Spatial Genomic Resource Reveals Molecular Insights into Key Bioactive-Metabolite Biosynthesis in Endangered Angelica glauca Edgew

Angelica glauca Edgew, which is an endangered medicinal and aromatic herb, is a rich source of numerous industrially important bioactive metabolites, including terpenoids, phenolics, and phthalides. Nevertheless, genomic interventions for the sustainable utilization and restoration of its genetic resources are greatly offset due to the scarcity of the genomic resources and key regulators of the underlying specialized metabolism. To unravel the global atlas of the specialized metabolism, the first spatial transcriptome sequencing of the leaf, stem, and root generated 109 million high-quality paired-end reads, assembled de novo into 81,162 unigenes, which exhibit a 61.53% significant homology with the six public protein databases. The organ-specific clustering grouped 1136 differentially expressed unigenes into four subclusters differentially enriched in the leaf, stem, and root tissues. The prediction of the transcriptional-interactome network by integrating enriched gene ontology (GO) and the KEGG metabolic pathways identified the key regulatory unigenes that correspond to terpenoid, flavonoid, and carotenoid biosynthesis in the leaf tissue, followed by the stem and root tissues. Furthermore, the stem and root-specific significant enrichments of phenylalanine ammonia lyase (PAL), cinnamate-4-hydroxylase (C4H), and caffeic acid 3-O-methyltransferase (COMT) indicate that phenylalanine mediated the ferulic acid biosynthesis in the stem and root. However, the root-specific expressions of NADPH-dependent alkenal/one oxidoreductase (NADPH-AOR), S-adenosyl-L-methionine-dependent methyltransferases (SDMs), polyketide cyclase (PKC), and CYP72A15 suggest the “root” as the primary site of phthalide biosynthesis. Additionally, the GC-MS and UPLC analyses corresponded to the organ-specific gene expressions, with higher contents of limonene and phthalide compounds in the roots, while there was a higher accumulation of ferulic acid in the stem, followed by in the root and leaf tissues. The first comprehensive genomic resource with an array of candidate genes of the key metabolic pathways can be potentially utilized for the targeted upscaling of aromatic and pharmaceutically important bioactive metabolites. This will also expedite genomic-assisted conservation and breeding strategies for the revival of the endangered A. glauca.


Introduction
The Indian Himalayan Region (IHR) is an important biodiversity hotspot, with an abundance of 1748 medicinal and aromatic plant species (MAPs) that have significant utility in Indian traditional medicines [1,2]. The gradual rising demands for these MAPs have resulted in the destructive harvesting and depletion of their natural genetic resources, consequently shifting them onto the IUCN's RET list [3][4][5][6].
Angelica glauca Edgew (syn: Angelica nuristanica; family: Apiaceae; common names: "Chora", "Gandhrayan", and "Smooth angelica") is an important medicinal and aromatic herb that is endemic to the IHR. It is an endangered perennial diploid (2n = 22) herb with an extensively larger genome size (11.7 Gb), and it is distributed throughout the Western Himalayan regions at an altitudinal range of 2000-3800 m above sea level (amsl) [7][8][9][10]. The plant is glabrous, tall, and erect, having 1-3 pinnately compound leaves, with a thick fistular stem and long conic roots. The clustered flowers in the form of umbel inflorescence are among the main characteristics of the plant, which attain maturity from July to August, mediated through cross-pollination [9,11,12].
The active accumulations of phthalide (butylidene phthalide and ligustilide), ferulic acid, and terpenoids (nerolidol, menthol, and carvone) have been traditionally used for the treatment of various disorders (cardiac, renal, digestive, pulmonary, rheumatism, menorrhea, cancer, and inflammation), and they have been used widely in aromatherapy [8,[12][13][14][15]. Phthalide biosynthesis involves either the condensation of malonyl CoA with acetyl-CoA or propionyl-CoA molecules, followed by the SAM-methylation-mediated production of tetraketide intermediate. Subsequently, several biochemical reactions, including cyclization, hydroxylation, carboxylation, and reduction, result in the accumulation of butylidene phthalide and ligustilide [16,17]. Similarly, the phenylpropanoid-mediated ferulic acidbiosynthesis pathway consists of the involvement of key enzymes, including phenylalanine ammonia lyase (PAL), cinnamic acid 4-hydroxylase (C4H), coumarate 3-hydroxylase (C3H), and caffeic acid 3-O-methyltransferase (COMT) [18,19]. In plants, the cytosolic MVA pathway has been suggested to contribute to sesqui-and triterpene biosynthesis, while the plastidial MEP pathway mainly synthesizes mono-and diterpenes, with limited crosstalk with the MVA pathway [20]. Nevertheless, most of these inferences were derived based on preliminary phytochemical and pharmacological studies [14,21]. Having evolved with a highly heterozygous complex genome (11.7 GB), A. glauca has possibly been omitted from global whole-genome-sequencing (WGS) efforts [7,10,22]. The paradigm shifts in sequencing technologies with the availability of multiple cost-effective high-throughput next-generation-sequencing (NGS) platforms has enormously contributed towards unraveling the functional and genomic insights into the specialized metabolism, irrespective of model or nonmodel plants [23,24], wherein organ-specific spatial-transcriptome-sequencing profiling has been proven to be an effective approach to the creation of comprehensive genomic resources and the elucidation of the complex biological/regulatory networks involved in the biosynthesis and transport of the specialized metabolism [25][26][27].
Therefore, global organ-specific transcriptome-sequencing efforts have been carried out for the creation of comprehensive genomic resources in the endangered Himalayan plant species A. glauca. Subsequently, the integration of spatial gene expressions with predicted protein interactome network analysis has assisted in the identification of the organ-specific key genes and regulators involved in the terpenoid, ferulic acid, and phthalide biosynthesis pathways with aromatic and pharmaceutical importance. The inferences derived in the current study will be a footstep for futuristic functional genomics and synthetic biology efforts for the nondestructive and sustainable production of the bioactive metabolites of A. glauca. In addition, novel genomic-resource creation can be utilized for the development of functionally relevant molecular-marker resources to strategize the conservation and domestication efforts in A. glauca.

