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Journal Articles Cell Year : 2022

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 Buée , 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)
Uri Neri
Adrienne B Narrowe
  • Function : Author
Alexander J Probst
  • Function : Author
Alexander Sczyrba
  • Function : Author
Annegret Kohler
  • Function : Author
Armand Séguin
  • Function : Author
Ashley Shade
  • Function : Author
Barbara J Campbell
  • Function : Author
Björn D Lindahl
  • Function : Author
Brandi Kiel Reese
  • Function : Author
Breanna M Roque
  • Function : Author
Chris Derito
  • Function : Author
Colin Averill
  • Function : Author
Daniel Cullen
  • Function : Author
David A.C. Beck
  • Function : Author
David A Walsh
  • Function : Author
David M Ward
  • Function : Author
Dongying Wu
  • Function : Author
Emiley Eloe-Fadrosh
  • Function : Author
Eoin L Brodie
  • Function : Author
Erica B Young
  • Function : Author
Erik A Lilleskov
  • Function : Author
Federico J Castillo
  • Function : Author
Francis M Martin
  • Function : Author
Gary R Lecleir
  • Function : Author
Graeme T Attwood
  • Function : Author
Hinsby Cadillo-Quiroz
  • Function : Author
Holly M Simon
  • Function : Author
Ian Hewson
  • Function : Author
Igor V Grigoriev
  • Function : Author
James M Tiedje
  • Function : Author
Janet K Jansson
  • Function : Author
Janey Lee
  • Function : Author
Jean S Vandergheynst
  • Function : Author
Jeff Dangl
  • Function : Author
Jeff S Bowman
  • Function : Author
Jeffrey L Blanchard
  • Function : Author
Jennifer L Bowen
  • Function : Author
Jiangbing Xu
  • Function : Author
Jillian F Banfield
  • Function : Author
Jody W Deming
  • Function : Author
Joel E Kostka
  • Function : Author
John M Gladden
  • Function : Author
Josephine Z Rapp
  • Function : Author
Joshua Sharpe
  • Function : Author
Katherine D Mcmahon
  • Function : Author
Kathleen K Treseder
  • Function : Author
Kay D Bidle
  • Function : Author
Kelly C Wrighton
  • Function : Author
Kimberlee Thamatrakoln
  • Function : Author
Klaus Nusslein
  • Function : Author
Laura K Meredith
  • Function : Author
Lucia Ramirez
  • Function : Author
Marc Buée
Marcel Huntemann
  • Function : Author
Marina G Kalyuzhnaya
  • Function : Author
Mark P Waldrop
  • Function : Author
Matthew B Sullivan
  • Function : Author
Matthew O Schrenk
  • Function : Author
Matthias Hess
  • Function : Author
Michael A Vega
  • Function : Author
Michelle A O’malley
  • Function : Author
Monica Medina
  • Function : Author
Naomi E Gilbert
  • Function : Author
Nathalie Delherbe
  • Function : Author
Olivia U Mason
  • Function : Author
Paul Dijkstra
  • Function : Author
Peter F Chuckran
  • Function : Author
Petr Baldrian
  • Function : Author
Philippe Constant
  • Function : Author
Ramunas Stepanauskas
  • Function : Author
Rebecca A Daly
  • Function : Author
Regina Lamendella
  • Function : Author
Robert J Gruninger
  • Function : Author
Robert M Mckay
  • Function : Author
Samuel Hylander
  • Function : Author
Sarah L Lebeis
  • Function : Author
Sarah P Esser
  • Function : Author
Silvia G Acinas
  • Function : Author
Steven S Wilhelm
  • Function : Author
Steven W Singer
  • Function : Author
Susannah S Tringe
  • Function : Author
Tanja Woyke
  • Function : Author
T.B.K. Reddy
  • Function : Author
Terrence H Bell
  • Function : Author
Thomas Mock
  • Function : Author
Tim Mcallister
  • Function : Author
Vera Thiel
  • Function : Author
Vincent J Denef
  • Function : Author
Wen-Tso Liu
  • Function : Author
Willm Martens-Habbena
  • Function : Author
Xiao-Jun Allen Liu
  • Function : Author
Zachary S Cooper
  • Function : Author
Zhong Wang
  • Function : Author
Mart Krupovic
Uri Gophna
  • Function : Correspondent author

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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Dates and versions

pasteur-03816108 , version 1 (15-10-2022)

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Attribution - NonCommercial - NoDerivatives

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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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