Genome and Comparative Transcriptome Analysis of Growth and Developmental Changes in the Pileus of the Cyclocybe chaxingu

<i>Cyclocybe chaxingu</i> is a well-known edible fungus in China, in which pileus size and color are key traits determining its commercial value. However, the molecular genetic mechanisms underlying the morphological development of its pileus remains limited at present. To address this, our study first completed the high-quality genome assembly of the monokaryotic strain Ag.c0002-1 of albino <i>C. chaxingu</i>, anchoring it to 13 chromosomes via Hi-C technology. The final genome size was 51.7 Mb with a GC content of 51.06%, and 11,332 protein-coding genes were annotated. Phenotypic observations and comparative transcriptome analyses were then conducted on the pilei of the brown cultivar Ag.c0067 and the white cultivar Ag.c0002 at the primordium, elongation, and mature stages. Phenotypic analysis revealed continuous pileus expansion accompanied by progressive color lightening in both cultivars during development. Comparative transcriptomic analyses revealed significant differences in gene expression patterns between the two cultivars across developmental stages. KEGG enrichment analysis indicated that pileus expansion is closely associated with pathways related to DNA replication, cell cycle of yeast, carbon metabolism, and carbohydrate digestion and absorption. Among these, differentially expressed genes involved in cell division tended to be downregulated, whereas genes associated with energy metabolism and substance transport were upregulated, providing the necessary energy and material support for pileus growth. Changes in pileus pigmentation were primarily associated with tyrosine metabolism, betalain biosynthesis, tryptophan metabolism, and melanogenesis pathways. Notably, the downregulation of tyrosinase genes and the upregulation of glutathione S-transferase genes during development may represent major molecular mechanisms underlying pileus color lightening. Overall, this study provides important insights into the molecular mechanisms regulating pileus development and pigmentation in <i>C. chaxingu</i>, while also offering valuable theoretical support for genetic analysis of basidiomycete morphogenesis and the molecular breeding of edible mushrooms.