Research article

Classification of Myoviridae bacteriophages using protein sequence similarity

Rob Lavigne¹ , Paul Darius¹ , Elizabeth J Summer² , Donald Seto³ , Padmanabhan Mahadevan³ , Anders S Nilsson⁴ , Hans W Ackermann⁵ and Andrew M Kropinski^6,7

¹  Biosystems Department, Katholieke Universiteit Leuven, Kasteelpark Arenberg 21, Leuven, B-3001, Belgium

²  Center for Phage Therapeutics, Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA

³  Department of Bioinformatics and Computational Biology, George Mason University, Manassas, VA20110, USA

⁴  Department of Genetics, Microbiology and Toxicology, Stockholm University, S-106 91 Stockholm, Sweden

⁵  Felix d'Herelle Reference Center for Bacterial Viruses, Department of Medical Biology, Faculty of Medicine, Laval University, Quebec, QC, G1K 4C6, Canada

⁶  Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, 110 Stone Road West, Guelph, ON, N1G 3W4, Canada

⁷  Department of Molecular & Cellular Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada

author email corresponding author email

BMC Microbiology 2009, 9:224doi:10.1186/1471-2180-9-224

Published:	26 October 2009

Abstract

Background

We advocate unifying classical and genomic classification of bacteriophages by integration of proteomic data and physicochemical parameters. Our previous application of this approach to the entirely sequenced members of the Podoviridae fully supported the current phage classification of the International Committee on Taxonomy of Viruses (ICTV). It appears that horizontal gene transfer generally does not totally obliterate evolutionary relationships between phages.

Results

CoreGenes/CoreExtractor proteome comparison techniques applied to 102 Myoviridae suggest the establishment of three subfamilies (Peduovirinae, Teequatrovirinae, the Spounavirinae) and eight new independent genera (Bcep781, BcepMu, FelixO1, HAP1, Bzx1, PB1, phiCD119, and phiKZ-like viruses). The Peduovirinae subfamily, derived from the P2-related phages, is composed of two distinct genera: the "P2-like viruses", and the "HP1-like viruses". At present, the more complex Teequatrovirinae subfamily has two genera, the "T4-like" and "KVP40-like viruses". In the genus "T4-like viruses" proper, four groups sharing >70% proteins are distinguished: T4-type, 44RR-type, RB43-type, and RB49-type viruses. The Spounavirinae contain the "SPO1-"and "Twort-like viruses."

Conclusion

The hierarchical clustering of these groupings provide biologically significant subdivisions, which are consistent with our previous analysis of the Podoviridae.