Abstract
BackgroundOne 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.ResultsThe 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.ConclusionWith 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.
Highlights
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
We present here a phylogenetic analysis of large DNA viruses with the Composition Vector (CV) method [20,27,28] and discuss their relationships at a deep level
Phylogenetic relationships of all 124 dsDNA viruses coming from 33 genera, 10 families are well consistent with the taxonomy by International Committee on the Taxonomy of Viruses (ICTV) [1] and other phylogenetic studies [9] with few exceptions
Summary
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. Infectious, obligate intracellular parasites that are capable of replicating themselves within their host cells. They are even smaller than the smallest elementary biosystem, yet still possess some properties of living systems such as having a genome and the ability to adapt to changing environments. Viruses were characterized by morphological features including capsid size, shape, structure, etc., as well as physicochemical and antigenic properties. The virus taxonomy system is approved and updated by the International Committee on the Taxonomy of Viruses (ICTV)
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