## 3 Results
### Gene Ontology and KEGG Annotation  
In the leaf tissue of _C. keiskei_, a gene ontology (GO) category study revealed 182 biological process terms. Among these, 51.73% of the unigenes were involved in the organic substance metabolic process, while 45.64% were categorized under the primary metabolic pathway. In terms of the secondary metabolic processes, 2.23% of the genes were associated with chlorophyll metabolism, 1.4% with carotenoid metabolism and 0.88% with xanthophyll metabolism, and 3.32% were found to respond to jasmonic acid.  
For the flower tissue, 110 GO categories were identified. Of these, 22.28% of the genes were involved in the developmental process, 21.62% in anatomical structural development and 12.08% in reproduction. In terms of secondary metabolic categories, 1.25% of the genes were associated with flavonoid metabolism and 0.65% with iso-pentenyl diphosphate (IPP) metabolism.  
In the root tissue, 198 biological function categories were observed. Among these, 28.34% of the unigenes were involved in chemical responses, while 20.38% were involved in inorganic substance responses. The root unigenes also exhibited secondary metabolic processes related to salicylic and jasmonic acid synthesis, with 1.08% of the genes involved in ethylene metabolism.  
When considering the combined assembled unigenes from all tissues, 228 GO categories were shared. Among these, 59.13% were related to metabolic process. In the plant secondary metabolic process, 3.18% were involved in isoprenoid metabolism, and 2.94% were associated with terpenoid metabolism (Supplementary Figure S3).  
Through the KEGG annotation, it was found that terpene cyclases from linear oligo-prenyl diphosphate precursors were responsible for the production of the largest class of natural products. The complete assembly of _C. keiskei_ generated 237,129 unigenes, of which 36.9% (68,282 unigenes) were identified in different routes through KEGG analysis (Supplementary Figure S4). Overall, 1047 of the unigenes were associated with metabolic pathways, and 165 of the unigenes were related to the biosynthesis of secondary metabolisms in diverse environments.  
The terpenoid backbone biosynthesis analysis revealed 31 databases matched to the KEGG database in the combined _C. keiskei_ unigenes. The pathway involved the production of various terpenoids, starting from acetyl-CoA to IPP, which produced FPP and GPP, leading to the production of different terpenoids. In the monoterpenoid pathway, compounds such as linalool and neomenthol were found in the flowers and leaves of _C. keiskei_ (Figure 1). In the diterpenoid pathway, eleven types of Gibberellic acid (GA53,44,19,20,29,51,9,24,15,12,34) were identified in the flower, leaf and root of _C. keiskei_. Sesquiterpenoid oils, including neorlidol, squalane and germacre B, were found in the flower samples, while neorlidol, neomenthol, germacre B and the triterpenoid oil amyrin were present in the leaf samples. The root transcriptome exhibited a higher abundance of monoterpenoids such as limonene, citronella, citronella, oxo gerani, caryophyllene and germacre B compared to the leaf and flower (Figure 1).  
\begin{table}
\begin{tabular}{c c c c c c c} \hline \multirow{2}{*}{**S. no**} & _C. keiskei_ & \multirow{2}{*}{**Unigene**} & \multirow{2}{*}{**N50**} & \multirow{2}{*}{**TAIR**} & \multirow{2}{*}{**Pfam**} & \multirow{2}{*}{**KEGG**} \\  & & & & & & \\  & & & & & & \\ \hline
1 & leaf & 72,044 & 1058.54 & 14,413 & 46,578 & 42,221 \\ \hline
2 & flower & 116,434 & 972.03 & 15,679 & 55,244 & 50,597 \\ \hline
3 & root & 146,550 & 802.03 & 14,880 & 58,909 & 45,363 \\ \hline  & all & 237,129 & 811.21 & 33,021 & 59,121 & 68,282 \\ \hline \end{tabular}
\end{table}
Table 1: Trinity de novo assembled unigenes and annotation statistics for _C. keiskei_.