Expansion of known ssRNA phage genomes: from tens to over a thousand

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dc.contributor.authorCallanan, Julieen
dc.contributor.authorStockdale, Stephen R.en
dc.contributor.authorStockdale, Stephen R.en
dc.contributor.authorDraper, Lorraine A.en
dc.contributor.authorRoss, R. Paulen
dc.contributor.authorHill, Colinen
dc.contributor.funderScience Foundation Irelanden
dc.date.accessioned2024-03-26T09:34:16Z
dc.date.available2024-03-26T09:34:16Z
dc.date.issued2020en
dc.description.abstractThe first sequenced genome was that of the 3569-nucleotide single-stranded RNA (ssRNA) bacteriophage MS2. Despite the recent accumulation of vast amounts of DNA and RNA sequence data, only 12 representative ssRNA phage genome sequences are available from the NCBI Genome database (June 2019). The difficulty in detecting RNA phages in metagenomic datasets raises questions as to their abundance, taxonomic structure, and ecological importance. In this study, we iteratively applied profile hidden Markov models to detect conserved ssRNA phage proteins in 82 publicly available metatranscriptomic datasets generated from activated sludge and aquatic environments. We identified 15,611 nonredundant ssRNA phage sequences, including 1015 near-complete genomes. This expansion in the number of known sequences enabled us to complete a phylogenetic assessment of both sequences identified in this study and known ssRNA phage genomes. Our expansion of these viruses from two environments suggests that they have been overlooked within microbiome studiesen
dc.description.statusPeer revieweden
dc.description.versionPublished Versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.citationCallanan, J., Stockdale, S.R., Shkoporov, A., Draper, L.A., Ross, R.P. and Hill, C. (2020) ‘Expansion of known ssRNA phage genomes: From tens to over a thousand’, Science Advances, 6(6), (8pp). doi: 10.1126/sciadv.aay5981en
dc.identifier.doi10.1126/sciadv.aay5981en
dc.identifier.endpage8en
dc.identifier.issued6en
dc.identifier.journaltitleScience Advancesen
dc.identifier.startpage1en
dc.identifier.urihttps://hdl.handle.net/10468/15699
dc.identifier.volume6en
dc.language.isoenen
dc.publisherAmerican Association for the Advancement of Scienceen
dc.relation.projectinfo:eu-repo/grantAgreement/SFI/SFI Research Centres/12/RC/2273/IE/Alimentary Pharmabiotic Centre (APC) - Interfacing Food & Medicine/en
dc.rights© 2020 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC)en
dc.rights.urihttps://creativecommons.org/licenses/by-nc/4.0/en
dc.subjectssRNA phage genomesen
dc.subjectMetatranscriptomic datasets
dc.titleExpansion of known ssRNA phage genomes: from tens to over a thousanden
dc.typeArticle (peer-reviewed)en
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