Mycogone perniciosa is the main causative agent of wet bubble disease, which causes severe damage to the production of the cultivated mushroom Agaricus bisporus around the world. Whole-genome sequencing of 12 isolates of M. perniciosa was performed using the Illumina sequencing platform, and the obtained paired-end reads were used to assemble complete mitochondrial genomes. Intraspecific comparisons of conserved protein-coding genes, transfer RNA (tRNA) and ribosomal RNA (rRNA) genes, introns, and intergenic regions were conducted. Five different mitochondrial DNA (mtDNA) haplotypes were detected among the tested isolates, ranging from 89,080 to 93,199 bp in length. All of the mtDNAs contained the same set of 14 protein-coding genes and 2 rRNA and 27 tRNA genes, which shared high sequence similarity. In contrast, the number, insertion sites, and sequences of introns varied greatly among the mtDNAs. Eighteen of 43 intergenic regions differed among the isolates, reflecting 65 single nucleotide polymorphisms, 76 indels, and the gain/loss of nine long fragments. Intraspecific comparison revealed that two introns were located within tRNA genes, which is the first detailed description of mitochondrial tRNA introns. Intronic sequence comparison within the same insertion sites revealed the formation process of two introns, which also illustrated a fast evolutionary rate of introns among M. perniciosa isolates. Based on the intron distribution pattern, a pair of universal primers and four pairs of isolate-specific primers were designed and were used to identify the five mtDNA types. In summary, the rapid gain or loss of mitochondrial introns could be an ideal marker for population genetics analysis.

多年生霉菌是湿泡病的主要病原体，对全世界栽培的蘑菇双孢蘑菇的生产造成严重损害。12种多年生分支杆菌的全基因组测序使用Illumina测序平台进行测序，并将获得的配对末端读数用于组装完整的线粒体基因组。进行了保守蛋白编码基因，转移RNA（tRNA）和核糖体RNA（rRNA）基因，内含子和基因间区域的种内比较。在测试的分离物中检测到五种不同的线粒体DNA（mtDNA）单倍型，长度为89080到93199 bp。所有的mtDNA都包含同一组14个蛋白质编码基因以及2个rRNA和27个tRNA基因，它们具有高度的序列相似性。相反，内含子的数量，插入位点和序列在mtDNA之间差异很大。在43个基因间区域中有18个在分离物中有所不同，反映出65个单核苷酸多态性，76个插入缺失和9个长片段的得失。种内比较显示，两个内含子位于tRNA基因内，这是线粒体tRNA内含子的第一个详细描述。在相同插入位点内的内含子序列比较揭示了两个内含子的形成过程，这也说明了内含子之间的快速进化速率。多年生支原体分离株。根据内含子分布模式，设计了一对通用引物和四对分离物特异性引物，并用于鉴定五种mtDNA类型。总之，线粒体内含子的快速增减可能是进行群体遗传学分析的理想标记。