Comparative transcriptomics reveals stage-specific regulatory pathways of ear thickening in Auricularia polytricha

Auricularia polytricha is an economically important edible and medicinal mushroom widely cultivated in China. Ear thickness, as a core commercial trait of this mushroom, directly determines its product quality and economic value. To explore the potential molecular regulatory mechanisms governing ear thickness, we performed comparative transcriptome sequencing on fruiting bodies of the main cultivar 'Zhang'er 4328' and its stable thick-ear mutant 'B2872' at three key developmental stages: primordium stage (PD), young ear stage (IF), and mature stage (MF). Differentially expressed genes (DEGs) were screened, followed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. GO enrichment results showed that DEGs were mainly enriched in biological processes associated with metabolic activity, cellular component formation, and catalytic function. KEGG enrichment analysis revealed a distinct stage-specific pattern: DEGs at the PD stage were primarily enriched in energy and substance synthesis pathways (e.g., thiamine metabolism, carbon metabolism); at the IF stage, DEGs were concentrated in pathways related to cell proliferation and structure formation (e.g., amino acid metabolism, nitrogen metabolism); and at the MF stage, DEGs were enriched in pathways involved in protein synthesis and cellular homeostasis maintenance (e.g., ribosome, endoplasmic reticulum protein processing). Our findings indicate that pathways related to energy metabolism, cell proliferation, and protein synthesis provide essential energy and material support for ear thickness in A. polytricha. This exploratory study preliminarily fills the research gap in the molecular mechanism underlying ear thickness variation in A. polytricha and provides a preliminary theoretical reference for molecular marker-assisted breeding of thick-ear varieties.