The DOI matches its Crossref record; 81 of the 81 references it cites were found in a registry or an index.
Viral dark matter and virus–host interactions resolved from publicly available microbial genomes
Open accessAbstract
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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Cites
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Cited by
Single-cell genome sequencing: current state of the science
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Horizontal gene transfer and adaptive evolution in bacteria.
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Lysogeny in nature: mechanisms, impact and ecology of temperate phages
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Self-citationThe Human Gut Virome Is Highly Diverse, Stable, and Individual Specific
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Identifying viruses from metagenomic data using deep learning
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Metadata
- Authors
- Roux, S., Hallam, S. J., Woyke, T., & Sullivan, M. B.
- Venue
- eLife
- Publisher
- eLife Sciences Publications, Ltd
- Published
- 2015-07-22
- Volume
- 4
- ISSN
- 2050-084X (ISSN-L)
- OpenAlex
- W2169899471
- Cited by
- 478
- References
- 81
- FWCI
- 36.14
- Type
- journal article
- Language
- en
- Open access
- gold
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- Roux, S., Hallam, S. J., Woyke, T., & Sullivan, M. B. (2015). Viral dark matter and virus–host interactions resolved from publicly available microbial genomes. eLife. https://doi.org/10.7554/elife.08490
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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