The microsatellites of Escherichia coli: rapidly evolving repetitive DNAs in a non-pathogenic prokaryote.

We have demonstrated hypervariability of native short-motif repeats (microsatellites) in Escherichia coli. Twenty-five of the longest microsatellites in the E. coli genome were identified. These were analysed for length variability among 22 wild-type (non-mutator) isolates from the E. coli collection of reference (ECOR). Non-coding mononucleotide repeats are consistently polymorphic among these genetically diverse E. coli. Length differences in variable microsatellites allowed all E. coli strains examined to be uniquely differentiated. Phylogenetic analysis of the variable repeats shows ubiquitous homoplasy at the level of divergence represented by the sample set, suggesting that these markers are hypermutable and should prove valuable for the discrimination of closely related strains that are not otherwise genetically differentiable. Genomic analyses suggest that similar markers are also likely to be found in all other prokaryotes.