GO-Enrichment Analysis
The organ-specific GO-enrichment analysis provided insights into the transcriptional dynamics of the significantly enriched transcripts in the leaf, stem, and root tissues of A. glauca. Among the biological processes, the response to gibberellin (GO:0009739), the abscisic acid-activated signaling pathway (GO:0009738), and the regulation of the cellular macromolecule biosynthetic process (GO:2000112) were recorded with significantly higher enrichments in the root tissues. However, the photosynthesis-related GO terms (GO:0009769, GO:0009768, GO:0009773, GO:0015979, GO:0009657), along with stomatal regulation (GO:0090333, GO:0010119), the cellular protein metabolic process (GO:0044267), and the organonitrogen compound biosynthetic process (GO:1901566) were significantly enriched in the leaf. Meanwhile, the stem exhibited a significantly higher enrichment of cell-wall biogenesis (GO:0042546), the cellular polysaccharide biosynthetic process (GO:0033692), and ion transport (GO:0006811). Interestingly, the secondary metabolic process (GO:0019748) showed significant enrichment in both the stem and root tissues ( Figure 3A, Table S4).

Organ-Specific Gene-Expression Elucidation of Key Metabolite Biosynthesis
The organ-specific KEGG-pathway-enrichment analysis recorded a significantly higher enrichment of the photosynthesis-related metabolic pathways, including carbon fixation and porphyrin and chlorophyll metabolism in the leaf tissue. However, diterpenoid and phenylpropanoid biosynthesis, including ferulic acid synthesis, were found to be enriched in both the stem and root ( Figure 5). Moreover, the transcripts involved in the biosynthesis of terpenoid backbone, flavonoids, and carotenoids confined their enrichment in the leaf, followed by the stem and root ( Figures 5 and 6).

