Evolution of genome organization in Oenococcus oeni revealed by physical and genetic map comparison

Abstract

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 was also examined by a bottom-up approach, using sequence data accessible from Joint Genome Institute, which enabled the confirmation of gene location and assessment of transcription direction. Comparison of genomic maps revealed O. oeni as a homogeneous species and supported the existence of two different genomic groups, although in a too much early phase of divergence to be considered as subspecies. O. oeni genomic organization 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 may be observed in O. oeni chromosomes, being the neighbouring region of the replication terminus the most conserved one. Since most of the structural polymorphisms can be correlated to the presence of transposase genes and sites of prophage integration, occurrence of macrodiversity events, as insertions-deletions, duplications or inversions of larger genomic regions seems to be ruled out in O. oeni evolution.