Chemical composition and transcriptomic analysis revealed the dynamic changes of saponins during the growth of <i>Panax japonicus</i> var. <i>major</i>

<i>Panax japonicus</i> is a valuable medicinal plant whose rhizomes are rich in diverse ginsenosides. However, its perennial growth habit can significantly influence the quality and consistency of the herbal product. Despite its medicinal importance, the molecular regulatory mechanisms underlying saponin biosynthesis during different growth stages remain largely unknown. In this study, we conducted a comprehensive analysis of saponin content and transcriptomic profiles in <i>P. japonicus</i> rhizomes from plants aged 2-5 years. High-performance liquid chromatography revealed significant variations in saponin levels across different growth stages. Specifically, the concentrations of the major saponins, Ginsenoside Ro and Chikusetsusaponin IVa, decreased with increasing plant age, while the minor components, Zingibroside R1 and Calenduloside E, showed an upward trend. Transcriptome sequencing generated 78.53 Gb of clean reads and assembled 90 912 unigenes, of which 61 268 unigenes were successfully annotated. Comparative analysis indicated that <i>P. japonicus</i> shares the highest sequence homology with <i>Daucus carota</i> subsp. <i>sativa</i>. In addition, 37 enzymes involved in the triterpenoid saponin biosynthesis pathway were identified through differential gene expression analysis. Weighted Gene Co-expression Network Analysis further identified seven gene modules significantly associated with triterpenoid saponin content. Notably, genes encoding Cytochrome P450s and Uridine diphosphate-glycosyltransferases, which are key enzymes in saponin biosynthesis, were highlighted for further investigation. This study fills a critical knowledge gap in the genetic regulation of saponin biosynthesis in <i>P. japonicus</i> throughout its developmental stages and provides novel insights into the molecular mechanisms regulating ginsenoside accumulation. These findings offer a valuable foundation for future genetic improvement and quality control of <i>P. japonicus</i> as a traditional medicinal herb.