High variability of mitochondrial gene order among fungi

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 (mt...

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Bibliographic Details
Published in:Genome biology and evolution 2014-02, Vol.6 (2), p.451-465
Main Authors: Aguileta, Gabriela, de Vienne, Damien M, Ross, Oliver N, Hood, Michael E, Giraud, Tatiana, Petit, Elsa, Gabaldón, Toni
Format: Article
Language:English
Subjects:
DNA, Mitochondrial - genetics
Fungal Proteins - genetics
Fungi - classification
Fungi - genetics
Gene Order
Gene Rearrangement
Genes, Mitochondrial
Genetic Variation
Genome, Mitochondrial
Introns
Life Sciences
Mitochondria - genetics
Molecular Sequence Data
Open Reading Frames
Phylogeny
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Summary: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.
ISSN:1759-6653
1759-6653
DOI:10.1093/gbe/evu028