期刊
ELIFE
卷 4, 期 -, 页码 -出版社
ELIFE SCIENCES PUBLICATIONS LTD
DOI: 10.7554/eLife.08490
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资金
- Gordon and Betty Moore Foundation [3790]
- Natural Sciences and Engineering Research Council of Canada (Conseil de Recherches en Sciences Naturelles et en Genie du Canada)
- Canada Foundation for Innovation (Fondation canadienne pour l'innovation)
- Canadian Institute for Advanced Research (L'Institut Canadien de Recherches Avancees)
- Tula Foundation
- Ambrose Monell Foundation
- G. Unger Vetlesen Foundation
- U.S. Department of Energy (Department of Energy) [DE-AC02-05CH11231]
The ecological importance of viruses is now widely recognized, yet our limited knowledge of viral sequence space and virus-host interactions precludes accurate prediction of their roles and impacts. In this study, we mined publicly available bacterial and archaeal genomic data sets to identify 12,498 high-confidence viral genomes linked to their microbial hosts. These data augment public data sets 10-fold, provide first viral sequences for 13 new bacterial phyla including ecologically abundant phyla, and help taxonomically identify 7-38% of 'unknown' sequence space in viromes. Genome-and network-based classification was largely consistent with accepted viral taxonomy and suggested that (i) 264 new viral genera were identified (doubling known genera) and (ii) cross-taxon genomic recombination is limited. Further analyses provided empirical data on extrachromosomal prophages and coinfection prevalences, as well as evaluation of in silico virus-host linkage predictions. Together these findings illustrate the value of mining viral signal from microbial genomes.
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