## 3 Results
### Differential Expression Analysis of the Leaf, Flower and Root Samples of C. keiskei  
An analysis of differentially expressed unigenes in the leaf, flower and root of _C. keiskei_ using the Trinity pipeline revealed a total of 3152 genes that showed significant differential expression (Supplementary Figure S7; Supplementary Table S3). Among these genes, 956 unigenes were significantly upregulated in the leaf, 236 in the flower and 417 in the root, and 50 unigenes were significantly upregulated in all the tissues (Figure 3A). Additionally, 367 unigenes were upregulated in both the flower and leaf, while 187 unigenes were upregulated in both the flower and root of _C. keiskei_. On the other hand, 471 genes showed down-regulation from the leaf to the flower (Figure 3B). The analysis of differentially expressed genes between the root and flower identified 1001 significantly downregulated genes, with 259 unigenes showing downregulation from the root to leaf. An annotation analysis of the top differentially expressed genes revealed that the upregulated unigenes in the leaf were mainly related to the photosynthesis process and phenylpropanol biosynthesis in _C. keiskei_.  
In the flowers, the upregulated unigenes were associated with lipid biosynthesis, terpene synthase genes, and the auxin response. In the root, the upregulated unigenes were primarily involved in organic chemical compound metabolism and terpene synthase genes (Figure 4; Supplementary Table S4). The downregulation analysis showed that the genes involved in lipid biosynthesis were downregulated in the leaf. Genes related to methyltransferase, metallothioneein and glycohydrolase 32 classes in the flower were highly downregulated. In the root, genes involved in glucosidase, GAP-dehydrogenase, photosynthesis and chalcone-flavanone isomerase were downregulated (Figure 4; Supplementary Table S5). The volcano plots of the differentially expressed _TPS_ genes revealed tissue-specific expression patterns in _C. keiskei_, highlighting the novel functions of _ckTPS2_, _ckTPS7_, _ckTPS14_ and _ckTPS23_ (Figure 4). These four _TPS_ genes showed significant expression differences in the comparative analysis and exhibited conserved motifs (Figure 4; Supplementary Figure S8).  
Figure 3: Venn diagram of the overlap of DE unigenes among the leaf, flower, and root of _C. keiskei_. (**A**) Upresulated genes and (**B**) downregulated genes.  
Among them, _ckTPS2_ and _ckTPS23_ were upregulated in the flower and downregulated in the leaf and root. _ckTPS14_ was significantly upregulated in the leaf and downregulated in the flower and root. _ckTPS7_ showed high upregulation in the root and downregulation in the leaf and flower of _C. keiskei.__ckTPS2_, belonging to the TPS-g class, is potentially related to geraniol synthase involved in the production of mono-terpenoids responsible for the floral scent in _C. keiskei_ flowers. _ckTPS23_, belonging to the TPS-a class, is upregulated in flowers, and may play a role in unknown floral scent functions in _C. keiskei_.  
Figure 4: Volcano plot showing comparative differential expression of unigenes and the top four _TPS_ genes in _C. keiskei_.