## 1 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 glauc_ 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 terpenids (nerolidol, menthol, and carvone) have been traditionally used for the treatment of various disorders (cardiac, renal, digestive, pulmonary, rheumat, memoria, cancer, and inflammation), and they have been used widely in aoratherapy [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 phenylpropanol-mediated ferulic acid-biosynthesis pathway consists of the involvement of key enzymes, including phenylalanine ammonia lyase (PAL), cinnamic acid 4-hydroxylase (C4H), comamate 3-hydroxylase (C3H), and caffe acid 3-O-methyltransferasease (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. glauc_ 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. glauc_. 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.