Integrated transcriptome and metabolome analysis decrypting molecular insights of specialized metabolism in Valeriana jatamansi Jones

Valeriana jatamansi Jones ranks among the top-selling herbs utilized globally to treat neurological disorders. Nevertheless, limited genomic resources remain a major constraint for genetic interventions and improvement. Therefore, deep transcriptomics and metabolomics investigations were conducted to create a comprehensive genomic resource to unravel organ-specific biosynthesis of specialized bioactive metabolites in leaf, flower, stem, and root_rhizome. Over 112 million organ-specific paired-end reads were de novo assembled into 73,894 unigenes with successful annotations (61.7%) in multiple public databases. Furthermore, 417 untargeted putative metabolites exhibited with organ-specific accumulation in UHPLC-QTOF-IMS (361) and GC-MS (56) analysis. Interestingly, 10,197 unigenes revealed spatial differential expression including significant upregulated expressions of key genes involved in the biosynthesis of terpenoid backbone (HMGR, DXS, DXR), monoterpenoids (LLS, GERS, MSY), sesquiterpenoids (SBS, VFS, VDS), triterpenoids (SQMO, SQS, LSY), carotenoids (PTSY, PDS, BCI), phenylpropanoids (PAL, 4CL, COMT) and flavonoids (CHS, CHI, DFR). Upregulated expression of pharmaceutically important valepotriates related genes (G10H, IDS,7DLGT, SLS) across all the tissue, while their maximal accumulation in root_rhizome possibly suggests source (aerial tissues) to sink (root_rhizome) transportation of key bioactive metabolites. Additionally, the prediction of pivotal regulators (bHLH, NAC, MYB, ERF, bZIP, WRKY, CH3) in gene regulatory network, and their complementation with expression and metabolome data can be genetically manipulated for upscale production of potential bioactive metabolites at industrial scale. Furthermore, comprehensive genomic resource created in the current study can be used for development of functionally relevant genome-wide molecular markers to strategize gene bank and implementation of molecular breeding efforts for commercial cultivations of V. jatamansi.