Genomic structure and content of Agrocybe aegerita mitochondrial DNA contain essential information regarding the evolution of this gourmet mushroom. In this study, eight isolates of A. aegerita were sequenced and assembled into complete mitochondrial genomes. The mtDNA of the isolate Ag0067 contained two genotypes, both of which were quadripartite architecture consisting of two identical inverted repeats, separated by a small single-copy region and a large single-copy region. The only difference was opposite directions of the small single-copy region. The mtDNAs ranged from 116,329 bp to 134,035 bp, harboring two large identical inverted repeats. Genes of plasmid-origin were present in regions flanked by inverted repeat ID2. Most of the core genes evolved at a relatively low rate, whereas five tRNA genes located in corresponding regions of Ag0002:1-14000 and Ag0002:50001-61000 showed higher diversity. A long fragment inversion (10 Kb) was suggested to have occurred during the differentiation of two main clades, leading to two different gene orders. The number and distribution of the introns varied greatly among the A. aegerita mtDNAs. Fast invasion of short insertions likely resulted in the diversity of introns as well as other non-coding regions, increasing the variation of the mtDNAs. We raised a model about the evolution of the large repeats to explain the unusual features of A. aegerita mtDNAs. This study constructed quadripartite architecture of A. aegerita mtDNAs analogous to chloroplast DNA, proposed an interconversion model of the divergent mitochondrial genotypes with large inverted repeats. The findings could increase our knowledge of fungal evolution.

茶树菇线粒体DNA的基因组结构和含量包含有关这种美味蘑菇进化的重要信息。在这项研究中，对八个A. aegerita分离株进行了测序，并将其组装成完整的线粒体基因组。分离株Ag0067的mtDNA包含两种基因型，这两种基因型都是四联结构，由两个相同的反向重复序列组成，由一个小的单拷贝区域和一个大的单拷贝区域分开。唯一的区别是小单拷贝区域的方向相反。mtDNA 的长度范围为 116,329 bp 至 134,035 bp，包含两个大的相同反向重复序列。质粒来源的基因存在于反向重复 ID2 侧翼的区域中。大多数核心基因的进化速度相对较低，而位于Ag0002：1-14000和Ag0002：50001-61000相应区域的5个tRNA基因表现出较高的多样性。有人认为在两个主要进化枝的分化过程中发生了长片段倒置（10 Kb），导致了两个不同的基因顺序。A. aegerita mtDNA中内含子的数量和分布差异很大。短插入的快速入侵可能导致内含子和其他非编码区域的多样性，增加线粒体DNA的变异。我们提出了一个关于大重复序列进化的模型来解释A. aegerita mtDNA 的不寻常特征。本研究构建了类似于叶绿体 DNA 的A. aegerita mtDNA 的四方结构，提出了具有大反向重复序列的不同线粒体基因型的相互转换模型。这些发现可以增加我们对真菌进化的了解。