Abstract
BackgroundThe Nucleo-Cytoplasmic Large DNA Viruses (NCLDV) constitute an apparently monophyletic group that consists of at least 6 families of viruses infecting a broad variety of eukaryotic hosts. A comprehensive genome comparison and maximum-likelihood reconstruction of the NCLDV evolution revealed a set of approximately 50 conserved, core genes that could be mapped to the genome of the common ancestor of this class of eukaryotic viruses.ResultsWe performed a detailed phylogenetic analysis of these core NCLDV genes and applied the constrained tree approach to show that the majority of the core genes are unlikely to be monophyletic. Several of the core genes have been independently acquired from different sources by different NCLDV lineages whereas for the majority of these genes displacement by homologs from cellular organisms in one or more groups of the NCLDV was demonstrated.ConclusionsA detailed study of the evolution of the genomic core of the NCLDV reveals substantial complexity and diversity of evolutionary scenarios that was largely unsuspected previously. The phylogenetic coherence between the core genes is sufficient to validate the hypothesis on the evolution of all NCLDV from a common ancestral virus although the set of ancestral genes might be smaller than previously inferred from patterns of gene presence-absence.
Highlights
The Nucleo-Cytoplasmic Large DNA Viruses (NCLDV) constitute an apparently monophyletic group that consists of at least 6 families of viruses infecting a broad variety of eukaryotic hosts
We present the results of this analysis which suggest that, the existence of a common ancestor of the NCLDV is beyond reasonable doubt, most of the conserved NCLDV genes had complex evolutionary histories
Approach and rationale Maximum likelihood reconstruction of the gene repertoire of the putative ancestral NCLDV has revealed a core consisting of approximately 50 viral genes (Table 1)
Summary
The Nucleo-Cytoplasmic Large DNA Viruses (NCLDV) constitute an apparently monophyletic group that consists of at least 6 families of viruses infecting a broad variety of eukaryotic hosts. Not a single gene is conserved in the genomes of all known viruses a small group of “viral hallmark genes” encoding some of the key proteins involved in genome replication and virion structure formation are shared by large, diverse subsets of viruses [1,2]. Several large groups of viruses infecting diverse hosts do appear to share common ancestry in the strict sense, that is, to have evolved from the same ancestral virus, as indicated by the conservation of sets of genes encoding proteins responsible for many functions essential for virus reproduction. Hereinafter we speak of 7 NCLDV families for the sake of simplicity
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