Comparison of the mitochondrial genome sequences of six Annulohypoxylon stygium isolates suggests that short fragment insertions as a potential factor leading to larger genomic size
2018
Deng, Youjin | Hsiang, Tom | Li, Shuxian | Lin, Longji | Wang, Oingfu | Chen, Qinghen | Xie, Baoqui | Ming, Ray
Mitochondrial DNA (mtDNA) is a core non-nuclear genetic material found in all eukaryotic organisms, the size of which varies extensively in eumycota, even within species. In this study, mitochondrial genomes of six isolates of Annulohypoxylon stygium were assembled from raw reads from PacBio and Illumina sequencing. Comparisons of mtDNAs of six isolates were conducted to analyze the diversity of genomic structures, conserved genes, intergenic regions and introns. Mitochondrial genomes of six isolates of A. stygium ranged from 132 kb to 147 kb in size, contained same sets of conserved protein-coding, tRNA and rRNA genes, and shared the same gene arrangements and orientation. In addition, most intergenic regions were homogeneous and had similar size except for the region between cytochrome b (cob) and cytochrome c oxidase I (cox1) genes. Sixty-six intron insertion sites and 100 different introns were detected in these genomes. Each genome contained more than 46 introns, which varied in distribution and content. Introns from homologous insertion sites also showed high diversity in size, type and content. Comparison of introns within the same insertion site revealed some complex introns, such as twintrons and orf-less introns. There were 45 short fragment insertions which were detected within introns, intergenic regions, or as introns, some of them located at critical conserved domain regions in the intron. Insertions of short fragment such as small inverted repeats might affect or hinder the movement of introns, which allow for intron accumulation in mitochondrial genomes, and enlarge their size. This study revealed that the evolution of fungal mitochondrial introns was complex, and the results suggested short fragment insertions as potential sources of large mitochondrial genomes in A. stygium.
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