Physical Mapping of Bacterial Genomes

The use of physical maps for the description and comparison of bacterial genomes has dramatically increased in the last few years with the advent of powerful tools for the construction of physical maps of large DNA molecules. The availability of restriction enzymes that cut whole bacterial genomes only a few times together with the use of pulsed-field gel electrophoresis to resolve and size the resulting fragments has allowed the direct restriction mapping of bacterial genomes. Nearly 50 bacterial genomes have been mapped for one or more of these enzymes. The isolation of complete ordered clone banks (encyclopedias) has been achieved for Escherichia coli, Rhodobacter capsulatus, Mycoplasma pneumoniae, Mycobacterium leprae, Halobacterium sp. and Haloferax volcanii PS2. By merging maps of the clones, high-resolution restriction maps of complete bacterial genomes have been obtained. Also, the accessibility of sequence databases, software tools, and curated databases for particular genomes has improved the usefulness and expanded the utility of both the maps and the encyclopedias. In this paper I review (i) the low-resolution maps of E. coli and other bacterial genomes obtained directly by fragmentation and measurement of fragments on pulsed-field gels of whole bacterial DNA, (ii) the bacterial genome encyclopedias and methods for isolating these complete ordered clone banks, and (iii) uses to which the maps and the encyclopedias can be put.