Fig. 10

Diversity and interactions between predicted prophages and CRISPR-Cas systems across industrial clostridia. (A) Prophage CCP-like tree with prevalence across host species. The tree was based on a concatenated alignment following the CCP model⁸⁴. (B) Schematic representation of the two types of CRISPR-Cas loci detected across industrial clostridia. Cas genes were annotated and colored as described earlier³⁴. (C) Prevalence and spacer content of CRISPR arrays. For each species, the boxplots show the distribution of number of spacer for each array (middle panel) and the frequency detection of each spacer across CRISPR-encoding genomes from the same species (right panel). The number of CRISPR-encoding genomes is indicated to the left of the middle panel, and spacer detection frequency across the species were not included when only a single CRISPR-Cas genome was available (C. butyricum). (D) Global prophage:genome network. Genome nodes (circle) are connected to prophage nodes (squares) when a spacer from this genome matches the prophage with 0 or 1 mismatch. Genomes and prophages are colored based on the (host) species, edges are colored based on the prophage carriage of the genome: black for spacers matching a prophage from the same genome, gray for spacers matching a prophage from a different genome. The inset bar chart shows the distribution of connection type: matches to prophages from other species, matches to prophages from the same species but a different genome, and matches to prophages from the same genome, i.e. “self-hit”.