## 2 Results
### Differentially Expressed Gene Analysis in Leaf vs. Root, and Stem vs. Root Tissue  
Differentially expressed genes (DEGs) within stem, leaf, and root tissues were screened using Poisson distribution methods with the parameters fold change (FC) \(\geq\) 2.00 and false discovery rate (FDR) \(\leq\) 0.001. Based on a Poisson distribution, 3372 unigenes showed expression in leaf tissues, 3287 unigenes showed expression in stem tissues, and 70,284 shared unigenes were identified in each of the three tissues (Figure 5A). Substantial transcription differences were observed in pairwise comparisons between different tissues. Forty-five-thousand-nine-hundred-and-sxty-one DEGs were commonly expressed in leaf and root tissue, while 14,951 DEGs were upregulated and 31,010 were downregulated in the leaf compared with the root. Comparison of stem and root tissue resulted in 33,110 DEGs, of which 12,570 were upregulated and 20,540 were downregulated in the stem compared with the root (Figure 5B).  
Figure 4: Spatial structure models of \(\beta\)-AS and the highly conserved motifs. (**A**–**C**) are the spatio-structural models of \(\beta\)-AS (CL2196.Contig2, CL5601.Contig1, and CL17709.Contig1; template: 1w6j.1.A; sequence identity: 43.10%, 39.88%, and 44.94%, respectively). The highly conserved MWCYCR (Motif I) and DCTAE (Motif II) residues are depicted as spheres in red and blue, respectively. (**D**) Alignment of \(\beta\)-AS amino acid sequences. Dark blue indicates identical amino acids, and red and lightskyblue indicate similar amino acids. Multiple sequence alignment was performed using the DNAMAN 6.0.3.99 software.  
Using KEGG enrichment, 33,088 DEGs were identified in leaf versus root, and 23,782 DEGs identified in stem versus root were mapped to 138 pathways, which were mainly enriched in \"metabolic pathways\", \"biosynthesis of secondary metabolites\", and \"plantpathogen interaction\" (Figure 6). Moreover, we identified 199 DEGs involved in terpenoid and polyketide metabolism, including 69 upregulated DEGs derived from leaf versus root and 36 upregulated DEGs derived from stem versus root (Figure 7).  
GO enrichment analysis showed that 25,024 DEGs derived from leaf versus root analysis in the \"biological process\" category were mainly mapped to \"photosynthesis\", \"cell wall organization or biogenesis\", \"carbohydrate metabolic process\", and \"cellular polysaccharide metabolic process\" (Supplementary Table S5). \"Drug catabolic process\", \"hydrogen peroxide metabolic process\", \"photosynthesis\", and \"hydrogen peroxide catabolic process\" were the major enriched GO terms of DEGs derived from stem versus root analysis (Supplementary Table S6). Furthermore, 40,108 DEGs in molecular function were mainly assigned to \"oxidoreductase activity\" in leaf versus root and stem  
Figure 5: Expression of unigenes in C. chinense leaf, stem and root tissues. (**A**) Venn diagram of the number of unigenes expressed in stem, leaf and root tissues. (**B**) Number of upregulated and downregulated DEGs in leaf vs. root, stem vs. root and leaf vs. stem datasets.  
Figure 6: Enrichment of differentially expressed genes (DEGs) in KEGG pathway. (**A**) Significantly enriched pathways for DEGs in leaf versus root tissues. (**B**) Significantly enriched pathways for DEGs in stem versus root tissues. The x-axis represents the rich factor (the value of the enrichment factor, which is the quotient of the foreground value (number of DEGs) and background value (total gene amount)), and the y-axis represents KEGG pathways.  
versus root analyses (Supplementary Tables S7 and S8). In general, a p-value for each term for which FDR \(\leq\) 0.01 was defined as significant enrichment.