Several methods can be used to study genome evolution. Most of the time, genome evolution is studied through nucleotide sequence polymorphism. However, in some species, mutation rate is low and polymorphisms are mainly caused by chromosomal rearrangements. In such a case, chromosomal rearrangement is the only informative marker to study genome evolution. In this study, we focused on plant mitochondrial genome evolution at the structural level. Plant mitochondrial genomes have been described as highly rearranged, but no study has been conducted on their rearrangement evolution. We chose to analyze the diversity of plant mitochondrial genomes at the intraspecific level to work on a short evolutive scale, limiting rearrangement events among genomes. The study was conducted on two species : Zea mays and Beta vulgaris. Moreover, besides structural polymorphisms, plant mitochondrial genomes contain large number of duplicated elements which are not taken into account by rearrangement tools if orthologous and paralogous relations are not established. Based on the hypothesis that the duplicated elements were caused by tandem duplication events, we proposed a new approach to find, sort and differentiate duplicated elements. This method led to phylogenies based on rearrangement events consistent with phylogenies based on nucleotide sequences. The comparison of genome evolution between maize and beet allowed us to show the existence of different evolution histories and mechanisms between these two species. We also observed evolutionary differences at the intraspecific level, raising the question of sampling strategy when genomes are compared at the interspecific level.
