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Open Access Research

The complete genomes of three viruses assembled from shotgun libraries of marine RNA virus communities

Alexander I Culley1, Andrew S Lang2 and Curtis A Suttle13*

Author Affiliations

1 University of British Columbia, Department of Botany, 3529-6270 University Blvd, Vancouver, B.C. V6T 1Z4, Canada

2 Department of Biology, Memorial University of Newfoundland, St. John's, NL A1B 3X9, Canada

3 University of British Columbia, Department of Earth and Ocean Sciences, Department of Microbiology and Immunology, 1461-6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada

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Virology Journal 2007, 4:69  doi:10.1186/1743-422X-4-69

Published: 6 July 2007

Abstract

Background

RNA viruses have been isolated that infect marine organisms ranging from bacteria to whales, but little is known about the composition and population structure of the in situ marine RNA virus community. In a recent study, the majority of three genomes of previously unknown positive-sense single-stranded (ss) RNA viruses were assembled from reverse-transcribed whole-genome shotgun libraries. The present contribution comparatively analyzes these genomes with respect to representative viruses from established viral taxa.

Results

Two of the genomes (JP-A and JP-B), appear to be polycistronic viruses in the proposed order Picornavirales that fall into a well-supported clade of marine picorna-like viruses, the characterized members of which all infect marine protists. A temporal and geographic survey indicates that the JP genomes are persistent and widespread in British Columbia waters. The third genome, SOG, encodes a putative RNA-dependent RNA polymerase (RdRp) that is related to the RdRp of viruses in the family Tombusviridae, but the remaining SOG sequence has no significant similarity to any sequences in the NCBI database.

Conclusion

The complete genomes of these viruses permitted analyses that resulted in a more comprehensive comparison of these pathogens with established taxa. For example, in concordance with phylogenies based on the RdRp, our results support a close homology between JP-A and JP-B and RsRNAV. In contrast, although classification of the SOG genome based on the RdRp places SOG within the Tombusviridae, SOG lacks a capsid and movement protein conserved within this family and SOG is thus likely more distantly related to the Tombusivridae than the RdRp phylogeney indicates.