vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria
Taxonomic classification of archaeal and bacterial viruses is challenging, yet also fundamental for developing a predictive understanding of microbial ecosystems. Recent identification of hundreds of thousands of new viral genomes and genome fragments, whose hosts remain unknown, requires a paradigm...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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PeerJ Inc.
2017-05-01
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| Series: | PeerJ |
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| Online Access: | https://peerj.com/articles/3243.pdf |
| _version_ | 1797425714701533184 |
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| author | Benjamin Bolduc Ho Bin Jang Guilhem Doulcier Zhi-Qiang You Simon Roux Matthew B. Sullivan |
| author_facet | Benjamin Bolduc Ho Bin Jang Guilhem Doulcier Zhi-Qiang You Simon Roux Matthew B. Sullivan |
| author_sort | Benjamin Bolduc |
| collection | DOAJ |
| description | Taxonomic classification of archaeal and bacterial viruses is challenging, yet also fundamental for developing a predictive understanding of microbial ecosystems. Recent identification of hundreds of thousands of new viral genomes and genome fragments, whose hosts remain unknown, requires a paradigm shift away from traditional classification approaches and towards the use of genomes for taxonomy. Here we revisited the use of genomes and their protein content as a means for developing a viral taxonomy for bacterial and archaeal viruses. A network-based analytic was evaluated and benchmarked against authority-accepted taxonomic assignments and found to be largely concordant. Exceptions were manually examined and found to represent areas of viral genome ‘sequence space’ that are under-sampled or prone to excessive genetic exchange. While both cases are poorly resolved by genome-based taxonomic approaches, the former will improve as viral sequence space is better sampled and the latter are uncommon. Finally, given the largely robust taxonomic capabilities of this approach, we sought to enable researchers to easily and systematically classify new viruses. Thus, we established a tool, vConTACT, as an app at iVirus, where it operates as a fast, highly scalable, user-friendly app within the free and powerful CyVerse cyberinfrastructure. |
| first_indexed | 2024-03-09T08:20:09Z |
| format | Article |
| id | doaj.art-e93ac4e15112412484a704aa9e5dfccd |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T08:20:09Z |
| publishDate | 2017-05-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
| series | PeerJ |
| spelling | doaj.art-e93ac4e15112412484a704aa9e5dfccd2023-12-02T21:54:09ZengPeerJ Inc.PeerJ2167-83592017-05-015e324310.7717/peerj.3243vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and BacteriaBenjamin Bolduc0Ho Bin Jang1Guilhem Doulcier2Zhi-Qiang You3Simon Roux4Matthew B. Sullivan5Department of Microbiology, Ohio State University, Columbus, OH, United StatesDepartment of Microbiology, Ohio State University, Columbus, OH, United StatesInstitut de Biologie de l’ENS (IBENS), École normale supérieure, PSL Research University, Paris, FranceDepartment of Chemistry and Biochemistry, Ohio State University, Columbus, OH, United StatesDepartment of Microbiology, Ohio State University, Columbus, OH, United StatesDepartment of Microbiology, Ohio State University, Columbus, OH, United StatesTaxonomic classification of archaeal and bacterial viruses is challenging, yet also fundamental for developing a predictive understanding of microbial ecosystems. Recent identification of hundreds of thousands of new viral genomes and genome fragments, whose hosts remain unknown, requires a paradigm shift away from traditional classification approaches and towards the use of genomes for taxonomy. Here we revisited the use of genomes and their protein content as a means for developing a viral taxonomy for bacterial and archaeal viruses. A network-based analytic was evaluated and benchmarked against authority-accepted taxonomic assignments and found to be largely concordant. Exceptions were manually examined and found to represent areas of viral genome ‘sequence space’ that are under-sampled or prone to excessive genetic exchange. While both cases are poorly resolved by genome-based taxonomic approaches, the former will improve as viral sequence space is better sampled and the latter are uncommon. Finally, given the largely robust taxonomic capabilities of this approach, we sought to enable researchers to easily and systematically classify new viruses. Thus, we established a tool, vConTACT, as an app at iVirus, where it operates as a fast, highly scalable, user-friendly app within the free and powerful CyVerse cyberinfrastructure.https://peerj.com/articles/3243.pdfVirusBacteriophageArchaeal virusesTaxonomy |
| spellingShingle | Benjamin Bolduc Ho Bin Jang Guilhem Doulcier Zhi-Qiang You Simon Roux Matthew B. Sullivan vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria PeerJ Virus Bacteriophage Archaeal viruses Taxonomy |
| title | vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria |
| title_full | vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria |
| title_fullStr | vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria |
| title_full_unstemmed | vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria |
| title_short | vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria |
| title_sort | vcontact an ivirus tool to classify double stranded dna viruses that infect archaea and bacteria |
| topic | Virus Bacteriophage Archaeal viruses Taxonomy |
| url | https://peerj.com/articles/3243.pdf |
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