Molecular mechanism of postharvest quality deterioration in Stropharia rugosoannulata based on transcriptomics and metabolomics

Stropharia rugosoannulata is a major commercial mushroom species. After harvest, the mushroom is prone to rapid quality deterioration, such as browning, water loss, and softening, thereby significantly limiting its shelf life and commercial value. This study utilized cap tissues at three storage stages (immediately postharvest (0 d), 7 days postharvest, and 14 days postharvest, stored at 15°C) for transcriptome sequencing and untargeted metabolome analysis with integrated data analysis. Comparative transcriptome analysis identified 2,955 differentially expressed genes exhibiting consistent upregulation or downregulation trends during postharvest storage. Metabolome analysis screened 43 non-redundant differentially abundant metabolites. Joint KEGG pathway mapping of differentially expressed genes and differentially abundant metabolites identified several metabolic pathways significantly enriched at both transcriptome and metabolome levels, including carbohydrate metabolism, cell wall polysaccharide degradation, and reactive oxygen species metabolism. Within these pathways, expression trends of key enzyme-encoding genes demonstrated significant consistency with changes in abundances of corresponding substrates, key intermediates, and energy molecules. This study provides important data for elucidating postharvest stress responses and enzymatic regulatory mechanisms of S. rugosoannulata, offering potential molecular targets and theoretical support for developing postharvest preservation technology systems.