Comprehensive transcriptomic and metabolomic analyses reveal developmental changes in one-year-old and two-year-old Polygonatum cyrtonema hua

Polygonatum cyrtonema Hua is traditional Chinese herbal medicine rich in active ingredients, such as polysaccharides, flavonoids, alkaloids, and others that contribute to human health. As a perennial plant, its culture duration may influence the accumulation of these functional active ingredients in its tissues. To investigate how secondary metabolites and gene expression levels change with plant growth age, we carried out metabolomic analysis on root tissues of 1-year-old and 2-year-old plants, alongside transcriptome analysis was of leaf tissues. Using LC-MS, we identified identified 81 and 80 differentially expressed metabolites（DEMs）in positive and negative ion modes, respectively. Of these, 80 differential metabolites showed higher accumulation in 2-year-old plants. The relative contents of nucleotides and analogues, lipids, organic acids, phenylpropanoids, alkaloids, and organic oxygen molecules increased with increasing growth age. Transcriptome analysis further revealed 2,068 differentially expressed genes, including 1,026 up-regulated and 1,042 down-regulated genes. A total of 102 metabolic pathways were enriched, with glucose metabolism, phenylpropanoid biosynthesis and flavonoid biosynthesis, being among the most enriched metabolic pathways. These results show that longer culture duration enhances the active of metabolic pathways components. Overall, this study study integrates multi-omics techniques to demonstrate age-related changes in metabolites and genes profiles in P. cyrtonema, providing valuable insights for the identification of candidate genes involved in the biosynthesis of active substances. • Transcriptome sequencing is integrated with corresponding metabolomic analysis. • Growth duration is a critical factor influencing the medicinal value of Polygonatum cyrtonema Hua. • Compared to the control group, the DEMs were associated with key metabolites such as organic acids, phenylpropanoids, and alkaloids. • DEGs within the phenylalanine biosynthetic pathway play a pivotal role in the accumulation of active components.