Hotel Estoril Eden, Monte Estoril,
Portugal
5-8 October 2005

 

 
 

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P
hysical and Genetic Mapping in Whole Genome Sequencing Era: an Overview

Lbia Z-Z
University of Lisbon, Sequencing Unit, ICAT, Portugal

Nowadays, a huge amount of genomic sequence information becomes available everyday through genome sequencing projects. However, the physical methods for the construction of bacterial chromosome maps, by a top-down approach using pulsed field gel electrophoresis (PFGE) remains a powerful tool in the study of genome structure and plasticity, namely in the framework of phylogenetics and comparative evolutionary studies.

Comparative analysis of genome structure at intraspecific level enables the identification of the genetic events (namely, homologous recombination, insertion/deletion, duplication, transposition) and some DNA sequences possibly involved in rearrangements (as IS elements, prophages and duplicated regions/genes). This macrodiversity is displayed through the comparative analysis of gene positioning and macrorestriction polymorphisms in the chromosome maps of each strain. Comparison of genomes of strains belonging to divergent groups can also give some insights of the genomic mechanisms driving evolution in a bacterial phylogenetic group.

The laboratory procedures for the construction of bacterial genomic maps, namely with examples of Lactic Acid Bacteria chromosome mapping, will be presented. The advantages of a combined statistical approach during map construction in determining the overlapping probabilities of macrorestriction fragments and directing experimental procedures (saving time and money) will be discussed.