Table_1_Global Characterization of Fungal Mitogenomes: New Insights on Genomic Diversity and Dynamism of Coding Genes and Accessory Elements.XLSX

Fungi comprise a great diversity of species with distinct ecological functions and lifestyles. Similar to other eukaryotes, fungi rely on interactions with prokaryotes and one of the most important symbiotic events was the acquisition of mitochondria. Mitochondria are organelles found in eukaryotic cells whose main function is to generate energy through aerobic respiration. Mitogenomes (mtDNAs) are double-stranded circular or linear DNA from mitochondria that may contain core genes and accessory elements that can be replicated, transcribed, and independently translated from the nuclear genome. Despite their importance, investigative studies on the diversity of fungal mitogenomes are scarce. Herein, we have evaluated 788 curated fungal mitogenomes available at NCBI database to assess discrepancies and similarities among them and to better understand the mechanisms involved in fungal mtDNAs variability. From a total of 12 fungal phyla, four do not have any representative with available mitogenomes, which highlights the underrepresentation of some groups in the current available data. We selected representative and non-redundant mitogenomes based on the threshold of 90% similarity, eliminating 81 mtDNAs. Comparative analyses revealed considerable size variability of mtDNAs with a difference of up to 260 kb in length. Furthermore, variation in mitogenome length and genomic composition are generally related to the number and length of accessory elements (introns, HEGs, and uORFs). We identified an overall average of 8.0 (0–39) introns, 8.0 (0–100) HEGs, and 8.2 (0–102) uORFs per genome, with high variation among phyla. Even though the length of the core protein-coding genes is considerably conserved, approximately 36.3% of the mitogenomes evaluated have at least one of the 14 core coding genes absent. Also, our results revealed that there is not even a single gene shared among all mitogenomes. Other unusual genes in mitogenomes were also detected in many mitogenomes, such as dpo and rpo, and displayed diverse evolutionary histories. Altogether, the results presented in this study suggest that fungal mitogenomes are diverse, contain accessory elements and are absent of a conserved gene that can be used for the taxonomic classification of the Kingdom Fungi.

真菌拥有极为丰富的物种多样性，且具备各异的生态功能与生活方式。与其他真核生物类似，真菌依赖与原核生物的相互作用，其中最重要的共生事件之一便是线粒体的获得。线粒体是真核细胞内的细胞器，其核心功能是通过有氧呼吸产生能量。线粒体基因组（Mitogenomes, mtDNAs）源自线粒体的双链环状或线性DNA，可携带核心基因与附属元件，且能够独立于核基因组进行复制、转录与翻译。尽管线粒体基因组具有重要研究价值，但针对真菌线粒体基因组多样性的调查研究仍较为匮乏。本研究评估了NCBI数据库中收录的788条经过整理注释的真菌线粒体基因组，以解析不同线粒体基因组间的差异与相似性，并深入理解真菌线粒体基因组变异的潜在机制。在所涵盖的12个真菌门中，有4个门尚无可用的线粒体基因组代表，这凸显了当前数据中部分类群的代表性不足。研究基于90%相似性阈值筛选出具有代表性的非冗余线粒体基因组，共剔除81条线粒体DNA。比较基因组分析结果显示，真菌线粒体基因组存在显著的长度变异，长度差异最高可达260 kb。此外，线粒体基因组的长度与基因组组成的差异通常与附属元件（内含子、归巢内切酶基因（HEGs）、上游开放阅读框（uORFs））的数量和长度相关。本研究统计得到，每个线粒体基因组平均含8.0个内含子（范围0~39）、8.0个归巢内切酶基因（范围0~100）以及8.2个上游开放阅读框（范围0~102），且不同真菌门间的差异显著。尽管核心蛋白编码基因的长度整体较为保守，但约36.3%的被评估线粒体基因组缺失了14个核心编码基因中的至少一个。此外，研究结果显示，不存在所有线粒体基因组共有的单一基因。研究还在众多线粒体基因组中检测到了其他非典型基因，如dpo、rpo，并发现它们呈现出多样的进化历史。综上，本研究结果表明，真菌线粒体基因组具有高度多样性，且携带各类附属元件，同时不存在可用于真菌界分类学鉴定的保守共有基因。