Organ-Specific Gene-Expression Elucidation of Key Metabolite Biosynthesis
The organ-specific KEGG-pathway-enrichment analysis recorded a significantly higher enrichment of the photosynthesis-related metabolic pathways, including carbon fixation and porphyrin and chlorophyll metabolism in the leaf tissue. However, diterpenoid and phenylpropanoid biosynthesis, including ferulic acid synthesis, were found to be enriched in both the stem and root ( Figure 5). Moreover, the transcripts involved in the biosynthesis of terpenoid backbone, flavonoids, and carotenoids confined their enrichment in the leaf, followed by the stem and root (Figures 5 and 6).
The root-specific higher expressions of the key candidates (NADPH-AOR, SDM, PKC, and CYP72A15) suggest the 'root' as the site of the synthesis and accumulation of phthalide biosynthesis. Likewise, the confined expressions of DHQ-SDH, EPSP, CM, ADT, PAL, C4H, and COMT in the stem and root complement the PPIN inference of the phenylpropanoidpathway-mediated ferulic acid biosynthesis. Furthermore, the leaf-specific expressions of DXS, MCT, and HDR suggest the MEP-mediated biosynthesis of aromatic mono-and sesquiterpenoids. Notably, the committed step (catalyzed by GPPS) was specific to the leaf tissue, while the downstream monoterpene-diversification-related genes, including LS, NMD, and CD, exhibited higher expressions in the stem and root. Nevertheless, STS and NES, involved in sesquiterpene biosynthesis, confined their expressions in the leaf (Figure 7). This transcriptional-level study was further complemented by the metabolite profiling of the leaf, stem, and root tissues.

Expression Dynamics of Transcription Factors
Transcription factors (TFs) are key elements that regulate the spatiotemporal ex pression of bioactive-metabolite biosynthesis [28]. Overall, 33,040 transcripts encoding 58 TF families, with significant abundances of bHLH (3386)

Differential Expressions of CYPs, UGTs, and Transporters
The CYPs and UGTs, which are a specific class of oxidoreductases and transferases, have been proven to be multifunctional candidates that regulate the biosynthesis and diversification of secondary metabolites [29,30]. In total, 602 transcripts encoding 44 CYP families were identified in A. glauca, with abundances of CYP71, CYP72, CYP76, CYP704,
Furthermore, eight candidate genes (viz., ADT, PAL, C4H, COMT, NADH-AOR, SDM, PKC, and CYP72A15) were validated with four diverse genotypes of A. glauca, and the qRT-PCR expression profiles follow a similar trend of expression as that recorded in the RNA-Seq expression data ( Figure 10, Table 5). However, the expression variations recorded across the genotypes may be due to the genotypic diversity and unique features of the methods.   Table S8). However, the expression differences (0.23) between the RNA-Seq and qRT-PCR are owing to intrinsic properties, such as the detection ranges and sensitivities of these methods [32,33] ( Figure 9A-C, Table S8).

GC-MS and UPLC Analysis
GC-MS analysis was used to determine the volatile compounds in the leaf, stem, and root tissues of A. glauca. The root tissue reported higher contents of limonene, with an area percent of 7.213%, as well as ligustilide (40.48%) and butylidenephthalide (0.66%), while germacrene D (5.01%), alpha farnesene (1.96%), and alpha bergamotene, with 2.39% area, exhibited dominance presence in the leaf tissue. Moreover, the results of the UPLC analysis recorded a higher accumulation of ferulic acid in the stem (206.66 μg/100 mg), followed by the root (22.82 μg/100 mg) and leaf (15.61 μg/100 mg) tissues ( Figures  11, S1 and S2).

GC-MS and UPLC Analysis
GC-MS analysis was used to determine the volatile compounds in the leaf, stem, and root tissues of A. glauca. The root tissue reported higher contents of limonene, with an area percent of 7.213%, as well as ligustilide (40.48%) and butylidenephthalide (0.66%), while germacrene D (5.01%), alpha farnesene (1.96%), and alpha bergamotene, with 2.39% area, exhibited dominance presence in the leaf tissue. Moreover, the results of the UPLC analysis recorded a higher accumulation of ferulic acid in the stem (206.66 µg/100 mg), followed by the root (22.82 µg/100 mg) and leaf (15.61 µg/100 mg) tissues (Figures 11, S1 and S2).

