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Identification of RNA Virus-Derived RdRp Sequences in Publicly Available Transcriptomic Data Sets.

Published version
Peer-reviewed

Type

Article

Change log

Authors

Abstract

RNA viruses are abundant and highly diverse and infect all or most eukaryotic organisms. However, only a tiny fraction of the number and diversity of RNA virus species have been catalogued. To cost-effectively expand the diversity of known RNA virus sequences, we mined publicly available transcriptomic data sets. We developed 77 family-level Hidden Markov Model profiles for the viral RNA-dependent RNA polymerase (RdRp)-the only universal "hallmark" gene of RNA viruses. By using these to search the National Center for Biotechnology Information Transcriptome Shotgun Assembly database, we identified 5,867 contigs encoding RNA virus RdRps or fragments thereof and analyzed their diversity, taxonomic classification, phylogeny, and host associations. Our study expands the known diversity of RNA viruses, and the 77 curated RdRp Profile Hidden Markov Models provide a useful resource for the virus discovery community.

Description

Keywords

Orthomyxoviridae, RNA virus, RdRp, pHMM, splicing, virus discovery, Transcriptome, RNA Viruses, RNA-Dependent RNA Polymerase, Phylogeny, RNA, Viral, Genome, Viral

Journal Title

Mol Biol Evol

Conference Name

Journal ISSN

0737-4038
1537-1719

Volume Title

40

Publisher

Oxford University Press (OUP)
Sponsorship
Wellcome Trust (106207/Z/14/Z)
Wellcome Trust (220814/Z/20/Z)
European Research Council (646891)