title: A novel virus genome discovered in an extreme environment suggests recombination between unrelated groups of RNA and DNA viruses.
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.
  
  
  METHODS
  This article was reviewed by EK, MK (nominated by PF) and AM. For the full reviews, please go to the Reviewers' comments section.
authors.affiliation: 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.
authors.forename: Geoffrey S
authors.initials: GS
authors.lastname: Diemer
authors.forename: Kenneth M
authors.initials: KM
authors.lastname: Stedman
mesh_terms: D000595:Amino Acid Sequence; D002140:California; D004267:DNA Viruses / Q000235:genetics*; D004783:Environmental Microbiology; D016679:Genome, Viral / Q000235:genetics*; D045482:Hot Springs / Q000821:virology; D060106:Lakes / Q000821:virology; D010802:Phylogeny; D012328:RNA Viruses / Q000235:genetics*; D011995:Recombination, Genetic / Q000235:genetics*; D016415:Sequence Alignment; D014764:Viral Proteins / Q000737:chemistry / Q000235:genetics
chemical_list: D014764:Viral Proteins