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Genomic and phylogenetic analysis of a single-stranded RNA virus infecting Rhizosolenia setigera (Stramenopiles: Bacillariophyceae)
Shirai, Y.; Takao, Y.; Mizumoto, H.; Tomaru, Y.; Honda, D.; Nagasaki, K. (2006). Genomic and phylogenetic analysis of a single-stranded RNA virus infecting Rhizosolenia setigera (Stramenopiles: Bacillariophyceae). J. Mar. Biol. Ass. U.K. 86(3): 475-483. dx.doi.org/10.1017/S0025315406013373
In: Journal of the Marine Biological Association of the United Kingdom. Cambridge University Press/Marine Biological Association of the United Kingdom: Cambridge. ISSN 0025-3154, more
Peer reviewed article  

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Keywords
    Rhizosolenia setigera Brightwell, 1858 [WoRMS]; Marine

Authors  Top 
  • Shirai, Y.
  • Takao, Y.
  • Mizumoto, H.
  • Tomaru, Y.
  • Honda, D.
  • Nagasaki, K.

Abstract
    We report the first complete genome sequence of the marine diatom-infecting, positive-sense single-stranded RNA (ssRNA) virus, Rhizosolenia setigera RNA virus (RsRNAV). The genome is 8877 nucleotides (nt), polyadenylated, lacking a cap structure, and has two large open reading frames (ORFs): ORF-1 (4818 nt), a polyprotein gene coding for replicases, e.g. RNA helicase, RNA-dependent RNA polymerase (RdRp); and ORF-2 (2883 nt), a polyprotein gene coding for structural proteins. The ORFs are separated by a 323 nt intergenic region (IGR), flanked by a 624 nt 5'-untranslated region (UTR) and a 229 nt 3'-UTR. The deduced amino acid sequences for ORF-1 and ORF-2 respectively show considerable similarities to the non-structural and structural proteins of a marine raphidophyte-infecting virus HaRNAV (Heterosigma akashiwo RNA virus). Phylogenetic analyses of concatenated amino acid sequences of RNA helicase and RdRp domains supported the monophyly of RsRNAV, HaRNAV and a marine protist-infecting virus SssRNAV (Schizochytrium single-stranded RNA virus) with moderate bootstrap values of 79-83%, but not at the family level, whilst their monophyly was only weakly supported (50-55%) in the phylogenetic tree based on RdRp whole domain. As a result, comparison of the genome organization and sequence suggests RsRNAV is not a member of any currently defined virus family. In the RdRp tree, the positive-sense ssRNA viruses infecting Stramenopiles (RsRNAV, HaRNAV and SssRNAV) and Alveolata (HcRNAV (Heterocapsa circularisquama RNA virus)) were categorized into phylogenetically distant clades, which suggests a host/virus coevolution. Our study supports the hypothesis that a diverse array of ssRNA viruses exists in marine environments.

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