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 | RNA Virus Discovery Consortium | Narrowe, Adrienne B. | Ramírez Nasto, Lucía | Wang, Zhong | Nusslein, Klaus | Meredith, Laura K. | Buée, 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, Mónica | Gilbert, Naomi E. | Delherbe, Nathalie | Mason, Olivia U. | Probst, Alexander J. | Sczyrba, Alexander | Kohler, Annegret | Séguin, Armand | Shade, Ashley | Campbell, Barbara J. | Lindahl, Björn D. | Reese, Brandi Kiel | Roque, Breanna M. | DeRito, Christopher | Averill, Colin | Cullen, Daniel | Beck, David A.C. | Walsh, David A. | Ward, David M. | Wu, Dongying | Eloe-Fadrosh, Emiley | Brodie, Eoin L. | 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. | Young, Erica B. | Lilleskov, Erik A. | Castillo, Federico J. | Martin, Francis | 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 | Wilhelm, Steven S. | Singer, Steven W. | Tringe, Susannah S. | Woyke, Tanja | Reddy, T.B.K. | Bell, Terrence H. | Mock, Thomas | McAllister, Tim | Thiel, Vera | Denef, Vincent J. | Liu, Wen-Tso | Martens-Habbena, Willm | Liu, Xiao-Jun Allen | Cooper, Zachary S. | Agronomía, Biotecnología y Alimentación | Agronomia, Bioteknologia eta Elikadura | Institute for Multidisciplinary Research in Applied Biology - IMAB
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.
Показать больше [+] Меньше [-]U.G. and U.N. are supported by the European Research Council (ERC-AdG 787514). U.N. is supported by a fellowship from the Edmond J. Safra Center for Bioinformatics at Tel Aviv University. Y.I.W. and E.V.K. are supported through the Intramural Research Program of the US National Institutes of Health (National Library of Medicine). V.V.D. was partially supported by NIH/NLM/NCBI Visiting Scientist Fellowship. The work of the U.S. Department of Energy Joint Genome Institute (S.R., A.P.C., I.M.C., N.I., D.P.-E., N.C.K., and all JGI co-authors), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy under contract no. DE-AC02-05CH11231. M.K. was supported by l’Agence Nationale de la Recherche grants ANR-20-CE20-009-02 and ANR-21-CE11-0001-01. D.K. was funded by the European Social Fund under no. 09.3.3-LMT-K-712-14-0027. D.A.B. is supported by grant NNX16SJ62G from the NASA Exobiology program, and by grant DE-FG02-94ER20137 from the Photosynthetic Systems Program, Division of Chemical Sciences, Geosciences, and Biosciences (CSGB), Office of Basic Energy Sciences of the U.S. Department of Energy.
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