## 2 Results
### Morphological Characterization of Glandular and Non-Glandular Trichomes of T. sinensis
**(b1–b3)**, abaxial side of leaf surface from the tip, middle and base of CAF0845 respectively; **(b1–b3’)**, abaxial side of leaf surface from the tip, middle, and base of CAF0845 respectively; **(c1–c3’)**, abaxial side of leaf surface from the tip, middle and base of CAF0830 respectively; **(d1–c3’)**, abaxial side of leaf surface from the tip, middle, and base of CAF0830 respectively. **(d)** Statistical analysis of the glandular and non-glandular trichomes on the adaxial and abaxial surfaces of the mid-section of the leaves of CAF0845 and CAF0830, in which the number of epidermal trichomes within an area of 1.5 mm\({}^{2}\) was counted. N, non-glandular; G, glandular. **(e)** The volatile components in the leaves of CAF0646 and CAF0830 were measured by GC-MS, and the components accounting for more than 1% of the total content were listed. The components corresponding to the chemical formulas are shown in Table 1. The red arrow shows the sesquiterpene component. We further performed gene expression analysis to obtain the differentially expressed genes (DEGs) (Log (FC) \(\geq\) 1 and FDR \(\leq\) 0.05) for several comparisons. The results showed that in different comparison combinations, the number of DEGs in the top and middle regions between the two varieties was high, while the number of DEGs in the middle and bottom regions of the same variety was significantly less (Figure 4a); moreover, it can be found that in the combinations between two genotypes, the number of DEGs was significantly higher (Figure 4a). In order to explore the distribution of DEGs, we conducted multiple combination analyses. First, we identified the DEGs that were compared at the same locations on the CAF0845 and CAF0830 leaves and identified 408 shared differential genes (Figure 4b). GO and KEGG enrichment analysis of the shared DEGs indicated that secondary metabolic pathways, including sulfur-containing substances, lipids, and amino acid metabolism, were involved in the differential process (Figure 4c). Second, we selected five combinations with a high number of DEGs for analysis, from which we identified 1112 shared DEGs (Figure 4d). The following GO and KEGG enrichment analyses of these 1112 DEGs revealed that similar to previous analyses, multiple secondary metabolic pathways are also the main pathways involved in these differential genes (Figure 4e). Taking these results, we suggest that the variations in trichome density in _T. sinensis_ are closely related to the process of the biosynthesis and regulation of secondary metabolites and may share a common regulatory pathway. Figure 4: Comparative transcriptome analysis of the different leaf zones in the _T. sinensis_ varieties with differential trichome density. (**a**) Summary of the distribution of the DEGs among comparisons of the samples. (**b**) A Venn diagram illustrating the DEGs at the same site across two genotypes. (**c**) GO function enrichment (\(p\)-value \(<\) 0.01) and KEGG pathway enrichment (\(p\)-value \(<\) 0.05) results from the bubble plots for the common genes in Figure 4b. (**d**) A Venn diagram depicting the top five groups with the highest number of DEGs. (**e**) GO function enrichment (\(p\)-value \(<\) 0.01) and KEGG pathway enrichment (\(p\)-value \(<\) 0.05) plots for the common genes in Figure 4d. Characterization of TPS Genes in T. sinensis Identify Candidates Involved in Sesquiterpenoid Biosynthesis  
We focused on the variation in the sesquiterpene content in the T. sinensis varieties and analyzed the expression levels of the TPS gene family (Table S2). In total, we obtained 44 _TPS_ genes in _T. sinensis_ based on our transcriptome data, and their expression patterns varied among varieties and regions (Figure S2). We analyzed the expression levels of TPS genes differentially among the varieties and identified 10 TPS genes that were differentially expressed in all three corresponding regions of the two varieties (Figure 5a).