Comprehensive nutritional metabolomics and transcriptomics reveal varietal differences and drying effects on health-related metabolites in Amomum tsao-ko, a traditional medicinal and culinary plant.

Amomum tsao-ko, a valued traditional medicinal and culinary plant, lacks a systematic characterization of its primary nutritional metabolites across different varieties and processing methods. This study employed widely-targeted metabolomics (UPLC-MS/MS) combined with transcriptome sequencing to comprehensively profile amino acids, vitamins, carbohydrates, and lipids in fresh and dried fruits of three morphologically distinct A. tsao-ko accessions. We identified 474 nutritional metabolites, uncovering significant varietal specificity; the round-fruited accession consistently accumulated higher relative levels of amino acids and vitamins. The drying process profoundly altered the nutritional composition, notably increasing carbohydrates and specific lipids. Integrated network pharmacology and molecular docking analyses pinpointed S-adenosylmethionine (SAM) as a key metabolite with high binding affinity to immunity-related targets (EZH2, DNMT1, DNMT3B). Furthermore, multi-omics correlation revealed that the differential accumulation of SAM among accessions is likely regulated by the transcriptional divergence of key genes (ACS1, ACO) in the ethylene biosynthesis pathway, suggesting a metabolic flux diversion mechanism. Our work provides a comprehensive nutritional baseline for A. tsao-ko, elucidates the impact of processing, and identifies a transcriptionally regulated, immunomodulatory metabolite, offering a scientific foundation for its tailored use in functional foods and nutraceuticals.