@article{ba4f83cf3b3a4637a112820f7d5d64bd,
title = "Expansion of the global RNA virome reveals diverse clades of bacteriophages",
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.",
keywords = "Bactriophage, Functional protein annotation, Metatranscriptomics, RNA Virus, RNA dependent RNA polymerase, Viral Ecology, Virus, Virus - Host prediction, viral phylogeny",
author = "{RNA Virus Discovery Consortium} and Uri Neri and Wolf, {Yuri I.} and Simon Roux and Camargo, {Antonio Pedro} and Benjamin Lee and Darius Kazlauskas and Chen, {I. Min} and Natalia Ivanova and {Zeigler Allen}, Lisa and David Paez-Espino and Bryant, {Donald A.} and Devaki Bhaya and Narrowe, {Adrienne B.} and Probst, {Alexander J.} and Alexander Sczyrba and Annegret Kohler and Armand S{\'e}guin and Ashley Shade and Campbell, {Barbara J.} and Lindahl, {Bj{\"o}rn D.} and Reese, {Brandi Kiel} and Roque, {Breanna M.} and Chris DeRito and Colin Averill and Daniel Cullen and Beck, {David A.C.} and Walsh, {David A.} and Ward, {David M.} and Dongying Wu and Emiley Eloe-Fadrosh and Brodie, {Eoin L.} and Young, {Erica B.} and Lilleskov, {Erik A.} and Castillo, {Federico J.} and Martin, {Francis M.} and LeCleir, {Gary R.} and Attwood, {Graeme T.} and Hinsby Cadillo-Quiroz and Simon, {Holly M.} and Ian Hewson and Grigoriev, {Igor V.} and Tiedje, {James M.} and Jansson, {Janet K.} and Janey Lee and VanderGheynst, {Jean S.} and Jeff Dangl and Bowman, {Jeff S.} and Blanchard, {Jeffrey L.} and Bowen, {Jennifer L.} and Jiangbing Xu",
note = "Funding Information: The authors would like to thank Shai Zilberzwige-Tal, David Burstein, Adi Stern, Leah Reshef, and Omry Lieber for helpful discussions. 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{\textquoteright}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 . We gratefully acknowledge the contributions of many scientists and principal investigators, who sent extracted genetic material for isolate genomes, environmental metagenomes, and metatranscriptomes, or sequencing results as part of the Department of Energy Joint Genome Institute Community Science Program and allowed us to include in our study the RNA virus sequences detected in these publicly available data sets regardless of publication status. Publisher Copyright: {\textcopyright} 2022 The Authors",
year = "2022",
month = oct,
day = "13",
doi = "10.1016/j.cell.2022.08.023",
language = "English (US)",
volume = "185",
pages = "4023--4037.e18",
journal = "Cell",
issn = "0092-8674",
publisher = "Cell Press",
number = "21",
}