Classification of Myoviridae bacteriophages using protein sequence similarity

Abstract

BackgroundWe 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.ResultsCoreGenes/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."ConclusionThe hierarchical clustering of these groupings provide biologically significant subdivisions, which are consistent with our previous analysis of the Podoviridae.

Identification and characterization of ϕH111-1

“…Comparing ϕH111-1 and P2 with CGUG (Table 2), the proteomes are 25.58% similar with respect to P2, placing ϕH111-1 in the same subfamily (Peduovirinae) but a different genus. 15 We could not identify any previously characterized phages with ≥ 40% similarity that would belong to the same genus as ϕH111-1. Currently, phages with the most similar proteomes are AcaML1 of Acidithiobacillus caldus (JX507079.1; 28.17% similar) and the "Vhmllikevirus" phages VHML of Vibrio harveyi (NC_004456.1; 28.07% similar) and both [16][17][18][19] Although these phages share subfamily-level similarity, they are very distinct with respect to aspects such as host, gene content, and lifestyle.…”

“…26,[30][31][32] Genome and proteome relatedness were assessed using BLASTN and CoreGenesUniqueGenes (CGUG) with a cutoff score of 75, respectively. 14,15,26 The genome map was constructed using Geneious. 33 The ϕH111-1 prophage sequence can be found in the GenBank database under B. cenocepacia H111 accession number NZ_CAFQ01000043.1 (bp 156,838-199,809).…”

Chimeric viruses blur the borders between the major groups of eukaryotic single-stranded DNA viruses

“…Genetic mosaicism has been previously pointed out as a factor impeding meaningful classification of tailed bacteriophages (order Caudovirales) 54 . However, the coding capacity of tailed bacteriophages is typically large enough to accommodate a representative core gene set 55,56 sufficient for hierarchical clustering of these viruses into biologically significant subdivisions 57,58 . For viruses with small genomes, on the other hand, the effect of horizontal gene transfer on the 'identity' of a viral group is considerably more acute.…”

Bacteriophage P2

“…P2 is a member of the subfamily Peduovirinae, which has been further divided into the P2-like viruses and the more distantly related (based on sequence similarity) HP1-like viruses. 4 In this review, members of these 2 genera will be referred to as P2-like and HP1-like, and the group collectively as P2-related. A more extensive review by Nilsson and Hagga rd-Ljungquist can be found in The Bacteriophages.…”