Transcriptomics and Metabolomics Analyses of Chinese Artichoke Tubers (Stachys sieboldii Miq.) during the Developmental Period

Chinese Artichoke ( Stachys sieboldii Miq.), an indigenous vegetable in China, is renowned for its rich nutritional content and medicinal properties. With a significant cultivation history and promising prospects, this vegetable holds great potential for further development. In this study, we investigated changes in gene expression levels and metabolite content within relevant metabolic pathways during the development of Chinese Artichoke tubers. Tubers from three different periods—S1 (6 Aug), S2 (2 Sep), and S3 (1 Oct)—served as materials for the analysis. The results revealed that differentially expressed genes and differentially accumulated metabolites were predominantly enriched in pathways associated with secondary metabolite synthesis, carbohydrate metabolism, amino acid metabolism, and lipid metabolism. These pathways are known to play significant regulatory roles in the development of Chinese Artichoke tubers. Two crucial metabolic pathways identified through a comprehensive analysis of transcriptomics and metabolomics were further investigated. The genes GOLS , STS , AGAL , and INV potentially play crucial roles in stachyose accumulation. Additionally, the genes trpB ( Cluster-5100.0 ), GOT2 ( Cluster-7051.0 ), and TYRAAT ( Cluster-4023.14777 ) potentially influence the aromatic amino acid content at different developmental stages. However, the regulatory mechanisms of these genes and their relationship with metabolites require further investigation. The study findings provide a theoretical foundation for understanding the key pathways that influence the growth of Chinese Artichoke tubers, metabolic mechanisms of stachyose and amino acids, verification of gene functions, and genetic enhancement of Chinese Artichoke cultivars.