## 3 Discussion
The knowledge of biosynthetic genes and accumulation patterns for bioactive phytochemicals will inform future metabolic engineering efforts to enhance the production of antiviral compounds. Transcriptome sequencing technology has become an indispensable approach for comprehensively analyzing non-model medicinal plants like _A. paniculata_[52]. In the absence of a complete reference genome [16; 53], we utilized a de novo assembly with Trinity to generate the _A. paniculata_ leaf, stem, and root transcriptomes. This yielded 120,032 transcripts and 40,850 unigenes, providing a valuable genomic resource. Upon the availability of the complete _A. paniculata_ genome, the transcript assemblies could be further improved. Through transcriptome annotation, we identified 120 and 60 genes that were putatively involved in diterpene lactone and flavonoid biosynthesis, respectively. The predominant expression of diterpene lactone genes in leaves concurred with our metabolite profiling showing abundant lactone accumulation in leaves. These transcriptomic patterns suggest the involvement of these genes in tissue-specific terpenoid and flavonoid production. Diterpene lactone biosynthesis in _A. paniculata_ proceeds via cyclization and rearrangement reactions catalyzed by class II and class I terpene synthases [34]. While class II terpene synthases have been functionally characterized in vitro and in vivo [15], class I terpene synthases remain to be fully elucidated [16]. From the _A. paniculata_ transcriptomes, we mined 43 putative terpene synthase genes based on sequence conservation, translation to full-length proteins, and tissue expression patterns. Two class I terpene synthase candidates were prioritized for further functional validation to determine their role in lactone biosynthesis. _A. paniculata_ flavonoids also exhibit anti-platelet, anti-thrombotic, and anti-oxidant activities [54; 55]. While the flavonoid pathway is established in other medicinal plants [38; 39], the responsible genes in _A. paniculata_ have not been reported. Our integrated transcriptome and metabolite datasets provide the first insights into the transcriptional regulation of _A. paniculata_ flavonoid metabolism. In summary, the elucidated genes offer targets to engineer enhanced terpenoid and flavonoid production in this antiviral medicinal crop. Integrated transcriptomic and metabolomic analyses are powerful approaches to elucidate the biosynthetic pathways of medicinal plant natural products [56]. Deciphering the underlying genetics of metabolite accumulation can provide fundamental insights into pathway regulation and resources for industrial-scale production or generation of novel bioactive compounds [57; 58]. The present study identified putative genes associated with terpenoid and flavonoid metabolism in _A. paniculata_. Based on their tissue-specific expression patterns, several terpene synthase and flavonoid biosynthesis genes were revealed as candidates contributing to generating lactone and flavonoid phytochemical pools. However, further functional validation is required to conclusively determine the roles of these genes in governing terpenoid and flavonoid accumulation. Future studies should focus on enzyme assays in vitro and genetic manipulations in vivo to characterize the biosynthetic functions of the nominated genes. Elucidation of their metabolic contributions will provide the knowledge base to engineer an optimized production of antiviral phytochemicals in this important medicinal crop. Ultimately, the integrated multi-omics approaches implemented here serve as a framework to uncover biosynthetic pathways and enable biotechnological innovations in non-model plant natural product systems.