Discussion
A. glauca is a rich repository of secondary metabolites, and especially terpenoids, phenylpropanoids, and phthalides having cardioactive, carminative, stimulant, digestive, expectorant, anti-inflammatory, and anticancerous properties are its key constituents [15,34]. Consequently, the cumulative demand of the phytopharmaceutical and aroma industries has recklessly harvested the genetic resources of A. glauca from its natural habitat. Additionally, soil erosion and excessive animal grazing have caused A. glauca to be listed among the IUCN's endangered plants [35,36]. More recently, high-throughput cost-effective next-generation sequencing (NGS) has significantly assisted in the conservation efforts through the rapid creation of genomic resources and gene-expression patterns for the identification of the key biosynthetic pathways, irrespective of model or nonmodel medicinal plant species [23,27].
Therefore, in the current study, global organ-specific transcriptome sequencing was carried out, with the successful generation of 109 million paired-end reads, assembled into 81,162 unigenes in organ-specific NGS-assisted transcriptome sequencing, which were in consensus with the recent genomic efforts in related Angelica species [37,38]. Overall, a 61.53% functional annotation rate of the de novo assembled unigenes with public protein databases is comparable with Ferula asafoetida (58%) and Thapsia laciniata (61.9%) of the family Apiaceae [39,40]. Moreover, the integration of the predicted protein-interactome network with leaf-, stem-, and root-specific gene expressions has assisted in the identification of the key regulators for the successful elucidation of the specialized-metabolite-biosynthesis pathway.

Organ-Specific Transcriptional Dynamics in A. gluaca
The global understanding of organ-specific gene expression has been successfully utilized to reveal the intricate key biosynthetic pathways and biological mechanisms, including different gene families, at the genome and transcriptional levels [41][42][43]. Significant pair-wise DEGs (leaf vs. stem; leaf vs. root; stem vs. root) and KEGG-enrichment analysis, bolstered in deciphering the complex secondary-metabolite-biosynthesis path-

Discussion
A. glauca is a rich repository of secondary metabolites, and especially terpenoids, phenylpropanoids, and phthalides having cardioactive, carminative, stimulant, digestive, expectorant, anti-inflammatory, and anticancerous properties are its key constituents [15,34]. Consequently, the cumulative demand of the phytopharmaceutical and aroma industries has recklessly harvested the genetic resources of A. glauca from its natural habitat. Additionally, soil erosion and excessive animal grazing have caused A. glauca to be listed among the IUCN's endangered plants [35,36]. More recently, high-throughput cost-effective nextgeneration sequencing (NGS) has significantly assisted in the conservation efforts through the rapid creation of genomic resources and gene-expression patterns for the identification of the key biosynthetic pathways, irrespective of model or nonmodel medicinal plant species [23,27].
Therefore, in the current study, global organ-specific transcriptome sequencing was carried out, with the successful generation of 109 million paired-end reads, assembled into 81,162 unigenes in organ-specific NGS-assisted transcriptome sequencing, which were in consensus with the recent genomic efforts in related Angelica species [37,38]. Overall, a 61.53% functional annotation rate of the de novo assembled unigenes with public protein databases is comparable with Ferula asafoetida (58%) and Thapsia laciniata (61.9%) of the family Apiaceae [39,40]. Moreover, the integration of the predicted protein-interactome network with leaf-, stem-, and root-specific gene expressions has assisted in the identification of the key regulators for the successful elucidation of the specialized-metabolitebiosynthesis pathway.

Organ-Specific Transcriptional Dynamics in A. gluaca
The global understanding of organ-specific gene expression has been successfully utilized to reveal the intricate key biosynthetic pathways and biological mechanisms, including different gene families, at the genome and transcriptional levels [41][42][43]. Significant pair-wise DEGs (leaf vs. stem; leaf vs. root; stem vs. root) and KEGG-enrichment analysis, bolstered in deciphering the complex secondary-metabolite-biosynthesis pathways in A. glauca, have been complemented with various previous studies, including those on Podophyllum hexandrum [44], Trillium govanianum [45], and Fritillaria roylei [27]. Subsequently, the prediction of the transcriptional-interactome network complementing the organ-specific expression-profiling-assisted elucidation of the complex specialized-metabolite pathways has been performed successfully in earlier studies [27,[46][47][48].
The cumulative enrichment of the terpenoids, flavonoids, and carotenoids in the leaf, and the phenylpropanoid and diterpenoid biosynthesis in the root and stem tissues, suggest the intra-/intercellular trafficking of key bioactive metabolites via membrane transporters [49,50]. This was further supported by the successful prediction of the transcriptional-interactome network, which suggests phenylpropanoid-mediated ferulic acid biosynthesis in the root and stem tissues with the active involvement of caffeoyl CoA methyl transferase, phenylalanine ammonnia lyase, cinnamoyl CoA reductase, and 4-coumarate: CoA ligase. Nevertheless, the root-specific enrichment of regulators having significant interactions with the key candidates that correspond to ferulic acid synthesis further support the 'stem and root' as the sites of ferulic acid biosynthesis. However, the enrichment of the photosynthesis and the stomatal regulation in the predicted network in the leaf tissue indicates enough primary-metabolite flux to synthesize and accumulate secondary metabolites [51,52].

