## 3 Discussion
### Elucidation of Key Biosynthetic Pathways  
Phenylpropanol biosynthesis is one of the most important pathways in secondary metabolism, and it contributes to the biosynthesis of a wide range of bioactive metabolites in plants [59]. The significant stem- and root-specific enrichments of phenylalanine ammonia lyase, cinnamate-4-hydroxylase, and caffe acid 3-O methyl transferase suggest the tissue-specific biosynthesis and accumulation of ferulic acid. Considering that isoprenoids (C-5 isopopentenyl diphosphate (IPP), and its isomer dimethylallyl diphosphate (DMAPP) act as the precursors for the terpenoid pool in plant systems, the significant KEGG enrichment of the cytosolic MVA pathway in the stem and root tissues suggests MVA-mediated diterpenoid biosynthesis [60; 20]. Nevertheless, the higher enrichments of the transcripts involved in the MEP pathway in the leaf suggests MEP-mediated mono-, sesqui-, and triterpenoid and carotenoid biosynthesis in the leaf tissues, as reported earlier for _Salvia milliorhizia_[61] and _Cymbopogon winterianus_[62]. Furthermore, inferences in biosynthetic studies on the phthalide-like structure (marilone and mycophenolic acid) in fungi were used to elucidate the condensation-, methylation-, cyclization-, and hydroxylation-mediated putative biosynthesis pathway of phthalide in _A. glauca_[63; 64; 17; 65]. The higher accumulation of ferulic acid in the stem, followed by the root and leaf tissues, observed in the UPLC analysis, well complemented both the RNA-Seq and qRT expression analyses. Moreover, the root-specific higher accumulation of limonene, ligustilide, and butylidene, well corroborated by the transcriptional dynamics reported in the current investigation, indicates the root as a storage site for the accumulation of these bioactive metabolites, as reported earlier [8; 9].  
The cytochrome P450 monooxygenases (CYPs) and UDP-glycostransferases (UGTs) are known to play an imperative role in the structural and chemical diversity of plant secondary metabolites (phenylpropanes, terpenoids, alkaloids, and carotenoids) by catalyzing numerous hydroxylation reactions [66; 67; 68; 69]. The leaf-specific expressions of CYP71, 74, 77, 82, and 97, along with the UGTs (71, 84, and 85), suggest their key involvement in the modification of shikimate products, the 3-hydroxylation of carotenoid and flavonoid biosynthesis [70; 71; 72; 73]. Nonetheless, the root-specific expressions of the CYP families (72,76, 81, and 98) and UGT85 (A2, A3, and A4) signify their potential role in the biosynthesis, modification, and diversification of phthalide and phenylpropanol biosynthesis in _A. glauca_[74,75].  
The inter-/intracellular transport of plant secondary metabolites is a critical process to attain metabolic homeostasis for the maintenance of the spatiotemporal biosynthesis and storage of plant secondary metabolites [47]. The leaf-specific expressions of membrane transporters, such as ABCB.26, ABCF.5, and ABCG, indicate the involvement in the cellular transport of mono-sesquiterpenoids and volatile compounds [48,76]. However, the stem-specific enrichments of the ABCB.1, ABCG.29, and NRT families, while SWEET14 and MATE were expressed in the root, indicate their role in the metabolite-flux transportation from the biosynthetic sites to the storage site [31,48].