Identification and localization of differences between Escherichia coli and Salmonella typhimurium genomes by suppressive subtractive hybridization

The availability of bacterial genome sequences raises an important new prob lem - how can one move from completely sequenced microorganisms as a refere nce to the hundreds and thousands of other strains or isolates of the same or related species that will not be sequenced in the near future? An effici ent way to approach this task is the comparison of genomes by subtractive h ybridization. Recently we developed a sensitive and reproducible subtractio n procedure for comparison of bacterial genomes, based on the method of sup pression subtractive hybridization (SSH). In this work we demonstrate the a pplicability of subtractive hybridization to the comparison of the related but markedly divergent,bacterial species Escherichia coli and Salmonella ty phimurium. Clone libraries representing sequence differences were obtained and, in the case of completely sequenced E. coli genome, the differences we re directly placed in the genome map. About 60% of the differential clones identified by SSH were present in one of the genomes under comparison and a bsent from the other. Additional differences in most cases represent sequen ces that have diverged considerably in the course of evolution. Such an app roach to comparative bacterial genomics can be applied both to studies of i nterspecies evolution - to elucidate the "strategies" that enable different genomes to fit their ecological niches - and to development of diagnostic probes for the rapid identification of pathogenic bacterial species.