Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Greece.
Genome Biol Evol. 2020 Aug 1;12(8):1337-1354. doi: 10.1093/gbe/evaa126.
Fungal mitochondrial (mt) genomes exhibit great diversity in size which is partially attributed to their variable intergenic regions and most importantly to the inclusion of introns within their genes. These introns belong to group I or II, and both of them are self-splicing. The majority of them carry genes encoding homing endonucleases, either LAGLIDADG or GIY-YIG. In this study, it was found that these intronic homing endonucleases genes (HEGs) may originate from mt free-standing open reading frames which can be found nowadays in species belonging to Early Diverging Fungi as "living fossils." A total of 487 introns carrying HEGs which were located in the publicly available mt genomes of representative species belonging to orders from all fungal phyla was analyzed. Their distribution in the mt genes, their insertion target sequence, and the phylogenetic analyses of the HEGs showed that these introns along with their HEGs form a composite structure in which both selfish elements coevolved. The invasion of the ancestral free-standing HEGs in the introns occurred through a perpetual mechanism, called in this study as "aenaon" hypothesis. It is based on recombination, transpositions, and horizontal gene transfer events throughout evolution. HEGs phylogenetically clustered primarily according to their intron hosts and secondarily to the mt genes carrying the introns and their HEGs. The evolutionary models created revealed an "intron-early" evolution which was enriched by "intron-late" events through many different independent recombinational events which resulted from both vertical and horizontal gene transfers.
真菌的线粒体（mt）基因组在大小上表现出很大的多样性，这部分归因于它们可变的基因间区，更重要的是，它们的基因中包含内含子。这些内含子属于 I 组或 II 组，它们都可以自我剪接。它们中的大多数携带编码归巢内切核酸酶的基因，要么是 LAGLIDADG，要么是 GIY-YIG。在这项研究中，发现这些内含子归巢内切核酸酶基因（HEGs）可能源自 mt 独立的开放阅读框，这些阅读框如今可以在早期分化真菌的物种中找到，被称为“活化石”。总共分析了 487 个带有 HEG 的内含子，这些内含子位于代表所有真菌门的目属的公共可用的 mt 基因组中。它们在 mt 基因中的分布、插入靶序列以及 HEG 的系统发育分析表明，这些内含子及其 HEG 形成了一种复合结构，其中自私元件共同进化。这些内含子中祖先独立的 HEGs 的入侵是通过一种称为“aenaon”假说的永恒机制发生的。它基于重组、转座和水平基因转移事件在整个进化过程中的发生。HEGs 的系统发育聚类主要根据它们的内含子宿主，其次是携带内含子及其 HEG 的 mt 基因。创建的进化模型揭示了一种“内含子早期”进化，通过许多不同的独立重组事件，通过垂直和水平基因转移，丰富了“内含子晚期”事件。
