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

Bolduc, Benjamin; Jang, Ho Bin; Doulcier, Guilhem; You, Zhi-Qiang; Roux, Simon; Sullivan, Matthew B.

doi:10.7717/peerj.3243

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

Journal Article · Wed May 03 00:00:00 EDT 2017 · PeerJ

DOI:https://doi.org/10.7717/peerj.3243· OSTI ID:1368218

Bolduc, Benjamin ^[1]; Jang, Ho Bin ^[2]; Doulcier, Guilhem ^[3]; You, Zhi-Qiang ^[4]; Roux, Simon ^[2]; Sullivan, Matthew B. ^[5]

The Ohio State Univ., Columbus, OH (United States). Dept of Microbiology; University of Arizona
The Ohio State Univ., Columbus, OH (United States). Dept of Microbiology
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)
The Ohio State Univ., Columbus, OH (United States). Dept of Chemistry and Biochemistry
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

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.

View Accepted Manuscript (DOE)

Research Organization:: Univ. of Arizona, Tucson, AZ (United States)

Sponsoring Organization:: Gordon and Betty Moore Foundation; National Science Foundation (NSF); USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)

Grant/Contract Number:: SC0010580

OSTI ID:: 1368218

Journal Information:: PeerJ, Journal Name: PeerJ Vol. 5; ISSN 2167-8359

Publisher:: PeerJ Inc.Copyright Statement

Country of Publication:: United States

Language:: English

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Analysis of Spounaviruses as a Case Study for the Overdue Reclassification of Tailed Phages Barylski, Jakub; Enault, François; Dutilh, Bas E. ETH Zurich https://doi.org/10.3929/ethz-b-000387041	text	January 2020
Phage-centric ecological interactions in aquatic ecosystems revealed through ultra-deep metagenomics Kavagutti, Vinicius S.; Andrei, Adrian-Ştefan; Mehrshad, Maliheh BioMed Central https://doi.org/10.5167/uzh-183761	text	January 2019
Discovery of several thousand highly diverse circular DNA viruses Tisza, Michael J.; Pastrana, Diana V.; Welch, Nicole L. eLife, Vol. 9 https://doi.org/10.7554/elife.51971	journal	February 2020
Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity Roux, Simon; Emerson, Joanne B.; Eloe-Fadrosh, Emiley A. PeerJ, Vol. 5 https://doi.org/10.7717/peerj.3817	journal	January 2017
Long-read viral metagenomics captures abundant and microdiverse viral populations and their niche-defining genomic islands Warwick-Dugdale, Joanna; Solonenko, Natalie; Moore, Karen PeerJ, Vol. 7 https://doi.org/10.7717/peerj.6800	journal	January 2019

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