Abstract
BackgroundRNA 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.ResultsTwo 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.ConclusionThe 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.
Highlights
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
Comparison to known viral sequences shows that the protein sequence predicted to be encoded by open reading frames (ORFs) 1 of JP-A contains conserved sequence motifs characteristic of a type III viral Helicase, a 3C-like cysteine protease and a type I RNA-dependent RNA polymerase (RdRp) [11] (Figure 1A)
The top matches for ORF 1 were to RsRNAV [E value = 3 × 10-119, identities = 302/908 (33%)], a newly sequenced, unclassified positive-sense single-stranded RNA (ssRNA) virus that infects the widely distributed diatom Rhizosolenia setigera [3], HaRNAV [E value = 2 × 10-32, identities = 156/624 (25%)] and Drosophila C virus [E value = 1 × 10-29, identities = 148/603 (24%)], a positive-sense ssRNA virus that infects fruit flies
Summary
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
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