Multi-omics integration analysis reveals metabolic regulation of carbohydrate and secondary metabolites during goji berry (Lycium barbarum L.) maturation

Metabolism and the synthesis of bioactive compounds play crucial roles in goji berry fruits, renowned for their exceptional nutritional and medicinal value. However, understanding the metabolic dynamics during goji berry maturation remains limited. This study integrates physicochemical indicators, metabolomics, transcriptomics, and proteomics data across three distinct fruit maturation stages. Fruit ripening induces significant changes in sugar and secondary metabolite levels, enriched with differential metabolites, proteins, and genes. Co-expression network analysis identifies LbSPS, LbGLGC, and LbFBP genes associated with sugar contents. Conjunction analysis reveals D-glucose as a substrate promoting diverse sugar biosynthesis. The decrease in polysaccharide and sucrose, and the accumulation of galactose, fructose, and total sugar during the red fruit stage, are influenced by the expression levels of LbGLP, LbFBP, LbINV, LbGLGC, LbWAXY, LbSPS, LbRS, and their corresponding enzymes. Notably, LbGLGC and LbWAXY interact in the plasma membrane and nucleus. The reduction in secondary metabolites, flavonoids, and betaines is regulated by the downregulation of genes LbF3D and LbBADH in the synthesis pathway during this period. Significant expression correlations were observed between the LbSPS and transcription factor LbNAC. Yeast one-hybrid and dual-luciferase assays indicate that LbNAC binds directly to the LbSPS promoter and regulates its expression. This study provides a novel perspective on metabolic changes during goji berry maturation and postharvest, suggesting potential candidate genes for high-quality fruit cultivation.