Transcriptomic and metabolomic analyses reveal nutritional and flavor changes in shade-cultivated Zingiber striolatum Diels shoots

• Comparative transcriptomic and metabolomic analysis showed distinct gene expression patterns and metabolites accumulation in shade cultivated Z. striolatum. • The majority of metabolites in the classes of flavonoids, phenolic acids, terpenoids, lipids and tannins, were decreased under shade except amino acids and derivatives. • Aminoacyl-tRNA biosynthesis was significantly upregulated while phenylpropanoid biosynthesis and gingerol biosynthesis were significantly downregulated under shade. • Shade grown Z. striolatum accumulated more amino acids but less gingerols. The young shoots of Zingiber striolatum Diels are considered as a special vegetable in China. Shading cultivation is a key practice to improve the taste and quality of Z. striolatum shoot. However, the underlying mechanism remains poorly understood. In this study, we performed combined transcriptomic and metabolomic analyses of light and shade cultivated Z. striolatum shoot. As a result, 4330 differential genes (|log₂FC| ≥ 1, FDR < 0.05) and 821 differential metabolites (|log₂FC| ≥ 1, Variable Importance in Projection, VIP > 1) were identified. Notably, most metabolites in the classes of flavonoids, phenolic acids, terpenoids, lipids and tannins were decreased under shade, except those in the amino acids and derivatives classes. KEGG enrichment analysis indicated that aminoacyl-tRNA biosynthesis was significantly upregulated while phenylpropanoid biosynthesis and gingerol biosynthesis were significantly downregulated under shade. Consistently, the contents of many amino acids were increased while several key phenylpropanoid and gingerol related metabolites were decreased under shade. Together, our study provides molecular insights into how shade cultivation may influence nutrition and flavor of Z. striolatum shoots.