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Updated: Aug 28, 2026

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
Published on: June 24, 2021
Full-Length Transcriptome Reveals Alternative Splicing Regulation and Key Genes Underlying Differential Ginsenoside
Xinyang Liu1, Xinyi Zhao1, Han Wang1
1Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China.
Abstract:
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.
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