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Expansion of the global RNA virome reveals diverse clades of bacteriophages

Uri Neri 1 Yuri I Wolf 2 Simon Roux 3 Antonio Pedro Camargo 3 Benjamin Lee 2, 4 Darius Kazlauskas 5 I. Min Chen 3 Natalia Ivanova 3 Lisa Zeigler Allen 6 David Paez-Espino 3 Donald A Bryant 7 Devaki Bhaya 8 Adrienne B Narrowe Alexander J Probst Alexander Sczyrba Annegret Kohler Armand Séguin Ashley Shade Barbara J Campbell Björn D Lindahl Brandi Kiel Reese Breanna M Roque Chris Derito Colin Averill Daniel Cullen David A.C. Beck David A Walsh David M Ward Dongying Wu Emiley Eloe-Fadrosh Eoin L Brodie Erica B Young Erik A Lilleskov Federico J Castillo Francis M Martin Gary R Lecleir Graeme T Attwood Hinsby Cadillo-Quiroz Holly M Simon Ian Hewson Igor V Grigoriev James M Tiedje Janet K Jansson Janey Lee Jean S Vandergheynst Jeff Dangl Jeff S Bowman Jeffrey L Blanchard Jennifer L Bowen Jiangbing Xu Jillian F Banfield Jody W Deming Joel E Kostka John M Gladden Josephine Z Rapp Joshua Sharpe Katherine D Mcmahon Kathleen K Treseder Kay D Bidle Kelly C Wrighton Kimberlee Thamatrakoln Klaus Nusslein Laura K Meredith Lucia Ramirez Marc Buee Marcel Huntemann Marina G Kalyuzhnaya Mark P Waldrop Matthew B Sullivan Matthew O Schrenk Matthias Hess Michael A Vega Michelle A O’malley Monica Medina Naomi E Gilbert Nathalie Delherbe Olivia U Mason Paul Dijkstra Peter F Chuckran Petr Baldrian Philippe Constant Ramunas Stepanauskas Rebecca A Daly Regina Lamendella Robert J Gruninger Robert M Mckay Samuel Hylander Sarah L Lebeis Sarah P Esser Silvia G Acinas Steven S Wilhelm Steven W Singer Susannah S Tringe Tanja Woyke T.B.K. Reddy Terrence H Bell Thomas Mock Tim Mcallister Vera Thiel Vincent J Denef Wen-Tso Liu Willm Martens-Habbena Xiao-Jun Allen Liu Zachary S Cooper Zhong Wang Mart Krupovic 9 Valerian V Dolja 2, 10, * Nikos C Kyrpides 3, * Eugene V Koonin 2, * Uri Gophna 1, * 
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.
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https://hal-pasteur.archives-ouvertes.fr/pasteur-03816108
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Submitted on : Saturday, October 15, 2022 - 3:39:01 PM
Last modification on : Tuesday, October 18, 2022 - 4:08:15 AM

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Uri Neri, Yuri I Wolf, Simon Roux, Antonio Pedro Camargo, Benjamin Lee, et al.. Expansion of the global RNA virome reveals diverse clades of bacteriophages. Cell, 2022, 185 (21), pp.4023-4037.e18. ⟨10.1016/j.cell.2022.08.023⟩. ⟨pasteur-03816108⟩

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