Integrative Transcriptome and Metabolome Analysis Reveals the Regulatory Networks and Key Biosynthetic Pathway Genes of Wild and Cultivated Gentiana macrophylla Pall

Objectives: Gentiana macrophylla Pall. (Gentianaceae) is a medicinally important perennial herb. Iridoids are the main chemical constituents of G. macrophylla. The scarcity of the wild resource has led to increased attention to cultivated G. macrophylla. However, little is known about the metabolic differences and the regulatory mechanisms between cultivated and wild G. macrophylla. Methods: This study utilized untargeted metabolomics and transcriptomics to reveal differentially accumulated metabolites (DAMs) and differentially expressed genes (DEGs) between wild and cultivated. Results: The metabolomics profiling revealed 25,587 DAMs (p < 0.05) while the transcriptomic profiling identified 6830 DEGs. Analysis revealed that DEGs were predominantly enriched for processes associated with monoterpenoid biosynthesis and flavonoid biosynthesis. In addition, we word validated six DEGs involved in monoterpenoid biosynthesis and flavonoid biosynthesis by RT-qPCR. According to KEGG pathway analysis, 10HGO (8-hydroxygeraniol dehydrogenase) may be a key enzyme encoding secoiridoid biosynthesis. The comprehensive results of transcriptome and metabolomics analysis revealed significant correlation between metabolite content and gene expression, providing a foundation for further study the function of G. macrophylla Pall. and the regulation of biosynthesis of active components. Conclusions: These approaches aim to explore the consistency of medicinal quality between the two sources across different habitats and to develop cultivated gentian as a full substitute for its wild counterpart in medicinal value. This strategy will fundamentally alleviate the predatory harvesting pressure on wild resources, ease their depletion, provide a theoretical basis for further development and protection of wild species of G. macrophylla in the future.