Integrated transcriptomic and metabolomic analysis reveals stage-associated molecular profiles in Ophiocordyceps sinensis.

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is globally recognized for its exceptional nutritional and medicinal properties. Variations in the edible qualities and tonic values of at different harvesting stages remain poorly understood in terms of compositional changes and regulatory mechanisms. Utilizing UPLC-MS/MS and transcriptome sequencing (RNA-seq), this study unveiled discrepancies in metabolite accumulation and gene expression of across various harvesting stages. Metabolomics analysis identified 596 differentially accumulated metabolites (DAMs), primarily enriched in amino acid-related metabolic pathways such as tyrosine, tryptophan, cysteine, and methionine metabolism. The up accumulation of organic acids and derivatives with delayed harvesting led to distinct abundances and compositions of amino acids, peptides, analogs, and fatty acids and conjugates, ultimately influencing the quality of . Transcriptomic analysis revealed 2550 differentially expressed genes (DEGs) at different harvesting stages, with KEGG-based enrichment analysis highlighting their involvement in amino acid-related activities like tyrosine metabolism and fatty acid degradation. The upregulation of these DEGs in amino acid-related pathways presents a promising target for studying quality. Integrative metabolomic and transcriptomic analyses indicated potential roles for (), (), (), and () in the synthesis pathways of amino acids, peptides, and their analogs, suggesting a possible indirect association with quality. These findings offer novel insights into the molecular mechanisms underlying the quality formation and metabolic evolution of .

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The online version contains supplementary material available at 10.1186/s12864-025-11869-3.