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Title: vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria

Abstract

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.

Authors:
 [1];  [1];  [2];  [3];  [1];  [4]
  1. The Ohio State Univ., Columbus, OH (United States). Dept of Microbiology
  2. Paris Sciences et Lettres Research Univ. (PSL), Paris (France). Ecole Normale Superieure, Inst. de Biologie de l'ENS (IBENS); Paris Sciences et Lettres Research Univ. (PSL), Paris (France). City of Paris Industrial Physics and Chemistry Higher Educational Institution (ESPCI)
  3. The Ohio State Univ., Columbus, OH (United States). Dept of Chemistry and Biochemistry
  4. The Ohio State Univ., Columbus, OH (United States). Dept of Microbiology; The Ohio State Univ., Columbus, OH (United States). Dept of of Civil, Environmental and Geodetic Engineering
Publication Date:
Research Org.:
Univ. of Arizona, Tucson, AZ (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23); National Science Foundation (NSF); Gordon and Betty Moore Foundation
OSTI Identifier:
1368218
Grant/Contract Number:
SC0010580; OCE-1536989; 3790; 3305
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
PeerJ
Additional Journal Information:
Journal Volume: 5; Journal ID: ISSN 2167-8359
Publisher:
PeerJ Inc.
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Virus; Bacteriophage; Archaeal viruses; Taxonomy

Citation Formats

Bolduc, Benjamin, Jang, Ho Bin, Doulcier, Guilhem, You, Zhi-Qiang, Roux, Simon, and Sullivan, Matthew B. vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria. United States: N. p., 2017. Web. doi:10.7717/peerj.3243.
Bolduc, Benjamin, Jang, Ho Bin, Doulcier, Guilhem, You, Zhi-Qiang, Roux, Simon, & Sullivan, Matthew B. vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria. United States. doi:10.7717/peerj.3243.
Bolduc, Benjamin, Jang, Ho Bin, Doulcier, Guilhem, You, Zhi-Qiang, Roux, Simon, and Sullivan, Matthew B. Wed . "vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria". United States. doi:10.7717/peerj.3243. https://www.osti.gov/servlets/purl/1368218.
@article{osti_1368218,
title = {vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria},
author = {Bolduc, Benjamin and Jang, Ho Bin and Doulcier, Guilhem and You, Zhi-Qiang and Roux, Simon and Sullivan, Matthew B.},
abstractNote = {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.},
doi = {10.7717/peerj.3243},
journal = {PeerJ},
number = ,
volume = 5,
place = {United States},
year = {Wed May 03 00:00:00 EDT 2017},
month = {Wed May 03 00:00:00 EDT 2017}
}

Journal Article:
Free Publicly Available Full Text
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Cited by: 2works
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