The large-scale Agaricales genomes shed light on the unique origin, evolution, development characteristics of subterranean mushroom Agaricus sinodeliciosus

Grassland ecosystems contain approximately 40% of terrestrial organic carbon; however, the genomic mechanisms underlying fungal decomposer adaptation to these environments remain poorly understood. We sequenced 22 new genomes of Agaricales mushroom-forming fungi and compared them with 100 published genomes spanning diverse ecological niches to investigate the genomic innovations associated with substrate specialisation. Our analyses revealed distinct genomic signatures across ecological guilds, with ectomycorrhizal fungi showing a pronounced reduction in plant cell wall-degrading enzymes, whereas grassland saprotrophs exhibited convergent expansion of cellulose-degrading machinery, particularly the CBM1, CBM13, and AA9 families. Notably, several species displayed intermediate genomic profiles that challenge traditional ecological classifications, suggesting more complex evolutionary trajectories along the saprotrophy-symbiosis spectrum than previously recognised. We focused our detailed analysis on Agaricus sinodeliciosus, a wild mushroom endemic to the high-altitude Tibetan Plateau grasslands, which uniquely forms large fruiting bodies underground. Compared to its cultivated relative A. bisporus, A. sinodeliciosus showed substantial genome expansion through transposable element proliferation, a dramatic reduction in plant cell wall-degrading enzymes, and species-specific pathways, including expanded tyrosine metabolism for melanin synthesis and hypoxia-responsive HIF-1 signalling. Transcriptomic analysis revealed that underground fruiting involves the coordinated regulation of hydrophobins, environmental sensors responsive to pH and nutrient availability, and downregulation of cAMP signalling pathways, which typically suppress fruiting body formation. These findings illuminate the genomic basis of fungal niche adaptation and highlight how substrate chemistry and environmental extremes drive the evolutionary innovation of mushroom-forming fungi.