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Elife. 2015 Jul 22;4. doi: 10.7554/eLife.08490.

Viral dark matter and virus-host interactions resolved from publicly available microbial genomes.

Author information

1
Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, United States.
2
Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada.
3
U.S Department of Energy Joint Genome Institute, Walnut Creek, United States.

Abstract

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.

KEYWORDS:

ecology; evolutionary biology; genomics; none; phage; prophage; virus; virus-host adaptation

Comment in

PMID:
26200428
PMCID:
PMC4533152
DOI:
10.7554/eLife.08490
[Indexed for MEDLINE]
Free PMC Article

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