A novel virus genome discovered in an extreme environment suggests recombination between unrelated groups of RNA and DNA viruses

Geoffrey S Diemer,Kenneth M Stedman

doi:10.1186/1745-6150-7-13

Geoffrey S Diemer, Kenneth M Stedman

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https://doi.org/10.1186/1745-6150-7-13

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Journal: Biology Direct	Publication Date: Jan 1, 2012
Citations: 153	License type: cc-by

Affiliation: Portland State University

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BackgroundViruses are known to be the most abundant organisms on earth, yet little is known about their collective origin and evolutionary history. With exceptionally high rates of genetic mutation and mosaicism, it is not currently possible to resolve deep evolutionary histories of the known major virus groups. Metagenomics offers a potential means of establishing a more comprehensive view of viral evolution as vast amounts of new sequence data becomes available for comparative analysis.ResultsBioinformatic analysis of viral metagenomic sequences derived from a hot, acidic lake revealed a circular, putatively single-stranded DNA virus encoding a major capsid protein similar to those found only in single-stranded RNA viruses. The presence and circular configuration of the complete virus genome was confirmed by inverse PCR amplification from native DNA extracted from lake sediment. The virus genome appears to be the result of a RNA-DNA recombination event between two ostensibly unrelated virus groups. Environmental sequence databases were examined for homologous genes arranged in similar configurations and three similar putative virus genomes from marine environments were identified. This result indicates the existence of a widespread but previously undetected group of viruses.ConclusionsThis unique viral genome carries implications for theories of virus emergence and evolution, as no mechanism for interviral RNA-DNA recombination has yet been identified, and only scant evidence exists that genetic exchange occurs between such distinct virus lineages.ReviewersThis article was reviewed by EK, MK (nominated by PF) and AM. For the full reviews, please go to the Reviewers' comments section.

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Viruses are known to be the most abundant organisms on earth, yet little is known about their collective origin and evolutionary history
Initial analysis of the individual metagenomic DNA sequences from virus-sized particles obtained from Boiling Springs Lake (BSL) indicated the presence of a virus capsid protein (CP) gene related to the downy mildew-infecting Sclerophthora macrospora-A (SmV-A) and Plasmopara halstedii-A (PhV-A) viruses [23,24]
The BSL metagenomic sequences were assembled into contigs and, surprisingly, a putative rolling circle replicase protein (Rep) gene most closely related to the circular ssDNA Circoviridae Rep was located immediately upstream of the ssRNA virus-like CP gene

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Viruses are known to be the most abundant organisms on earth, yet little is known about their collective origin and evolutionary history. Given the fact that the paper is about virus evolution, the Background section could provide some information on the current hypotheses on the origin of viruses and the mechanisms of their evolution. This would allow the readers to more fully appreciate the significance of the findings presented in the Results section The authors might find useful the recent reviews on this subject by (Koonin and Dolja, 2011; Krupovic et al, 2011; Forterre and Prangishvili, 2009).

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