Abstract
Two genomic fragments (5,662 and 1,269 nt in size, GenBank accession no. JQ756122 and JQ756123, respectively) of novel, positive-strand RNA viruses that infect archaea were first discovered in an acidic hot spring in Yellowstone National Park (Bolduc et al., 2012). To investigate the diversity of these newly identified putative archaeal RNA viruses, global metagenomic datasets were searched for sequences that were significantly similar to those of the viruses. A total of 3,757 associated reads were retrieved solely from the Yellowstone datasets and were used to assemble the genomes of the putative archaeal RNA viruses. Nine contigs with lengths ranging from 417 to 5,866 nt were obtained, 4 of which were longer than 2,200 nt; one contig was 204 nt longer than JQ756122, representing the longest genomic sequence of the putative archaeal RNA viruses. These contigs revealed more than 50% sequence similarity to JQ756122 or JQ756123 and may be partial or nearly complete genomes of novel genogroups or genotypes of the putative archaeal RNA viruses. Sequence and phylogenetic analyses indicated that the archaeal RNA viruses are genetically diverse, with at least 3 related viral lineages in the Yellowstone acidic hot spring environment.Electronic supplementary materialThe online version of this article (doi:10.1186/s40064-015-0973-z) contains supplementary material, which is available to authorized users.
Highlights
Almost all life forms can be infected by viruses
Sequence assembly The nucleotide sequences of the putative archaeal RNA viruses
A pairwise sequence similarity comparison indicated that the assembled contigs in this study shared a similarity of 50 to 99% with JQ756122 or JQ756123 (Figure 2), suggesting the genetic diversity of the putative archaeal RNA viruses in the Yellowstone hot spring
Summary
Thousands of viruses have been identified (King et al 2012). Most of these viruses infect bacteria or eukaryotes. There are an average of 107 viruslike particles per milliliter of surface seawater (Bergh et al 1989), an estimated 5,000 viral genotypes in 200 liters of seawater (Breitbart et al 2002) and at Recently, sequences of putative archaeal RNA viruses were obtained using a metagenomic approach (Bolduc et al 2012). Two contigs were assembled and were demonstrated to be genomes of putative archaeal RNA viruses
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