究。基于完整基因组数据的无比对方法在系统发育分析中越来越受到关注。在无比对方法中，我们小组提出的动态语言（DL）方法已成功应用于细菌和叶绿体基因组的系统发育分析。
本文使用 DL 方法分析了 124 种大型双链 DNA 病毒和 30 种细小病毒的全蛋白组系统发育关系，这两个数据集的基因组大小差异很大。我们的分析结果与病毒分类国际委员会（ICTV）最新的大型双链 DNA 病毒和细小病毒分类一致。
本方法为大型双链 DNA 病毒和细小病毒的系统发育关系提供了一种新的恢复方法，也为一些未分类病毒的归属提供了一些见解。相比之下，一些无比对方法，如 CV Tree 方法，可用于恢复大型双链 DNA 病毒的系统发育关系，但不适合解析基因组较小的细小病毒的系统发育关系。
