Table_1_Comparative Analyses of Mitochondrial Genomes Provide Evolutionary Insights Into Nematode-Trapping Fungi.xlsx

Predatory fungi in Orbiliaceae (Ascomycota) have evolved a diversity of trapping devices that enable them to trap and kill nematodes, other small animals, and protozoans. These trapping devices include adhesive hyphae, adhesive knobs, adhesive networks, constricting rings, and non-constricting rings. Their diversity and practical importance have attracted significant attention from biologists, making them excellent model organisms for studying adaptative evolution and as biological control agents against parasitic nematodes. The putative origins and evolutionary relationships among these carnivorous fungi have been investigated using nuclear protein-encoding genes, but their patterns of mitogenome relationships and divergences remain unknown. Here we analyze and compare the mitogenomes of 12 fungal strains belonging to eight species, including six species representing all four types of nematode trapping devices and two from related but non-predatory fungi. All 12 analyzed mitogenomes were of circular DNA molecules, with lengths ranging from 146,101 bp to 280,699 bp. Gene synteny analysis revealed several gene rearrangements and intron transfers among the mitogenomes. In addition, the number of protein coding genes (PCGs), GC content, AT skew, and GC skew varied among these mitogenomes. The increased number and total size of introns were the main contributors to the length differences among the mitogenomes. Phylogenetic analyses of the protein-coding genes indicated that mitochondrial and nuclear genomes evolved at different rates, and signals of positive selection were found in several genes involved in energy metabolism. Our study provides novel insights into the evolution of nematode-trapping fungi and shall facilitate further investigations of this ecologically and agriculturally important group of fungi.

子囊菌门（Ascomycota）蜡钉菌科（Orbiliaceae）中的捕食性真菌演化出多样的捕食结构，可捕获并杀死线虫、其他小型动物及原生动物。这类捕食结构涵盖黏性菌丝、黏性结节、黏性网络、收缩环与非收缩环。其多样性与实际应用价值引发生物学家的广泛关注，使其成为研究适应性演化的优质模式生物，同时也可作为寄生线虫的生物防治剂。此前研究者已通过核编码蛋白基因，对这类食线虫真菌的潜在起源与演化关系展开探究，但目前学界对其线粒体基因组（mitogenome）的关联模式与分化特征仍不甚明晰。本研究对12株隶属于8个物种的真菌线粒体基因组进行分析与比较：其中6个物种覆盖全部4类线虫捕食结构，另外2株则来自亲缘关系相近但无捕食性的真菌。本次分析的12个线粒体基因组均为环状DNA分子，长度介于146101 bp至280699 bp之间。基因共线性分析显示，这些线粒体基因组间存在多组基因重排与内含子转移事件。此外，各线粒体基因组的蛋白质编码基因（protein coding genes, PCGs）数量、GC含量、AT偏倚及GC偏倚均存在差异。内含子数量与总长度的增加，是导致不同线粒体基因组间长度差异的主要因素。对蛋白质编码基因的系统发育分析表明，线粒体基因组与核基因组的演化速率存在显著差异，且多个参与能量代谢的基因呈现正选择信号。本研究为捕食线虫真菌的演化历程提供了全新见解，将推动这一在生态学与农业领域兼具重要意义的真菌类群的后续研究。