Abstract
Sizes of mitochondrial genomes vary extensively between fungal species although they typically contain a conserved set of core genes. We have characterised the mitochondrial genome of the conifer root rot pathogen Heterobasidion irregulare and compared the size, gene content and structure of 20 Basidiomycete mitochondrial genomes. The mitochondrial genome of H. irregulare was 114, 193 bp and contained a core set of 15 protein coding genes, two rRNA genes and 26 tRNA genes. In addition, we found six non-conserved open reading frames (ORFs) and four putative plasmid genes clustered in three separate regions together with 24 introns and 14 intronic homing endonuclease genes, unequally spread across seven of the core genes. The size differences among the 20 Basidiomycetes can largely be explained by length variation of intergenic regions and introns. The Agaricomycetes contained the nine largest mitochondrial genomes in the Basidiomycete group and Agaricomycete genomes are significantly (p < 0.001) larger than the other Basidiomycetes. A feature of the Agaricomycete mitochondrial genomes in this study was the simultaneous occurrence of putative plasmid genes and non-conserved ORFs, with Cantharellus cibarius as only exception, where no non-conserved ORF was identified. This indicates a mitochondrial plasmid origin of the non-conserved ORFs or increased mitochondrial genome dynamics of species harbouring mitochondrial plasmids. We hypothesise that two independent factors are the driving forces for large mitochondrial genomes: the homing endonuclease genes in introns and integration of plasmid DNA.
Highlights
Mitochondria are believed to have a monophyletic origin from an endosymbiotic α-proteobacterium that was engulfed, more than one billion years ago, by a eukaryotic common ancestor (Gray et al 2001; Bullerwell and Lang 2005; Koumandou et al 2013)
Our observations show that variation in exchangeable gene content and repeat regions are important contributors to differences in mt genome size
Many fungal and plant species have mt plasmid DNA integrated in their mt genomes, despite the fact that no genes coding for integrase activity has been found in mt plasmids so far (Cahan and Kennell 2005)
Summary
Mitochondria are believed to have a monophyletic origin from an endosymbiotic α-proteobacterium that was engulfed, more than one billion years ago, by a eukaryotic common ancestor (Gray et al 2001; Bullerwell and Lang 2005; Koumandou et al 2013). The mitochondrial (mt) genomes contain considerably fewer genes than freeliving α-proteobacteria and many of the genes that are required for its function seem to have been transferred to the nucleus or replaced by already existing nuclear genes with similar function (Adams and Palmer 2003). Mitochondrial genomes occur either as circular or linear molecules (Burger et al 2003). Genes encoded by the mt genome can be divided into two groups: core genes and exchangeable genes. Core genes are involved in respiration, oxidative phosphorylation and translation (Burger et al 2003), while exchangeable genes are characterised by variation in type and number among species. Mitochondrial plasmids are commonly found in plant and fungal mitochondria and are selfreplicating genetic elements that have little or no homology
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