Evolution of gene order conservation in prokaryotes

Gene order is extensively conserved between closely related species, but rapidly becomes less conserved among more distantly related organisms, probably in a cooperative fashion. This trend could be universal in prokaryotic genomes, as archaeal genomes are likely to behave similarly to bacterial genomes. Gene order conservation could therefore be used as a valid phylogenetic measure to study relationships between species. Even between very distant species, remnants of gene order conservation exist in the form of highly conserved clusters of genes. This suggests the existence of selective processes that maintain the organization of these regions. Because the clusters often span more than one operon, common regulation probably cannot be invoked as the cause of the maintenance of gene order.Gene order conservation is a genomic measure that can be useful for studying relationships between prokaryotes and the evolutionary forces shaping their genomes. Gene organization is extensively conserved in some genomic regions, and further studies are needed to elucidate the reason for this conservation.Completely sequenced genomes enable the study of relations between organisms in terms of the complete set of genes they possess. Genomic properties have been proposed as the most convenient tool for studying these relationships, as they are global properties that may circumvent many of the difficulties of classical molecular phytogenies [1]. Common gene content [2,3] or conservation of families of proteins [4] are examples of this kind of genomic information. From this genomic perspective, conservation of gene order is a very informative measure that may provide information both about the function and interactions of the proteins these genes encode [5,6], and about the evolution of the genomes and the organisms themselves.Gene order is generally well preserved at close phylogenetic distances [7]. When the species are not closely related, the degree of gene order conservation is usu