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

Geoffrey S Diemer and Kenneth M Stedman*

Author Affiliations

Department of Biology, and the Center for Life in Extreme Environments, Portland State University, 1719 SW 10th Avenue, SRTC room 246, Portland, OR, 97201, USA

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Biology Direct 2012, 7:13  doi:10.1186/1745-6150-7-13

Published: 19 April 2012

Abstract

Background

Viruses 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.

Results

Bioinformatic 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.

Conclusions

This 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.

Reviewers

This article was reviewed by EK, MK (nominated by PF) and AM. For the full reviews, please go to the Reviewers' comments section.

Keywords:
Non-retroviral RNA virus integration; RNA-DNA recombination; Viral metagenomics; Metaviromics; Virus ecology; Viral diversity; Modular theory of virus evolution; Interviral lateral gene transfer; RNA World; DNA World; Virus World