title: High variability of mitochondrial gene order among fungi.
abstract: 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 (mt) genomes (mtDNA), but fungi provide new opportunities to study highly differentiated mtDNAs. Here, we analyzed 38 complete fungal mt genomes to investigate the evolution of mtDNA gene order among fungi. In particular, we looked for evidence of nonhomologous intrachromosomal recombination and investigated the dynamics of gene rearrangements. We investigated 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 mt 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 associated ORFs. Our results support previous evidence for the presence of mt recombination in all fungal phyla, a process conspicuously lacking in most Metazoa. Overall, the patterns of rearrangements may be explained by the combined influences of recombination (i.e., most likely nonhomologous and intrachromosomal), accumulated repeats, especially at intergenic regions, and to a lesser extent, mobile element dynamics.
authors: Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona, Spain.
authors: Gabriela
authors: G
authors: Aguileta
authors: Damien M
authors: DM
authors: de Vienne
authors: Oliver N
authors: ON
authors: Ross
authors: Michael E
authors: ME
authors: Hood
authors: Tatiana
authors: T
authors: Giraud
authors: Elsa
authors: E
authors: Petit
authors: Toni
authors: T
authors: Gabaldón
mesh_terms: D004272:DNA, Mitochondrial / Q000235:genetics*; D005656:Fungal Proteins / Q000235:genetics*; D005658:Fungi / Q000145:classification / Q000235:genetics*; D023061:Gene Order; D015321:Gene Rearrangement; D050259:Genes, Mitochondrial; D014644:Genetic Variation; D054629:Genome, Mitochondrial; D007438:Introns; D008928:Mitochondria / Q000235:genetics; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D010802:Phylogeny
chemical_list: D004272:DNA, Mitochondrial; D005656:Fungal Proteins
keywords: Basidiomycota; basal fungi; endosymbiosis; fungal phylogeny; genome size reduction; rearrangement rates; sordariomycetes