## 1 Introduction  
_Andrographis paniculata_ is an annual herbaceous plant in the Acanthaceae family that is widely found in the tropics and subtropics, especially in China, India, Malaysia, and other places [1, 2]. In China, _A. paniculata_ is considered one of the \"Great Southern Medicine\" and is known as \"natural antibiotics\" for its effectiveness in treating inflammation, influenza, cancer, and other conditions [3, 4]. The chemical constituents of _A. paniculata_ primarily includeiterpene lactones and flavonoids, with the main active ingredients being andrographolide, neoadjuvant, and deoxyradrographolide [5; 6]. _A. Paniculata_ has many applications in medicine and the chemical industry [7; 8]. Notably, andrographolide from _A. paniculata_ has been approved as a key component in many Chinese patent medicines, including andrographolide dropping pills, andrographolide tablets, and andrographolide soft capsules [9]. The highly contagious SARS-CoV-2 pandemic has caused thousands of deaths due to the unavailability of specific medications [10]. The Xiyanping injection, made from andrographolide derivatives, has been recommended for severe patients [11]. Owing to the increasing commercial value of _A. paniculata_, large-scale cultivation has been established in southern China with many good agricultural practice (GAP) planting bases [12]. However, supply remains insufficient to meet market demand. Therefore, modern biotechnology to enable in vitro biosynthesis is imperative.  
Diterpene lactones are characteristic compounds in _A. paniculata_, and their upstream pathway of biosynthesis is relatively well understood, including two pathways: the mexulonic acid (MVA) pathway and the plastidial 2-C-methylerythrhitol 4-phosphate (MEP) pathway [13; 14]. The MVA pathway produces isopentenyl pyrophosphate (IPP) and dimethylally pyrophosphate (DMAPP) from acetyl-CoA, while the MEP pathway synthesizes IPP and DMAPP from pyruvate and glyceraldehyde-3-phosphate. These compounds are then converted into _ent_-copalyl diphosphate (_ent_-cpp) by geranylgeranyl diphosphate synthase (GGPS) and _ent_-copalyl diphosphate synthase (_ent_-cps), with subsequent enzymes believed to be cytochrome P450 and class I terpene synthase [15; 16; 17]. Although transcriptomic and genomic studies in recent years have examined the downstream biosynthesis pathway of _A. paniculata_, the key class I terpene synthase enzymes have not been identified, leaving the pathway unclear [16; 18]. Additionally, despite the abundance of flavonoids in _A. paniculate_, their biosynthesis has received scarce research attention, with limited literature on the topic available.  
In order to extract the key enzymes of biosynthesis of the active ingredients in _A. paniculata_ and clarify their biosynthetic pathways, a comprehensive and systematic profiling of _A. paniculata_ was conducted. A qualitative analysis of different parts of _A. paniculata_ was performed using HPLC-MS and found that the active ingredients are mainly diterpene lactones and flavonoids. The molecular docking of these active ingredients showed potential for treating SARS-CoV-2 and significant commercial value. Moreover, the quantitative analysis on the chemical constituents in different tissues was also performed to determine the tissue-specific differences. Concurrently, transcriptome sequencing was used to analyze _A. paniculata_. Combining DEG analysis with a quantitative analysis of the active ingredients in different tissues made it possible to speculate on the biosynthetic pathways and enzymes involved in producing active components in _A. paniculata_. This study fills a gap of flavonoid biosynthesis in _A. paniculata_, and the transcriptome analysis data will facilitate further research on the biosynthesis genes of natural products in _A. paniculata_, enriching its genetic information and providing insights for the subsequent in vitro biosynthesis of these diterpene lactones and flavonoids.