plosone-phylo
pone.0011126.g001.png
General features of the 4 distinct CRISPR loci.
(A) - Position of the 4 distinct CRISPR loci in the chromosomes. Core genes are represented in red; CRISPR in grey. (B) Evolution of the number of repeats of each CRISPR locus across the phylogenetic tree of the 27 E. coli, 7 Shigella, 16 Salmonella, and 1 E. fergusonii strains. The tree was reconstructed from the concatenated alignments of 1241 genes of the core genome of Escherichia and Salmonella strains (see Methods). The main nodes of these branches were supported with high bootstrap values (>90%). Phylogenetic groups of the strains are indicated with colors on the right part of the figure. Very closely related genomes, at distances lower than 0.02% substitutions per position are indicated by a vertical black line; black circles correspond to genomes removed of some analysis, as marked in the text, to avoid redundancy. (C) Sequence logo for all but terminal repeats of the CRISPR1-CRISPR2 arrays and those of the CRISPR3-CRISPR4 arrays. Predicted secondary structure of the most frequent sequence within each CRISPR pairs using RNAfold (see Methods). (D) Positive correlation between the number of repeats in the CRISPR1 and those of the CRISPR2 in each strain (R2 = 0.63; p<0.0001). Phylogenetic group of the strains is indicated with colors (see (B)); full circle: CRISPR/cas system is complete in the strain; open circle: the system is partial; cross: the system is absent.
pone.0011126.g001.png
General features of the 4 distinct CRISPR loci.
(A) - Position of the 4 distinct CRISPR loci in the chromosomes. Core genes are represented in red; CRISPR in grey. (B) Evolution of the number of repeats of each CRISPR locus across the phylogenetic tree of the 27 E. coli, 7 Shigella, 16 Salmonella, and 1 E. fergusonii strains. The tree was reconstructed from the concatenated alignments of 1241 genes of the core genome of Escherichia and Salmonella strains (see Methods). The main nodes of these branches were supported with high bootstrap values (>90%). Phylogenetic groups of the strains are indicated with colors on the right part of the figure. Very closely related genomes, at distances lower than 0.02% substitutions per position are indicated by a vertical black line; black circles correspond to genomes removed of some analysis, as marked in the text, to avoid redundancy. (C) Sequence logo for all but terminal repeats of the CRISPR1-CRISPR2 arrays and those of the CRISPR3-CRISPR4 arrays. Predicted secondary structure of the most frequent sequence within each CRISPR pairs using RNAfold (see Methods). (D) Positive correlation between the number of repeats in the CRISPR1 and those of the CRISPR2 in each strain (R2 = 0.63; p<0.0001). Phylogenetic group of the strains is indicated with colors (see (B)); full circle: CRISPR/cas system is complete in the strain; open circle: the system is partial; cross: the system is absent.