Expanding the Diversity of Mycobacteriophages: Insights into Genome Architecture and Evolution
Figure 11
Acquisition of an HNH homing endonuclease in mycobacteriophage Pumpkin.
A. Alignment of the Cluster E genomes 244, Pumpkin, and Cjw1 reveals the presence of a Pumpkin gene (40) that is absent from other Cluster E genomes. B. Phamily circles of Phams 1706, 1707, 1567, and 2942, which include Pumpkin genes 37, 38, 39, and 40. Pham1706 and 1707 have members exclusively within Cluster E genomes. Pham 1567 is more widely distributed with members in Subcluster A1, some in A2, F2, and singleton genomes, and is functionally a glutaredoxin. Pham 2942 is a homing endonuclease and is broadly distributed among the mycobacteriophages. Each of the 80 genomes is shown on the circumference of each circle – arranged by cluster – with arcs indicating pairs of genomes containing a pham member; thicker arcs indicate closer similarity. Red and blue arcs show BlastP and ClustalW comparisons respectively. C. Phylogenetic reconstruction of Pham2942. All members are distantly related, and Pumpkin gp40 probably was acquired independently from other Cluster E acquisitions (Porky gp109, 244 gp112). Members are colored according to cluster of parent genome: A1, green; F1, purple; E, orange; I1, blue; B3, yellow; Omega is a singleton. The neighbor-joining (NJ) tree was drawn by NJPlot using output from an alignment in ClustalW; bootstrap values from 1000 iterations are shown.