High variability of mitochondrial gene order among fungi

rates, genome size reduction, endosymbiosis From their origin as an early alpha proteobacterial endosymbiont to their current state as cellular organelles, large-scale genomic reorganization has taken place in the mitochondria of all main eukaryotic lineages. So far, most studies have focused on plant and animal mitochondrial genomes (mtDNA) but fungi provide new opportunities to study highly differentiated mtDNAs. Here we analyzed 38 complete fungal mitochondrial genomes to investigate the evolution of mtDNA gene order among fungi. In particular, we looked for evidence of non-homologous intrachromosomal recombination and investigated the dynamics of gene rearrangements. We analyzed the effect that introns, intronic open reading frames (ORFs) and repeats may have on gene order. Additionally, we asked whether the distribution of transfer RNAs (tRNAs) evolves independently to that of mt protein-coding genes. We found that fungal mitochondrial genomes display remarkable variation between and within the major fungal phyla in terms of gene order, genome size, composition of intergenic regions, and presence of repeats, introns and associate