Elucidation of Key Biosynthetic Pathways
Phenylpropanoid 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 caffeic acid 3-O methyl transferase suggest the tissue-specific biosynthesis and accumulation of ferulic acid. Considering that isoprenoids (C-5 isopentenyl 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 MVAmediated diterpenoid biosynthesis [20,60]. 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 miltiorrhiza [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 hydroxylationmediated putative biosynthesis pathway of phthalide in A. glauca [17,[63][64][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 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 stemspecific 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].

Plant Materials and RNA Isolation
For the tissue-specific transcriptomic sequencing, leaf, stem, and root tissues of A. glauca were collected from Ranikot, Chamba district, Himachal Pradesh, India (32.5601 • N, 76.1049 • E), at an elevation of 2708 amsl. The plant samples were snap-frozen in liquid nitrogen and stored at −80 • C till RNA isolation. Total high-quality RNA was extracted using the iRIS protocol [77]. The concentration of RNA was determined using a NanoDrop 2000 spectrophotometer (Thermo Scientific, Waltham, MA, USA), and the quality was checked in 1% formaldehyde MOPS gel electrophoresis. The integrity of the RNA was measured in terms of the RNA-integrity-number (RIN) value using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA), and samples having RIN values ≥ 7.0 were subsequently utilized for library preparation. The methodology adopted in this study is represented in Figure 12. 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 phenylpropanoid biosynthesis in A. gluaca [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].

Plant Materials and RNA Isolation
For the tissue-specific transcriptomic sequencing, leaf, stem, and root tissues of A. glauca were collected from Ranikot, Chamba district, Himachal Pradesh, India (32.5601° N, 76.1049° E), at an elevation of 2708 amsl. The plant samples were snap-frozen in liquid nitrogen and stored at −80 °C till RNA isolation. Total high-quality RNA was extracted using the iRIS protocol [77]. The concentration of RNA was determined using a NanoDrop 2000 spectrophotometer (Thermo Scientific, Waltham, MA, USA), and the quality was checked in 1% formaldehyde MOPS gel electrophoresis. The integrity of the RNA was measured in terms of the RNA-integrity-number (RIN) value using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA), and samples having RIN values ≥ 7.0 were subsequently utilized for library preparation. The methodology adopted in this study is represented in Figure 12.

Library Construction, Transcriptome Sequencing, and De Novo Assembly
Three RNA-Seq libraries corresponding to the leaf, stem, and root tissues were prepared using the Illumina TruSeq RNA sample prep kit v2 (Illumina Inc., San Diego, CA, USA), following the manufacturer's instructions, targeting 200-300 bp insert-sized libraries. The prepared libraries were quantified using a Qubit 2.0 Fluorimeter (Invitrogen, Waltham, MA, USA), followed by a quality assessment using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The paired-end sequencing (2 × 100 bp) was performed using the NovaSeq 6000 platform (Illumina Inc., San Diego, CA, USA). The raw sequencing data obtained from all three tissues were deposited to the SRA (Sequence Read Archive) in the NCBI database, with the accession number SRP359017, under Bio Project PRJNA 804685. The high-quality clean reads having Phred scores (Q value) > 30 were extracted using the NGS Toolkit [78], and they were subsequently assembled (de novo) using Trinity RNA-Seq version 2.4.0 with default parameters [79]. Furthermore, the assembled sequences were clustered based on a 90% sequence homology using CD-HIT-EST version 4.6 [80].

Differential Expression Analysis
To determine the tissue specificity of the differential-gene-expression patterns, the high-quality reads were mapped onto the NR transcripts using the Bowtie 2 tool [85]. The reads mapped onto the assembled transcripts were quantified in terms of FPKM using the RSEM tool [86]. Furthermore, the EdgeR package was used to assess the differential transcript expressions in the following pair-wise comparisons: leaf vs. stem; leaf vs. root; stem vs. root, with the false-discovery rate (FDR < 0.05) and log 2 fold change (≥2) as the differentially expressed genes [87]. The differential-pathway-enrichment analysis was performed by gene-enrichment analysis using the R Bioconductor package, as previously used [46]. The Fischer exact test (Hochberg FDR adjustment cutoff < 0.05) was used for the identification of the organ-specific significant differentially enriched pathways.

