Integrated Transcriptomics and Metabolomics Reveal Key Insights into Iridoid Biosynthesis in Gentiana crassicaulis Seeds during Germination

<b>Background:</b><i>Gentiana crassicaulis</i> Duthie ex Burk., a key species used in traditional Chinese medicine for treating rheumatic pain and stroke, contains iridoids as its primary active component. However, the biosynthetic mechanisms underlying iridoid production are not fully understood. <b>Methods:</b> This study focused on iridoid biosynthesis during the germination of <i>G. crassicaulis</i> seeds, integrating metabolomic and transcriptomic analyses to uncover the underlying pathways and key candidate genes. <b>Results:</b> 196,132 unigenes and 10 iridoid compounds were identified through RNA-seq and ultra performance liquid chromatography-quadrupole time of flight-mass spectrometer (UPLC-Q-TOF-MS), respectively. The intersection of results from Pearson correlation analysis and weighted gene co-expression network analysis (WGCNA) revealed a significant correlation between 26 genes and iridoid levels, suggesting their potential role in the iridoid metabolism. Notably, six highly expressed candidate genes (<i>DL7H</i>, <i>SLS</i>, <i>CYP76</i>, <i>CYP72A2</i>, <i>CYP84A1</i>, and <i>13-LOX3</i>) and five iridoids (loganic acid, sweroside, swertiamarin, gentiopicroside, and 6'-O-β-D-glucosyl-gentiopicroside) responded to methyl jasmonate stimulation in <i>G. crassicaulis</i> seedlings. <b>Conclusions:</b> by combining the known functions of candidate gene families, It is hypothesized that the <i>CYP716</i> and <i>LOX</i> families exert indirect influences on iridoid metabolism, while the <i>CYP71</i>, <i>CYP81</i>, <i>CYP72</i>, <i>CYP76</i>, <i>CYP710</i> families, <i>2OG-FeII</i> family, and the glucosyltransferase family are likely to play direct roles in the biosynthetic transformations of the five iridoids. This study provides a theoretical basis for further functional gene validation and metabolic engineering aimed at enhancing iridoid production. The insights gained could lead to improved iridoid production efficiency in medicinal plants, ultimately benefiting the quality and efficacy of medicinal materials.