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; McAllister, Tim; Thiel, Vera; Denef, Vincent J.; Liu, Wen-Tso; Martens-Habbena, Willm; Allen Liu, Xiao-Jun; Cooper, Zachary S.; Wang, Zhong

doi:10.1016/j.cell.2022.08.023

Expansion of the global RNA virome reveals diverse clades of bacteriophages

Journal Article · Wed Sep 28 00:00:00 EDT 2022 · Cell

DOI:https://doi.org/10.1016/j.cell.2022.08.023· OSTI ID:2570216

; 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 more »

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.

View Accepted Manuscript (DOE)

Research Organization:: Boston Univ., MA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES). Chemical Sciences, Geosciences & Biosciences Division (CSGB); USDOE Office of Science (SC), Biological and Environmental Research (BER)

Contributing Organization:: RNA Virus Discovery Consortium

Grant/Contract Number:: AC02-05CH11231; FG02-94ER20137; SC0020403

OSTI ID:: 2570216

Alternate ID(s):: OSTI ID: 1969343

Journal Information:: Cell, Journal Name: Cell Journal Issue: 21 Vol. 185; ISSN 0092-8674

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

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Journal Article · Sun Aug 25 20:00:00 EDT 2024 · Nature (London) · OSTI ID:2440394

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59 BASIC BIOLOGICAL SCIENCES
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