This is the abstract of a talk prepared for the Oeiras Mathematical and Computational Biology Workshop. June 20, 2003, Instituto Gulbenkian de Ciência
Abstract: The availability of 100 bacterial genomes allows the comparative analysis of genome structure and composition in relation to bacterial lifestyle and evolution. Replication plays a major role among the elements structuralizing Bacterial genomes. The replication asymmetries induce biases at the levels of nucleotide composition and gene distribution that strongly fashion the chromosome. As a consequence the latter seems more structured than previously thought. However, Bacterial genomes also contain a very significant number of repeats that may shuffle the chromosome. Such repeats may be present for many purposes. Hence, a trade-off is established between the advantage of having the potential for sequence variation and the disadvantages it produces, by stimulating rearrangements that disrupt the replication chromosomal structure. For example, it has been observed that repeats tend to be placed in the chromosome in such a way that the rearrangements they may induce provoke smaller disruptions to the chromosomal replication structure than expected by chance. Further, there is an important negative correlation between the number of repeats and the replication strand biases or the synteny conservation. In short, this is a talk on biases and repeats, but especially on order and disorder in bacterial genomes.