Integrated transcriptome and metabolome analysis reveals key genes and metabolic pathways regulating growth and...

Polygonatum cyrtonema Hua is a traditional Chinese medicine with the same origin as both medicine and food, and its medicinal components have considerable clinical value. Due to its substantial market demand, it is now primarily produced through artificial cultivation. To produce high-quality P. cyrtonema, we performed transcriptome and metabolome sequencing of one-year-old and three-year-old P. cyrtonema to explore the growth regulation mechanisms and key genes involved in improving its quality. A total of 1,957 differentially expressed genes (DEGs) and 163 differentially expressed metabolites (DEMs) were identified in this study. Integrated transcriptomic and metabolomic analyses suggested that the growth regulation of P. cyrtonema may be primarily associated with sphingolipid metabolism, phenylpropanoid biosynthesis, and starch and sucrose metabolism. Our data suggest that sucrose transport to sink organs may be facilitated by increased expression of the bidirectional sugar transporter SWEET14, and sucrose may be hydrolyzed by β-fructofuranosidase, potentially providing energy for plant growth on one hand and contributing to fructose accumulation on the other. Furthermore, the elevated abundance of L-phenylalanine may be associated with an increase in secondary metabolites, which could provide a metabolic basis for age-dependent growth and metabolite partitioning in rhizomes. The observed downregulation of sphingolipid metabolism-related genes may reflect the perennial growth habit of P. cyrtonema, whereby slower growth in the first year may promote sphingolipid-mediated root development. However, we emphasize that these inferences are based on correlative transcriptomic and metabolomic data, and functional validation is required to establish causal relationships.