Abstract
The origin and evolution of viruses is a subject of ongoing debate. In this study, we provide a full account of the evolutionary relationships between proteins of significant sequence and structural similarity found in viruses that belong to different classes according to the Baltimore classification. We show that such proteins can be found in viruses from all Baltimore classes. For protein families that include these proteins, we observe two patterns of the taxonomic spread. In the first pattern, they can be found in a large number of viruses from all implicated Baltimore classes. In the other pattern, the instances of the corresponding protein in species from each Baltimore class are restricted to a few compact clades. Proteins with the first pattern of distribution are products of so-called viral hallmark genes reported previously. Additionally, this pattern is displayed by the envelope glycoproteins from Flaviviridae and Bunyaviridae and helicases of superfamilies 1 and 2 that have homologs in cellular organisms. The second pattern can often be explained by horizontal gene transfer from the host or between viruses, an example being Orthomyxoviridae and Coronaviridae hemagglutinin esterases. Another facet of horizontal gene transfer comprises multiple independent introduction events of genes from cellular organisms into otherwise unrelated viruses.
Highlights
IntroductionViruses do not constitute a monophyletic group, in which the phylogenetic history can be traced back to a common ancestor
Unlike cellular organisms, viruses do not constitute a monophyletic group, in which the phylogenetic history can be traced back to a common ancestor
We provide a full account of the evolutionary relationships between proteins of significant sequence and structural similarity found in viruses that belong to different classes according to the Baltimore classification
Summary
Viruses do not constitute a monophyletic group, in which the phylogenetic history can be traced back to a common ancestor. The origin and relatedness of different virus families is currently a subject of active discussion It is unclear whether viruses have evolved by reduction of genes from cellular species, whether they descended from mobile elements of other organisms or whether they precede cellular life and are ancient self-replicating units. All of these hypotheses are true, for a subset of viral families [1]. Retroviruses are considered a separate group that includes DNA- and RNA-encoded viruses It is hypothesized that in certain cases, the conserved viral genes are witnesses of evolutionary processes as ancient as the origin of life itself [7]
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