Whole genome molecular phylogeny of large dsDNA viruses using composition vector method

Abstract

Background: 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.

Results: 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.

Conclusion: 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.

Figure 1

Tree of 124 large DNA viruses. Phylogenetic analysis of large DNA viruses based on CV method with K-string length K = 5. Altogether 33 genera from 10 families are presented. The nine unclassified dsDNA viruses are indicated by grey. Family names are placed close to the corresponding branches. Note that this is an unrooted tree and the branches are not to scale.

Figure 2

Trees of 4 virus families. Phylogenetic analysis of 4 virus families based on CV method with K-string length K = 5. a: Adenoviridae; b: Baculoviridae; c: Herpesviridae; d: Poxviridae. The unclassified dsDNA viruses are indicated by grey. Genus or subfamily names are placed close to the corresponding branches.