Classification of Myoviridae bacteriophages using protein sequence similarity.
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."


CONCLUSIONS
The hierarchical clustering of these groupings provide biologically significant subdivisions, which are consistent with our previous analysis of the Podoviridae.
Lavigne
Rob
R
Biosystems Department, Katholieke Universiteit Leuven, Kasteelpark Arenberg 21, Leuven, B-3001, Belgium. Rob.Lavigne@biw.kuleuven.be
Darius
Paul
P
Summer
Elizabeth J
EJ
Seto
Donald
D
Mahadevan
Padmanabhan
P
Nilsson
Anders S
AS
Ackermann
Hans W
HW
Kropinski
Andrew M
AM
D016000:Cluster Analysis; D019295:Computational Biology; D016679:Genome, Viral; D017900:Myoviridae / Q000145:classification* / Q000235:genetics; D010802:Phylogeny; D040901:Proteomics / Q000379:methods*; D020539:Sequence Analysis, Protein; D017386:Sequence Homology, Amino Acid; D014764:Viral Proteins / Q000235:genetics
D014764:Viral Proteins