Fig. 3

Porphyromonas gingivalis CRISPR arrays encode spacers that target phages in other strains. Predicted CRISPR-Cas systems in each strain of Pg are shown; quantities of each system are related to cell color saturation (A). CRISPR spacer hits from arrays found in Pg are mapped onto Pg phages shown in midpoint-rooted tree at the top (30 full, 5 partial; “b” suffix indicates version of an “a” phage found in a different assembly of the Pg strain (based on whole genome nucleotide BLAST distance and scaled by VICTOR [28] d0 formula, recommended for nucleic acid datasets) dark blue cells indicate 0-mismatch spacer-phage nucleotide identity, light blue indicates 1-mismatch, and vignetting indicates presence of the entire prophage in the bacteria (as shown in Fig. 1) (B). Percent of total spacers found in each Pg that have 0- or 1-mismatch to a predicted phage are shown; same coloring as panel B (C). CRISPR-Cas systems were identified by CCTyper [55] and mapped to phage genomes with Bowtie [56]. Phylogenetic relationships among Pg are shown on the left (79 strains; 88 leaves, including 3 substrains and 6 strains with independent assemblies), based on concatenated ribosomal protein genes