Introgression and gene family contraction drive the evolution of lifestyle and host shifts of hypocrealean fungi

Hypocrealean fungi (Ascomycota) are known for their diversity of lifestyles. Their vital influences on agricultural and natural ecosystems have resulted in a number of sequenced genomes, which provide essential data for genomic analysis. Totally, 45 hypocrealean fungal genomes constructed a phylogeny. The phylogeny showed that plant pathogens in Nectriaceae diverged earliest, followed by animal pathogens in Cordycipitaceae, Ophiocordycipitaceae and Clavicipitaceae with mycoparasites in Hypocreaceae. Insect/nematode pathogens and grass endophytes in Clavicipitaceae diverged at last. Gene families associated with host-derived nutrients are significantly contracted in diverged lineages compared with the ancestral species. Introgression was detected in certain lineages of hypocrealean fungi, and the main functions of the genes located in the introgressed regions are involved in host recognition, transcriptional regulation, stress response and cell growth regulation. These results indicate that contraction of gene families and introgression might be main mechanisms to drive lifestyle differentiation and evolution and host shift of hypocrealean fungi.

肉座菌目真菌（Hypocrealean fungi）隶属于子囊菌门（Ascomycota），以其多样的生活方式著称。这类真菌对农业与自然生态系统具有重要影响，因此已有大量相关测序基因组被解析，为基因组学分析提供了关键数据。本研究共整合45个肉座菌目真菌基因组构建系统发育树。结果显示，赤霉科（Nectriaceae）的植物病原菌为最早分化的类群；随后分化的是虫草科（Cordycipitaceae）、线虫草科（Ophiocordycipitaceae）和麦角菌科（Clavicipitaceae）的动物病原菌，以及肉座菌科（Hypocreaceae）的真菌重寄生物种；麦角菌科中昆虫/线虫病原菌与禾本科内生真菌则为最晚分化的类群。与祖先物种相比，分化谱系中与宿主来源营养相关的基因家族发生了显著收缩。研究还在部分肉座菌目真菌谱系中检测到基因渐渗（introgression）现象，渐渗区域内的基因主要参与宿主识别、转录调控、应激响应及细胞生长调控等生物学过程。上述结果表明，基因家族收缩与基因渐渗或为驱动肉座菌目真菌生活方式分化与演化、以及宿主转移的核心机制。