Integration of genomic and proteomic analyses in the classification of the Siphoviridae family

Evelien M Adriaenssens; Rob Edwards; John H E Nash; Padmanabhan Mahadevan; Donald Seto; Hans-Wolfgang Ackermann; Rob Lavigne; Andrew M Kropinski

doi:10.1016/j.virol.2014.10.016

Integration of genomic and proteomic analyses in the classification of the Siphoviridae family

Virology. 2015 Mar:477:144-154. doi: 10.1016/j.virol.2014.10.016. Epub 2014 Nov 14.

Authors

Evelien M Adriaenssens¹, Rob Edwards², John H E Nash³, Padmanabhan Mahadevan⁴, Donald Seto⁵, Hans-Wolfgang Ackermann⁶, Rob Lavigne⁷, Andrew M Kropinski⁸

Affiliations

¹ Centre for Microbial Ecology and Genomics, Genomics Research Institute, University of Pretoria, Lynnwood Road, Pretoria 0028, South Africa.
² Geology, Mathematics, and Computer Science, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA.
³ Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, 110 Stone Road West, Guelph, ON, Canada N1G 3W4.
⁴ Department of Biology, University of Tampa, Tampa, FL, 33606, USA.
⁵ Bioinformatics and Computational Biology Program, School of Systems Biology, George Mason University, 10900 University Blvd, Manassas, VA 20110, USA.
⁶ Département de Microbiologie-infectiologie et immunologie, Faculté de médecine, Université Laval, Québec, QC, Canada G1K 7P4.
⁷ Department of Biosystems, Laboratory of Gene Technology, KU Leuven, KasteelparkArenberg 21 - b2462, Heverlee 3001, Belgium. Electronic address: rob.lavigne@kuleuven.be.
⁸ Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, 110 Stone Road West, Guelph, ON, Canada N1G 3W4; Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada N1G 2A1. Electronic address: akropins@uoguelph.ca.

PMID: 25466308
DOI: 10.1016/j.virol.2014.10.016

Abstract

Using a variety of genomic (BLASTN, ClustalW) and proteomic (Phage Proteomic Tree, CoreGenes) tools we have tackled the taxonomic status of members of the largest bacteriophage family, the Siphoviridae. In all over 400 phages were examined and we were able to propose 39 new genera, comprising 216 phage species, and add 62 species to two previously defined genera (Phic3unalikevirus; L5likevirus) grouping, in total, 390 fully sequenced phage isolates. Many of the remainders are orphans which the Bacterial and Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV) chooses not to ascribe genus status at the time being.

Keywords: ClustalW; CoreGenes; ICTV; Phage Proteomic Tree; Siphoviridae; Taxonomy.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Bacteriophages / chemistry
Bacteriophages / classification*
Bacteriophages / genetics
Genome, Viral*
Genomics / methods
Proteome / analysis*
Proteomics / methods
Siphoviridae / chemistry
Siphoviridae / classification*
Siphoviridae / genetics
Viral Proteins / analysis*
Virology / methods

Substances

Proteome
Viral Proteins