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

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.

Figure 1

Map of southwestern British Columbia, Canada showing locations where samples were collected.Sites in coastal BC waters where the JP-A and JP-B genomes were detected are indicated and labelled. Both JP-A and JP-B were detected in samples from 5 of the 9 stations that were screened. The SOG station was not assayed for JP-A or JP-B. See Table 2 for additional information about the stations.

Figure 2

Analysis of genomes for putative open reading frames. In the ORF maps created with DNA Strider [28], for each reading frame, potential start codons (AUG) are shown with a half-height line and stop codons (UGA, UAA, and UAG) are shown by full-height lines. Recognizable conserved RNA virus protein domains (Hel = helicase, Pro = Protease, RdRp = RNA-dependent RNA polymerase) and other genomic features (UTR = untranslated region, IGR = intergenic region) are noted below each genome. See text for more detail. A. Map of the JP-A genome. B. Map of the JP-B genome. C. Map of the SOG genome.

Figure 3

Bayesian maximum likelihood trees of aligned RdRp amino acid sequences from the JP-A and JP-B genomes and representative members of the proposed order Picornavirales. Bayesian clade credibility values are shown for relevant nodes in boldface followed by bootstrap values based on neighbour-joining analysis. The Bayesian scale bar indicates a distance of 0.1. See Additional file 2 for complete virus names and accession numbers.

Figure 4

Bayesian maximum likelihood trees of aligned concatenated helicase, RdRp and VP3-like capsid amino acid sequences from the JP-A and JP-B genomes and other picorna-like viruses. Bayesian clade credibility values are shown for relevant nodes in boldface followed by bootstrap values based on neighbour-joining analysis. The Bayesian scale bar indicates a distance of 0.1. See Additional file 2 for complete virus names and accession numbers.

Figure 5

Bayesian maximum likelihood trees of aligned RdRp amino acid sequences from the SOG genome and members of the family Tombusviridae and unassigned genus Umbravirus. Bayesian clade credibility values are shown for relevant nodes in boldface followed by bootstrap values based on neighbour-joining analysis. The Bayesian scale bar indicates a distance of 0.1. See Additional file 2 for complete virus names and accession numbers.