## 3 Discussion
chinense_ datasets, and the alignment of six \(\beta\)-AS unigenes suggested that \(\beta\)-AS contains a highly conserved binding site and characteristic motif (Figure 4). These results were consistent with \(\beta\)-AS in other plants [28; 29]. Previous studies have shown that the \"DCTAE\" motif is the initiation site for the polycylization reaction. The Asp residue in this motif releases protons to trigger the cyclization reaction in the conversion of 2,3-oxidosqualene to \(\beta\)-amyrin [28; 30]. The \"MWCYCR\" motif is a characteristic motif of \(\beta\)-AS. the \"W\" residue controls the formation of \(\beta\)-amyrin by stabilization of an oleanyl cation, and the \"Y\" residue participates in forming pentacyclic triterpenes [29]. Moreover, the rich helix suggests that \(\beta\)-AS is a membrane-related protein [20]. Despite the sequence diversity of these genes, the protein 3D structures were conserved and had similar functions. The overall expression level of unigenes and content of total saponins in root tissue was lower than that in leaf and stem tissues. This result suggested that the aerial parts of _C. chinense_ might contain effective medicinal compounds. Based on DEG analysis, 69 DEGs involved in terpenoid backbone biosynthesis were upregulated in leaf versus root tissue, and 36 DEGs were upregulated in stem versus root tissue. The observation that these upregulated DEGs control the biosynthesis of the terpenoid backbone in leaf and stem tissue further confirmed that the aerial parts of _C. chinense_ possess important medicinal value. Many TFs are difficult to detect owing to their low expression levels; however, they are very important because small increases in expression levels of TFs can have drastic effects [31]. In our study, a total of 4381 candidate TFs were assigned to 59 TF families. These TFs might be crucial for plant metabolism and regulation. MYB TFs are crucial for biosynthesis of the terpenoid backbone. A previous investigation indicated that the overexpression of a MYB TF in tomato can upregulate the terpenoid metabolism [32]. The 572 candidate MYB TFs discovered in our dataset included 100 upregulated TFs in leaf versus root comparisons and 75 upregulated TFs in stem versus root comparisons (Table 3). Previous studies also showed that the overexpression of WRKY in transiently transformed _C. blinii_ resulted in improved total saponin content [33]. A total of 277 WRKY TFs were identified in this study, of which 76 upregulated TFs were identified in the leaf versus root comparisons and 29 upregulated TFs were identified in stem versus root comparisons. Specially regulated TFs might be responsible for modulating the content of triterpen saponins in _C. chinense_. Plant hormones are plant-specific key signaling molecules that respond to various stimuli and are involved in the synthesis of secondary metabolites [34]. JA can upregulate the expression level of the squalene synthase (BFSS1) gene, stimulate the accumulation of \(\beta\)-AS mRNA and increase the content of bupleurum saponins [35]. Additionally, the synthesis of sesquiterpene and monoter were promoted in GAs-mediated grapevine [36]. In the present study, we found 60 genes involved in JA biosynthesis, including eight and 24 upregulated genes in leaf vs. root and stem vs. root comparisons, respectively. Ten genes participated in GA biosynthesis, of which only one upregulated gene was identified in the stem versus root comparisons, which may indicate the importance of the biosynthesis of GA.