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. 2009 Oct 26:9:224.
doi: 10.1186/1471-2180-9-224.

Classification of Myoviridae bacteriophages using protein sequence similarity

Rob Lavigne  1 , Paul Darius, Elizabeth J Summer, Donald Seto, Padmanabhan Mahadevan, Anders S Nilsson, Hans W Ackermann, Andrew M Kropinski
Affiliations

Classification of Myoviridae bacteriophages using protein sequence similarity

Rob Lavigne et al. BMC Microbiol. .

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.

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Figures

Figure 1
Figure 1
Hierarchical cluster dendrogram of the analyzed Myoviridae. The relative dissimilarity between the phage proteomes (between 0.0 and 1.0) forms the basis for the proposed groupings. The dotted lines reflects the cut-off value used for the establishment of genera, used consistently for all Myoviridae and the previously defined Podoviridae [107]. Subfamily and tentative subfamily groupings are indicated in the grey and dotted boxes, respectively.
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