Figure 1

cas3 phylogeny and CRISPR repeat diversity. Condensed maximum likelihood phylogeny of cas3 nucleotide sequences reveals clades corresponding to Cas array subtype. The two major clades delineate known (I-E, I-C, I-B) and previously undescribed (I-U) subtypes. The order of genes for each subtype is displayed on the right. Gene annotations in parentheses designate hypothetical proteins with low identity to those indicated. In the I-B arrays, cas8b was replaced by a larger gene related to cst1. The total number of each array subtype among the 75 genomes is shown in the condensed nodes. Six arrays were missing several genes and therefore excluded from the analysis. Nodal support values (● above 80%, ▲ 100%) were obtained by 1000 bootstrap replicates (see Additional file 2 for the full tree including strain names and bootstrap values). Consensus repeat sequences in the associated CRISPR loci (indicated in gray) were specific to each array subtype and mostly showed considerable conservation.