Genome organization in Oenococcus oeni strains studied by comparison of physical and genetic maps

The genomic organization of nine strains of Oenococcus oeni belonging to two previously suggested divergent groups was examined by a top-down approach, including analysis of isolated genes and construction of physical and genetic maps. Genomic sequence data from Oenococcus oeni strain PSU-1 were also examined by a bottom-up approach, using sequence data accessible from the U.S. Joint Genome Institute (Walnut Creek, CA, USA), which enabled the confirmation of gene location and the assessment of transcription direction. A comparison of the genomic maps revealed that O. oeni is a homogeneous species and supported the existence of two different genomic groups, although in a phase of divergence much too early for the recognition of subspecies. The genomic organization of O. oeni is characterized by an unusual conserved distribution of the two rrn operons, located at least 500 kb apart from the putative chromosome replication origin. Differential degrees of conservation are observed in O. oeni chromosomes, the neighboring region of the replication terminus being the most conserved one. Since most of the structural polymorphisms can be correlated to the presence of transposase genes and sites of prophage integration, the occurrence of macrodiversity events, such as insertions-deletions, duplications, or inversions of larger genomic regions, can most likely be ruled out in O. oeni evolution.