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

PeerJ

article

Benjamin Bolduc¹  Ho Bin Jang¹  Guilhem Doulcier²  Zhi-Qiang You⁴  Simon Roux¹  Matthew B. Sullivan¹ 

[1] Department of Microbiology, Ohio State University;Institut de Biologie de l’ENS ,(IBENS), École normale supérieure, PSL Research University;ESPCI, PSL Research University;Department of Chemistry and Biochemistry, Ohio State University;Department of Civil, Environmental and Geodetic Engineering, Ohio State University

关键词: Virus;    Bacteriophage;    Archaeal viruses;    Taxonomy;   

DOI  :  10.7717/peerj.3243

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

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.

【 授权许可】

CC BY