Organ-specific transcriptional and untargeted metabolome analysis demystifies molecular insights and regulation of Gallic acid and flavonoid biosynthesis in Bergenia ciliata.

Bergenia ciliata is a priority medicinal plant, renowned for its antiviral, antibacterial, anticancer, and anti-inflammatory properties. Despite its extensive use, the underlying molecular mechanisms of specialized bioactive metabolites biosynthesis remain largely unexplored. Next-generation sequencing-assisted organ-specific in-depth transcriptional analysis of leaf, stem, and root rhizome yielded 259 million high-quality paired-end reads, which were de novo assembled into 73,039 unigenes and 28,599 isoforms. Functional annotation revealed extensive gene functions significantly enriched in KEGG pathways related to secondary metabolism, including flavonoid, terpenoid, and phenylpropanoid biosynthesis. Moreover, differential expression analysis identified 15,395 transcripts, including key gene families such as TFs (bHLH, NAC, and MYB-related), CYPs, and UGTs that exhibited notable tissue-specific dynamic expression driving the secondary metabolite biosynthesis. Further, pathway enrichment of candidate DEGs highlighted organ-specific unique gene expression patterns that substantially contributed toward the biosynthesis of gallic acid, bergenin, phenylpropanoid, and flavonoids. Untargeted metabolomic profiling further revealed DAMs that strongly correlated with transcriptome profiles, confirming the tissue-specific regulation of these metabolites. Integration of transcriptomic and metabolomic data unraveled distinct molecular signatures and regulatory hubs involved in specialized metabolite pathways. Additionally, the GRN predicted significant interactions between TFs (bHLH, C2H2, bZIP, ERF, and B3) and key biosynthetic genes. Further, qRT-PCR validation reinforces the transcriptomic data and emphasizes the importance of this study. Overall, this study provides the first comprehensive genomic resource for B. ciliata, revealing key genes, pathways, and regulators involved in gallic acid and flavonoid biosynthesis. These findings lay a robust foundation for metabolic engineering, conservation strategies, and industrial-scale exploitation of bioactive compounds.