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Makino (<jats:italic>G. pentaphyllum<\/jats:italic>) is a medicinal and edible plant with multiple functions of liver protection, anti-tumor, anti-inflammation, balancing blood sugar and blood lipids. The nutritional value of the <jats:italic>G. pentaphyllum<\/jats:italic> plant is mainly due to its rich variety of biologically active substances, such as flavonoids, terpenes and polysaccharides. In this study, we performed a comprehensive analysis combining metabolomics and root, stem and leaf transcriptomic data of <jats:italic>G. pentaphyllum<\/jats:italic>. We used transcriptomics and metabolomics data to construct a dynamic regulatory network diagram of <jats:italic>G. pentaphyllum<\/jats:italic> flavonoids and terpenoids, and screened the transcription factors involved in flavonoids and terpenoids, including basic helix-loop-helix (bHLH), myb-related, WRKY, AP2\/ERF. Transcriptome analysis results showed that among the DEGs related to the synthesis of flavonoids and terpenoids, dihydroflavonol 4-reductase (DFR) and geranylgeranyl diphosphate synthases (GGPPS) were core genes. This study presents a dynamic image of gene expression in different tissues of <jats:italic>G. pentaphyllum<\/jats:italic>, elucidating the key genes and metabolites of flavonoids and terpenoids. This study is beneficial to a deeper understanding of the medicinal plants of <jats:italic>G. pentaphyllum<\/jats:italic>, and also provides a scientific basis for further regulatory mechanisms of plant natural product synthesis pathways and drug development.<\/jats:p>","DOI":"10.1038\/s41598-024-57716-5","type":"journal-article","created":{"date-parts":[[2024,4,15]],"date-time":"2024-04-15T09:02:55Z","timestamp":1713171775000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":16,"title":["Integrative metabolomic and transcriptomic analyses reveals the accumulation patterns of key metabolites associated with flavonoids and terpenoids of Gynostemma pentaphyllum (Thunb.) 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