Viral dark matter and virus–host interactions resolved from publicly available microbial genomes
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 12,49...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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eLife Sciences Publications Ltd
2015-07-01
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| Series: | eLife |
| Subjects: | |
| Online Access: | https://elifesciences.org/articles/08490 |
| _version_ | 1818019124817690624 |
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| author | Simon Roux Steven J Hallam Tanja Woyke Matthew B Sullivan |
| author_facet | Simon Roux Steven J Hallam Tanja Woyke Matthew B Sullivan |
| author_sort | Simon Roux |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-14T07:48:17Z |
| format | Article |
| id | doaj.art-c8a3243277f746ec98f9ee6213f1ace8 |
| institution | Directory Open Access Journal |
| issn | 2050-084X |
| language | English |
| last_indexed | 2024-04-14T07:48:17Z |
| publishDate | 2015-07-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj.art-c8a3243277f746ec98f9ee6213f1ace82022-12-22T02:05:17ZengeLife Sciences Publications LtdeLife2050-084X2015-07-01410.7554/eLife.08490Viral dark matter and virus–host interactions resolved from publicly available microbial genomesSimon Roux0Steven J Hallam1Tanja Woyke2Matthew B Sullivan3Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, United StatesDepartment of Microbiology and Immunology, University of British Columbia, Vancouver, Canada; Graduate Program in Bioinformatics, University of British Columbia, Vancouver, CanadaU.S Department of Energy Joint Genome Institute, Walnut Creek, United StatesDepartment of Ecology and Evolutionary Biology, University of Arizona, Tucson, United StatesThe 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.https://elifesciences.org/articles/08490virusphageprophagevirus-host adaptation |
| spellingShingle | Simon Roux Steven J Hallam Tanja Woyke Matthew B Sullivan Viral dark matter and virus–host interactions resolved from publicly available microbial genomes eLife virus phage prophage virus-host adaptation |
| title | Viral dark matter and virus–host interactions resolved from publicly available microbial genomes |
| title_full | Viral dark matter and virus–host interactions resolved from publicly available microbial genomes |
| title_fullStr | Viral dark matter and virus–host interactions resolved from publicly available microbial genomes |
| title_full_unstemmed | Viral dark matter and virus–host interactions resolved from publicly available microbial genomes |
| title_short | Viral dark matter and virus–host interactions resolved from publicly available microbial genomes |
| title_sort | viral dark matter and virus host interactions resolved from publicly available microbial genomes |
| topic | virus phage prophage virus-host adaptation |
| url | https://elifesciences.org/articles/08490 |
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