Spatiotemporal transcriptome profiling of Panax ginseng Meyer across three cultivation ages

Background Korean ginseng ( Panax ginseng Meyer) is a valuable medicinal herb whose pharmacological properties accumulate with cultivation age. Comparative transcriptomic analyses focusing on commercially critical cultivation ages (4-8 years) and fine-scale tissue compartmentalization remain limited. We aimed to identify age- and tissue-specific gene expression patterns underlying developmental transitions and spatial specialization in cultivated ginseng. Methods We conducted comprehensive ribonucleic acid (RNA) sequencing of leaf, root, and flower tissues from P. ginseng plants cultivated for 4, 6, and 8 years. Differential gene expressions, functional enrichment, temporal clustering, and cross-tissue analyses were performed, with validation by quantitative reverse transcription PCR (qRT-PCR). Results Over 5,500 differentially expressed genes (DEGs) were identified in each tissue type. Spatial profiling revealed 886 outer root-enriched genes associated with nitrogen metabolism, flavonoid biosynthesis, and ginsenoside production, while 359 inner root-enriched genes were linked to vascular development and auxin signaling. Age-dependent analysis identified 1,210 leaf DEGs and 3,007 root DEGs. Gene Ontology enrichment showed tissue-specific functional specialization: photosynthesis in leaves, structural processes in roots, and developmental regulation in flowers. Time-course clustering revealed eight expression patterns, with age-upregulated genes enriched in stress and defense responses, and age-downregulated genes in photosynthesis and flavonoid metabolism. Cross-tissue analysis uncovered 124 genes consistently upregulated and 55 downregulated with age, representing pan-tissue developmental markers. qRT-PCR validation confirmed RNA-seq accuracy. Conclusion Our findings provide an integrated transcriptomic framework for understanding developmental regulation in P. ginseng and identifying biomarkers for tissue identity and cultivation age authentication.