Full-Length Transcriptome Reveals Alternative Splicing Regulation and Key Genes Underlying Differential Ginsenoside Accumulation Between Wild-Simulated and Cultivated Ginseng

Ginsenoside accumulation is tissue- and germplasm-specific, yet its transcriptional regulation remains unclear. We combined HPLC, PacBio full-length transcriptome, and Illumina RNA-seq to compare 4-year cultivated ginseng with 26-year wild-simulated ginseng. After clustering and error correction, we obtained 265,373 (CG) and 210,343 (WSG) non-redundant full-length transcript isoforms. Total saponins ranked leaves > roots > stems. In leaves, PPT type (Re and Rg1) predominated and was significantly higher in CG than WSG; in roots, PPD type dominated, and all monomer saponins in WSG were significantly higher. Transcriptome analysis revealed widespread alternative splicing (mainly retained introns), with key genes like CYP716A47 showing differential expression and splicing. WGCNA identified a yellow module positively correlated with PPD-type ginsenosides, enriched in terpenoid and CYP/UGT pathways and containing CYP716A47 and multiple UGT candidates. qRT-PCR validated 12 selected genes (6 known, 6 novel). Our findings reveal multilevel transcriptional and post-transcriptional regulation associated with the distinct production backgrounds of cultivated and wild-simulated ginseng and provide candidate targets for future functional studies and metabolic engineering.