Genome rearrangement by replication-directed translocation

Gene order in bacteria is poorly conserved during evolution(1-3). For examp le, although many homologous genes are shared by the proteobacteria Escheri chia coli. Haemophilus influenzae and Helicobacter pylori. their relative p ositions are very different in each genome, except local functional cluster s such as operons(3-6). The complete sequences of the more closely related bacterial genomes, such as pairs of Chlamydia(7-9), H. pylori(10,11) and My cobacterium species(12), now allow identification of the processes and mech anisms involved in genome evolution. Here we provide evidence that a substa ntial proportion of rearrangements in gene order results from recombination sites that are determined by the positions of the replication forks. Our o bservations suggest that replication has a major role in directing genome e volution.