Expansion of the global RNA virome reveals diverse clades of bacteriophages

Neri, Uri, Wolf, Yuri I., Roux, Simon, Camargo, Antonio Pedro, Lee, Benjamin, Kazlauskas, Darius, Chen, I. Min, Ivanova, Natalia, Zeigler Allen, Lisa, Paez-Espino, David, Bryant, Donald A., Bhaya, Devaki, Krupovic, Mart, Dolja, Valerian V., Kyrpides, Nikos C., Koonin, Eugene V., Gophna, Uri, Narrowe, Adrienne B., Probst, Alexander J., Sczyrba, Alexander, Kohler, Annegret, Séguin, Armand, Shade, Ashley, Campbell, Barbara J., Lindahl, Björn D., Reese, Brandi Kiel, Roque, Breanna M., Derito, Chris, Averill, Colin, Cullen, Daniel, Beck, David A. C., Walsh, David A., Ward, David M., Wu, Dongying, Eloe-Fadrosh, Emiley, Brodie, Eoin L., Young, Erica B., Lilleskov, Erik A., Castillo, Federico J., Martin, Francis M., Lecleir, Gary R., Attwood, Graeme T., Cadillo-Quiroz, Hinsby, Simon, Holly M., Hewson, Ian, Grigoriev, Igor V., Tiedje, James M., Jansson, Janet K., Lee, Janey, Vandergheynst, Jean S., Dangl, Jeff, Bowman, Jeff S., Blanchard, Jeffrey L., Bowen, Jennifer L., Xu, Jiangbing, Banfield, Jillian F., Deming, Jody W., Kostka, Joel E., Gladden, John M., Rapp, Josephine Z., Sharpe, Joshua, McMahon, Katherine D., Treseder, Kathleen K., Bidle, Kay D., Wrighton, Kelly C., Thamatrakoln, Kimberlee, Nusslein, Klaus, Meredith, Laura K., Ramirez, Lucia, Buee, Marc, Huntemann, Marcel, Kalyuzhnaya, Marina G., Waldrop, Mark P., Sullivan, Matthew B., Schrenk, Matthew O., Hess, Matthias, Vega, Michael A., O'Malley, Michelle A., Medina, Monica, Gilbert, Naomi E., Delherbe, Nathalie, Mason, Olivia U., Dijkstra, Paul, Chuckran, Peter F., Baldrian, Petr, Constant, Philippe, Stepanauskas, Ramunas, Daly, Rebecca A., Lamendella, Regina, Gruninger, Robert J., Mckay, Robert M., Hylander, Samuel, Lebeis, Sarah L., Esser, Sarah P., Acinas, Silvia G., Wilhelm, Steven S., Singer, Steven W., Tringe, Susannah S., Woyke, Tanja, Reddy, T. B. K., Bell, Terrence H., Mock, Thomas ORCID: https://orcid.org/0000-0001-9604-0362, McAllister, Tim, Thiel, Vera, Denef, Vincent J., Liu, Wen-Tso, Martens-Habbena, Willm, Allen Liu, Xiao-Jun, Cooper, Zachary S. and Wang, Zhong (2022) Expansion of the global RNA virome reveals diverse clades of bacteriophages. Cell, 185 (21). 4023-4037.e18. ISSN 0092-8674

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Abstract

High-throughput RNA sequencing offers broad opportunities to explore the Earth RNA virome. Mining 5,150 diverse metatranscriptomes uncovered >2.5 million RNA virus contigs. Analysis of >330,000 RNA-dependent RNA polymerases (RdRPs) shows that this expansion corresponds to a 5-fold increase of the known RNA virus diversity. Gene content analysis revealed multiple protein domains previously not found in RNA viruses and implicated in virus-host interactions. Extended RdRP phylogeny supports the monophyly of the five established phyla and reveals two putative additional bacteriophage phyla and numerous putative additional classes and orders. The dramatically expanded phylum Lenarviricota, consisting of bacterial and related eukaryotic viruses, now accounts for a third of the RNA virome. Identification of CRISPR spacer matches and bacteriolytic proteins suggests that subsets of picobirnaviruses and partitiviruses, previously associated with eukaryotes, infect prokaryotic hosts.

Item Type:	Article
Faculty \ School:	Faculty of Science > School of Environmental Sciences University of East Anglia Research Groups/Centres > Theme - ClimateUEA
UEA Research Groups:	Faculty of Science > Research Centres > Centre for Ecology, Evolution and Conservation Faculty of Science > Research Groups > Centre for Ocean and Atmospheric Sciences Faculty of Science > Research Groups > Environmental Biology
Depositing User:	LivePure Connector
Date Deposited:	11 Mar 2024 09:31
Last Modified:	11 Mar 2024 10:31
URI:	https://ueaeprints.uea.ac.uk/id/eprint/94613
DOI:	10.1016/j.cell.2022.08.023

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