2; BURPS1106A_3666 – 3701). However, this region also contains three transposases, and so was not considered

in the analysis reported here. Bacteriophage clusters Results from the Dotter analysis allowed a preliminary Cell Cycle inhibitor clustering of prophages and prophage-like regions. These groups were further refined by examination of BLASTP protein distance data, resulting in the clustering of 32 of the 37 PIs and prophages into each of four groups (data not shown). Cluster composition was very similar between selleck compound the three BLASTP-distance FITCH trees and agreed with DOTTER results, although branch positions varied slightly (Fig. 2). Seven prophages/PIs clustered into the Siphoviridae-like group, so named because of the inclusion of the previously published bacteriophages ϕ1026b [6] and ϕE125 [21]. Bacteriophage ϕ644-2, described in this study, is also a member of this group (Fig. 2). Prophages in this group have long non-contractile tails and termini with cohesive ends. The cos site, present in ϕ1026b and ϕE125, was identified in all other members of this group. The Myoviridae-like group consists of 15 prophages/PIs (Fig. 2). Phages in this group, identified by the inclusion of ϕK96243 (GI2) [3] and ϕ52237, typically have contractile tails and terminal repeats [48]. Three subgroups were identified within the Myoviridae-like class (Fig. 2). Subgroup A contains ϕK96243,

MM-102 ϕ52237, ϕE202, and four other prophages/PIs. Bacteriophage ϕE12-2 and five prophages/PIs clustered to form subgroup B, including two (PI-406E-2 and PI-S13-2) which appear to be more distantly related. The Mu-like Myoviridae group contains only two prophages: BcepMu [29] and ϕE255. Both left and right phage ends at the host/phage Protein kinase N1 junction in BcepMu [29] were located at the ends of ϕE255, with 95% and 91% identity, respectively. No significant identity was found between either of the two Mu-like prophages and any of the other prophages or prophage-like sequences. Two undefined groups were also identified: undefined-1 contains four PIs, and undefined-2 has five (Fig.2).

Interestingly, undefined-2 contains five of the eight PIs identified in the three B. multivorans strains. Finally, six sequences had no significant similarity to any other sequence and were thus considered unclustered, including PI-668-1, PI-406E-1, PI-LB400-1, GI3, Bcep22 and Bcep781. Burkholderia bacteriophages are populated by morons Genomic comparisons of all the phages in each class revealed that the genomes are arranged in mosaic structures. Each of the phylogenetic classes of phages contains distinct local collinear blocks (LCB), also called synteny blocks, which are differentially present among the phages in that group (Fig. 3). Within each group, the synteny blocks are shuffled among the genomes (Fig. 3), suggesting that several of the phages have undergone dramatic genomic rearrangements.