1. Expansion of the global RNA virome reveals diverse clades of bacteriophages
- Author
-
Neri, Uri, Wolf, Yuri I, Roux, Simon, Camargo, Antonio Pedro, Lee, Benjamin, Kazlauskas, Darius, Chen, I Min, Ivanova, Natalia, Allen, Lisa Zeigler, Paez-Espino, David, Bryant, Donald A, Bhaya, Devaki, Consortium, RNA Virus Discovery, 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 AC, 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, TBK, Bell, Terrence H, Mock, Thomas, McAllister, Tim, and Thiel, Vera
- Subjects
Microbiology ,Biological Sciences ,Bioinformatics and Computational Biology ,Genetics ,Infectious Diseases ,Biotechnology ,Microbiome ,Infection ,Bacteriophages ,DNA-Directed RNA Polymerases ,Genome ,Viral ,Phylogeny ,RNA ,RNA Viruses ,RNA-Dependent RNA Polymerase ,Virome ,RNA Virus Discovery Consortium ,Bactriophage ,Functional protein annotation ,Metatranscriptomics ,RNA Virus ,RNA dependent RNA polymerase ,Viral Ecology ,Virus ,Virus - Host prediction ,viral phylogeny ,Medical and Health Sciences ,Developmental Biology ,Biological sciences ,Biomedical and clinical sciences - 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.
- Published
- 2022