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

Roux, Simon; Hallam, Steven J.; Woyke, Tanja; Sullivan, Matthew B.

doi:10.7554/eLife.08490

Title: Viral dark matter and virus–host interactions resolved from publicly available microbial genomes

Journal Article · Wed Jul 22 00:00:00 EDT 2015 · eLife

DOI:https://doi.org/10.7554/eLife.08490· OSTI ID:1209986

Roux, Simon ^[1]; Hallam, Steven J. ^[2]; Woyke, Tanja ^[3]; Sullivan, Matthew B. ^[1]

Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, United States
Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada, Graduate Program in Bioinformatics, University of British Columbia, Vancouver, Canada
U.S Department of Energy Joint Genome Institute, Walnut Creek, United States

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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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: Joint Genome Institute (DE-AC02-05CH11231); AC02-05CH11231

OSTI ID:: 1209986

Alternate ID(s):: OSTI ID: 1209987; OSTI ID: 1628837

Journal Information:: eLife, Journal Name: eLife Vol. 4; ISSN 2050-084X

Publisher:: eLife Sciences Publications, Ltd.Copyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 272 works

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