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

Benjamin Bolduc, Ho Bin Jang, Guilhem Doulcier, Zhi Qiang You, Simon Roux, Matthew Sullivan

Research output: Contribution to journalArticle

33 Citations (Scopus)

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.

Original languageEnglish (US)
Article numbere3243
JournalPeerJ
Volume2017
Issue number5
DOIs
StatePublished - 2017
Externally publishedYes

Fingerprint

dsDNA viruses
DNA Viruses
Archaea
Viruses
Archaeal Viruses
Bacteria
Genes
Genome
genome
Viral Genome
DNA
bacteria
taxonomy
Taxonomies
Application programs
Ecosystem
viruses
Bacteriophages
microbial ecology
Research Personnel

Keywords

  • Archaeal viruses
  • Bacteriophage
  • Taxonomy
  • Virus

ASJC Scopus subject areas

  • Neuroscience(all)
  • Medicine(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

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.

In: PeerJ, Vol. 2017, No. 5, e3243, 2017.

Research output: Contribution to journalArticle

Bolduc, Benjamin ; Jang, Ho Bin ; Doulcier, Guilhem ; You, Zhi Qiang ; Roux, Simon ; Sullivan, Matthew. / vConTACT : An iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria. In: PeerJ. 2017 ; Vol. 2017, No. 5.
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