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

PeerJ. 2017 May 3;5:e3243. doi: 10.7717/peerj.3243. eCollection 2017.

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.

Keywords: Archaeal viruses; Bacteriophage; Taxonomy; Virus.

Grant support

This research was supported by awards to MBS from the US Department of Energy, Office of Science, Office of Biological and Environmental Research under the Genomic Science program (DE-SC0010580), the National Science Foundation (OCE-1536989), and the Gordon and Betty Moore Foundation (#3790, 3305) and computational resources provided by the Ohio Supercomputer Center (1987, http://osc.edu/ark:/19495/f5s1ph73). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.