Gao Lei, Qi Ji
The Institute of Theoretical Physics, Academia Sinica, Beijing 100080, China.
BMC Evol Biol. 2007 Mar 15;7:41. doi: 10.1186/1471-2148-7-41.
One important mechanism by which large DNA viruses increase their genome size is the addition of modules acquired from other viruses, host genomes or gene duplications. Phylogenetic analysis of large DNA viruses, especially using methods based on alignment, is often difficult due to the presence of horizontal gene transfer events. The recent composition vector approach, not sensitive to such events, is applied here to reconstruct the phylogeny of 124 large DNA viruses.
The results are mostly consistent with the biologist's systematics with only a few outliers and can also provide some information for those unclassified viruses and cladistic relationships of several families.
With composition vector approach we obtained the phylogenetic tree of large DNA viruses, which not only give results comparable to biologist's systematics but also provide a new way for recovering the phylogeny of viruses.
大型DNA病毒增加其基因组大小的一个重要机制是添加从其他病毒、宿主基因组或基因复制中获得的模块。由于存在水平基因转移事件，对大型DNA病毒进行系统发育分析，尤其是使用基于比对的方法，往往很困难。最近的组成向量方法对这类事件不敏感，在此用于重建124种大型DNA病毒的系统发育。
结果大多与生物学家的分类学一致，只有少数异常情况，并且还可以为那些未分类的病毒以及几个科的分支关系提供一些信息。
通过组成向量方法，我们获得了大型DNA病毒的系统发育树，其结果不仅与生物学家的分类学相当，而且为恢复病毒的系统发育提供了一种新方法。
