Molecular characterisation of a novel recombinant Ribgrass mosaic virus strain FSHS
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Molecular characterisation of a novel recombinant Ribgrass mosaic virus strain FSHS Ramesh R. Chavan and Michael N. Pearson*
Abstract Background: The genus Tobamovirus (Virgaviridae) comprises 33 accepted species with the recent addition of eight new viruses and is divided in to three subgroups based on the origin of assembly of the virion and host range. Within the subgroup 1 tobamoviruses the orchid-associated tobamovirus was hypothesized to be a chimeric derivative of recombinations between genome fragments from subgroup 3 and 1. Recombination events involving RdRp, movement and coat protein genes are recorded within subgroup 1 and 2. However natural recombinations have not previously been reported between subgroup 3 tobamoviruses. Findings: The organization and phylogenetic analyses of the complete genome and the different ORFs placed the new isolate within the Ribgrass mosaic virus clade of subgroup 3 tobamoviruses. Recombination detection analyses indicated that the isolate was a chimeric genome with fragments of high similarity to Ribgrass mosaic virus (RMV) strains NZ-439 (HQ667978) and Actinidia-AC (GQ401365.1) infecting herbaceous Plantago sp. and woody Actinidia spp., respectively. The recombinant differed across the whole genome by 3-8 % from other published RMV genomes. Conclusion: In this investigation we report an intra-specific recombination between RMV strains NZ-439 (HQ667978) and Actinidia-AC (GQ401365.1), in the replicase component between viral-methyltransferase and viral-helicase regions, resulting in a novel RMV strain FSHS (JQ319720.1) that represents the first described natural recombinant within the RMV cluster of subgroup 3 tobamoviruses. Keywords: RMV, RMV cluster, Subgroup 3 tobamovirus, Recombination detection analysis, Plantago, Actinidia
Body of text The viruses of the genus Tobamovirus (http://ictvonline.org/ virusTaxonomy.asp) that exhibit co-divergence and hostswitching have a widespread geographical distribution, an extensive host range and prevail even in abiotic natural ecosystems [8, 15, 21, 24]. Subgroup 1 tobamoviruses mostly infect solanaceous species, with the exception of the orchid infecting Odontoglossum ringspot virus (ORSV). The subgroup 2 viruses are highly diverse infecting members of Cactaceae, Cucurbitaceae, Fabaceae, Malvaceae and Passifloraceae, showing host range specificity and serological relatedness that may prelude an increased number of subgroups [14]. Subgroup 3 includes crucifer and plantain infecting viruses. In subgroup 1 the * Correspondence: [email protected] School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland, New Zealand
origin-of-assembly (OA) is located in the movement protein (ORF3), while in subgroup 2 it is in the coat protein (ORF4) and in subgroup 3 it’s located in the overlap between ORF3 and ORF4 [8, 15]. The subgroup 3 tobamoviruses are further classified into Ribgrass mosaic virus (RMV), Turnip vein clearing virus (TVCV) and Youcai mosaic virus (YoMV) clusters, based
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