Protein-Protein-Interactome-Network Prediction
The protein-protein-interactome network was predicted by using the predetermined PPI network of Arabidopsis thaliana [88]. The orthologs of the significant organ-specific enriched transcripts were obtained with the TAIR database using the BLASTx tool. The interactome network was built and analyzed using Cytoscape ver. 3.4.0 an open-source software maintained by National Institute of General Medical Sciences (NIGMS), U.S [89]. The nodes of the network represent transcripts, with the respective orthologs having significant correlation edges (FDR ≤ 0.05) of the predicted network. The R Bioconductor package was used to perform the pathway curation and gene-set enrichment of the predicted network [90].

qRT-PCR Validation of RNA-Seq Data
The validation of the RNA-Seq data was performed with the key genes of the pathways using qRT-PCR analysis (ST 8). Gene-specific primers were designed using Batch Primer 3 ver1.0 (Albany, NY, US) (http://probes.pw.usda.gov/batchprimer3/ (accessed on 2 July 2020)).
The cDNA was prepared from 2 µg of high-quality total RNA using a cDNA synthesis kit (Thermo Scientific, Waltham, MA, USA, Revert H Minus). The reaction mixture was composed of 1µL of template cDNA, 0.5 µL of gene-specific primers, 5 µL Power SYBR Green mix (Applied Biosystems, Thermo Fisher Scientific, Waltham, MA, USA), and 3 µL nuclease-free water, and the amplifications were performed in the real-time PCR system (QuantStudio 5, Applied Biosystems, Waltham, MA, USA). The relative expression levels of the genes were calculated from the cycle-threshold (ct) values using the 2 −∆∆ct method, considering EF-1α as a reference gene [91]. Additionally, the expression stabilities of the key candidate genes were validated in four diverse genotypes of A. glauca, collected from the natural habitats of the geographically separated populations of Western Himalaya, India  Table 5)).

Metabolite Profiling
The phytochemical analysis of the specialized metabolites in the leaf, stem, and root tissues was performed using gas chromatography-mass spectrometry (GC-MS) and ultraperformance liquid chromatography (UPLC-MS). Volatile compounds were extracted and analyzed by a mass spectrometer (QP2010 Shimadzu, Tokyo, Japan), attached with an AOC-5000 auto injector and a DB-5 (SGE International, Ringwood, Australia) fused-silica capillary column of a 30 m length, 0.25 mm i.d., and 0.25 µm film thickness. Helium was utilized as a carrier gas, with a constant flow rate of 1.1 mL/min, and the program was set as in a prior study [92].
Ultra-performance liquid chromatography (UPLC) was used to identify the ferulic acid, and the analysis was carried out using the Water Acquity UPLC-H class system, which includes a binary solvent manager, an autosampler, a column heater, and an eλ photodiode array detector (PDA). All the parameters used in the analysis followed a previous study [93], and the chromatographic data were recorded for each sample and were quantified based on internal standard curves.

Conclusions
The specialized metabolites of the high-altitude Himalayan endangered species A. glauca are a vital resource for the pharmaceutical and aromatic industries. The increasing demand has led to the indeterminate extraction of natural plant populations. Therefore, the creation of the first NGS-assisted comprehensive spatial genomic resource has assisted in the identification of the tissue-specific key regulators that influence the specialized-metabolite biosynthetic pathways in A. glauca, which will enable the identification of the targeted secondary-metabolite-biosynthesis pathways in other medicinal plants. Furthermore, the tissue-specific molecular insights into the terpenoid, ferulic acid, and phthalide biosynthesis will assist leaf-, stem-, and root-specific genetic interventions to upscale the targeted metabolite synthesis with the active involvement of TFs, CYPs, UGTs, and transporters that correspond to the biosynthesis, transportation, and diversification of secondary metabolites. The present study paves the way to understand the multifarious metabolic genes for the synthesis of diverse biomolecules in plant species. Creating genomic resources from the current study will formulate future steps to enhance metabolite production by genetic engineering and molecular functionally relevant marker resources for the population diversity and conservation planning of this important Himalayan medicinal plant.