## 1 Introduction  
_Panax notoginseng_ (Burk) [PERSON]. [PERSON] is a widely used herbal medicine with important pharmacological effects, such as anti-hypertensive, neuroprotective, anti-inflammatory estrogen-like, anti-atherosclerotic, anti-tumor, and hepatoprotective activities [1; 2; 3; 4]. The medicinal properties of _P. notoginseng_ are attributed to its bioactive constituents, namely, triterpene saponins, which are also known as ginseng. These saponins can be categorized into two groups based on the skeleton of their aglycones, namely, dammarane-type and oleanane-type saponins [5; 6]. Dammarane-type saponins commonly include notoginsenoside R1 and ginseng Rb1, Rb2, Rc, Rd, Re, Rd, Rf, and Rg1 [7]. Oleanane-type saponins mainly comprise ginseng Ro and Roa [8]. Different parts of _P. notoginseng_ contain various types of saponins and show diverse pharmacological activities [3; 9]. For example, _P. notoginseng_ roots have been widely used to treat cardiovascular diseases and other disorders [10]. _P. notoginseng_ leaves are used to cure insomnia and alleviate anxiety [4]. _P. notoginseng_ flowers have beneficial effects on hypertension, tinnitus, and vertigo therapy [11; 12]. These results indicate that the parts of _P. notoginseng_ elicit different therapeutic effects. The identification of the types and contents of these different parts is essential for its safe application in medicinal and health care products. The types and contents of saponin are correlated with the expression of key genes in the synthesis pathway [13]. Studies have reported that triterpene saponins are synthesized through the mevalonate (MVA) and 2-C-methyl-D-erythnitol-4-phosphate (MEP) pathways, and multiple genes are involved in saponin synthesis [14; 15]. Isoprenyl diphosphate and dimethylly pyrophosphate produced in these two pathways are then transformed to geranyl pyrophosphate (GPP) by geranyl diphosphates synthase (GDPS), the formed GPP is then transformed into farnesyl pyrophosphate by farnesyl diphosphate synthase (FPS) [16]. Two FPP (C\({}_{15}\)) molecules yield a C\({}_{30}\) isoprenoid squalene by squalene synthase (SS) [17]. The formed squalene is catalyzed to produce 2,3-oxidosqualene by squalene epoxidase (SE) [18]. 2,3-Oxidosqualene is catalyzed by dammareenediol-II synthase (DS) to form dammareenediol-II and subsequently undergo cytochrome (CYP) hydroxylation and UDP-glycostransferases (UGTs) [19]. FPS, SS, SE, and DS genes show tissue-specific expression patterns, which are correlated with saponin contents [13; 15]. CYP716 subfamily genes, namely, CYP716A47 and CYP716A53v2, participate in dammarane-type triterpen production, and CYP716A52v2 is implicated in oleanane-type triterpeneoid production in _P. ginseng_[20]. CYP716A47 hydroxylates dammareenediol-II at the C-12 position to yield protopanaxadiol in _P. ginseng_[21]. CYP716A53v2 catalyzes protopanaxadiol at the C-6 position to generate protopanaxatriol in _P. ginseng_[22]. CYP716A52v2 acts as \(\beta\)-amyrin 28-oxidase that modifies \(\beta\)-amyrin into oleanolic acid in _P. ginseng_[23]. These results indicate that CYPs play important roles in dammarane-type triterpeneoid synthesis in _P. ginseng_. However, reports regarding the expression patterns of CYP genes related to the distribution of protopanaxadiol- and protopanaxatriol-type saponins in different parts of _P. notoginseng_ are limited. This study aimed to identify the main genes regulating the distribution of protopanaxadiol- and protopanaxatriol-type saponins in different parts of _P. notoginseng_ based on the integrated analysis of high-performance liquid chromatography (HPLC) and transcriptome. First, the types and contents of saponins in different tissues of _P. notoginseng_ were detected through HPLC. Subsequently, the transcriptome of the six parts was examined using Illumina HiSeq 4000 to identify the key genes related to saponin distribution. RT-qPCR analysis was performed to further confirm the main gene expression patterns in the tissues of _P. notoginseng_.