Comparative Optical Mapping: A New Approach for Microbial Comparative Genomics

The recent plethora of sequenced genomes has just ushered in a new era of genetics-based research. Although an impressive number of species have been, or are planned to be sequenced, the full value of such efforts will be fully accrued when patterns of variation can be discerned and annotated for many strains or isolates within a given species. As such, bacteria are an ideal place to start investigations aimed at the discernment of genome rearrangements, chromosome deletions, and horizontal transfer of foreign DNA, since these events help drive bacterial evolution. For example, genome remodeling events may cause irreversible gene loss, or add novel functionalities to an organism. Unfortunately, current approaches do not adequately identify and characterize such large-scale genomic rearrangements. The Optical Mapping System, developed in our laboratory creates high resolution maps of entire genomes, using DNA directly extracted from cells—this approach obviates the need for libraries, PCR, and probe technologies. The system uses a complex blend of single molecule technologies to enable high throughput and the construction of reliable maps. This capability has been proven by the construction and sequence comparison of 13 bacterial optical maps, and 3 parasites. Recent advances in both throughput and resolution of the Optical Mapping System has enabled genomic comparisons amongst different strains of the same species or closely related species, allowing for the pinpoint discernment of insertions, deletions and rearrangements. Comparisons of optical maps vs. in silico maps, and in silico vs. in silico maps constructed for two strains of Yersinia pestis (CO-92 biovar Orientalis and KIM), E. coli K12 and Shigella flexneri 2a, two strains of S. flexneri (2a and Y), and two strains of Rhodobacter sphaeroides (2.4.1 and ATCC 17029) have revealed regions of homology, insertion sites and a panoply of rearrangements. These results portend the wide use of Optical Mapping to uniquely provide genome structural details for a large number of strains, isolates or even closely related species, in ways that would complement direct sequence analysis.