Additional file 1: Figure S1. of Reconstruction of the evolution of microbial defense systems

Gains and losses in ATGC068-Corynebacterium. Figure S2. Gains and losses in ATGC081-Clostridium. Figure S3. Gains and losses in ATGC159-Propionibacterium. Figure S4. Count output for ATGC068-Corynebacterium. Figure S5. Example of multiple independent substitutions of CRISPR-Cas system type II-C to type I-E. Figure S6. Example of predicted gain by COUNT of Abi2 gene in a large loci with multiple gains and losses. Figure S7. Example of TA gene loss. Figure S8. Count output for ATGC081-Clostridium. Figure S9. Example of gain of four DS genes in Clostridium botulinum A2 str Kyoto. Figure S10. Count output for ATGC159-Propionibacterium. Figure S11. Locus details for Fig. 7c. Figure S12. Example of TA gene gain (within a large locus) in Propionibacterium acnes C1. Figure S13. Density distribution of p-values from the randomization test. Figure S14. Distribution of defense systems and dynamic events in 18 genomes. Figure S15. Scheme of the methodology used to test randomness in the distribution defense genes and dynamic events in the chromosome. Table S1. Distribution of defense systems COGs in ATGCs. Table S2. Number of the defense systems normalized by the total number of genes (COGs). Table S3. Genome dynamics in defense systems, including gain, loss, expansion and reduction: (a) total number of events; (b) events relative to the number of COGs and (c) events relative to the number of COGs and genomes. Defense systems with less than 10 genes or less than 10 events are left empty. Table S4. Comparison of the genome dynamics in defense systems (relative to the dynamics in all genes) between life styles using the Welch Two Sample t-test implemented in R. Table S5. Comparison of the genome dynamics in defense systems (relative to the dynamics in all genes) between taxa using the Welch Two Sample t-test implemented in R. Table S6. Relative fluxes in defense systems. Table S7. Description of genes in Additional file 1: Figures. S1, S2 and S3. Table S8. Locus description of Additional file 1: Figure S9. Table S9. Locus description of Additional file 1: Figure S12. Table S10. P-values of Additional file 1: Figure S14. (DOCX 2297 kb)