Fig. 1

Genomic relationship of D29 to other Cluster A relatives. a. Pairwise BLAST-based whole genome alignments of D29 and several Cluster A mycobacteriophages, with the name and subcluster designation indicated. Grey boxes above and below the ruler in each map represent genes transcribed on the top and bottom strands, respectively. The color spectrum between genomes represents pairwise nucleotide similarity, from high similarity (violet) to no detectable similarity (white). Maps were generated using Phamerator (Cresawn et al. 2011). The positions of several genes highly conserved across Cluster A phages are indicated by arrows for reference (tmp = tape measure protein; pol = DNA polymerase; rnr = ribonucleotide reductase). b. Expanded view of StarStuff, Pomar16, and Kerberos genes deleted in D29. The predicted functions are shown, but note that the functions of most of the genes in this region are not known. c-e Whole genome alignments of the Subcluster A2 phages from panel A were created with Mauve, and mutation events (SNPs and alignment gaps) were identified. c. Phylogenetic tree was constructed based on the whole genome alignment. d. Alignment gaps were mapped to the phylogenetic branches in the D29 clade (enlarged from panel B) using Count to predict whether gaps were due to insertion or deletion events. Bar charts reflect the total number of predicted events per branch. e. Mutation events across the D29 clade are mapped onto the representative StarStuff genome. The histogram reflects the number of SNPs identified. The individual insertion (circle) and deletion (square) events predicted from Count are labeled below and shaded by size. Several highly-conserved genes are labeled as in panel A for reference. f. The precise coordinates of the deletion event in D29 that has rendered it lytic (Ford et al. 1998) are labeled in all phages in this clade, with the associated size of the deletion indicated below. Arrows indicate the 3 bp sequence that may have facilitated the deletion