Comparative analysis of mitochondrial genomes from closely related Rhynchosporium species reveals extensive intron invasion

[Display omitted] •We report the complete mitochondrial genomes of four closely related fungal species.•Three mitochondrial genomes significantly expanded as result of intron invasion.•The mitochondrial mutation rate was 77 times higher than the nuclear mutation rate.•Our study revealed a very dynam...

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Bibliographic Details
Published in:Fungal genetics and biology 2014-01, Vol.62, p.34-42
Main Authors: Torriani, Stefano F.F., Penselin, Daniel, Knogge, Wolfgang, Felder, Marius, Taudien, Stefan, Platzer, Matthias, McDonald, Bruce A., Brunner, Patrick C.
Format: Article
Language:English
Subjects:
Ascomycota - genetics
DNA, Mitochondrial - genetics
Genome architecture
Genome evolution
Genome, Mitochondrial
Horizontal intron transfer
Intron encoded proteins
Introns
Mutation Rate
PAC species
Phylogeny
Sequence Analysis, DNA - methods
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Summary:[Display omitted] •We report the complete mitochondrial genomes of four closely related fungal species.•Three mitochondrial genomes significantly expanded as result of intron invasion.•The mitochondrial mutation rate was 77 times higher than the nuclear mutation rate.•Our study revealed a very dynamic mitochondrial genome evolution. We sequenced and annotated the complete mitochondrial (mt) genomes of four closely related Rhynchosporium species that diverged ∼14,000–35,000years ago. During this time frame, three of the mt genomes expanded significantly due to an invasion of introns into three genes (cox1, cox2, and nad5). The enlarged mt genomes contained ∼40% introns compared to 8.1% in uninvaded relatives. Many intron gains were accompanied by co-conversion of flanking exonic regions. The comparative analysis revealed a highly variable set of non-intronic, free-standing ORFs of unknown function (uORFs). This is consistent with a rapidly evolving accessory compartment in the mt genome of these closely related species. Only one free-standing uORF was shared among all mt genomes analyzed. This uORF had a mutation rate similar to the core mt protein-encoding genes, suggesting conservation of function among the species. The nucleotide composition of the core protein-encoding genes significantly differed from those of introns and uORFs. The mt mutation rate was 77 times higher than the nuclear mutation rate, indicating that the phylogeny inferred from mt genes may better resolve the phylogenetic relationships among closely related Rhynchosporium species than phylogenies inferred from nuclear genes.
ISSN:1087-1845
1096-0937
DOI:10.1016/j.fgb.2013.11.001