## 2 Results
### Gene Annotation and Functional Classification
\begin{table}
\begin{tabular}{c c c c c c c} \hline \multirow{2}{*}{**Sample**} & **Total Raw** & **Total Clean** & **Total Clean** & **Clean Reads** & **Clean Reads** & **Total Mapping** \\  & **Reads (M)** & **Reads (M)** & **Bases (Gb)** & **Q20 (\%)** & **Q30 (\%)** & **(\%)** \\ \hline AYYS1 & 45.72 & 42.54 & 6.38 & 98.79 & 96.38 & 80.41 \\ AYYS2 & 45.72 & 42.45 & 6.37 & 98.82 & 96.46 & 79.94 \\ AYYS3 & 45.72 & 42.36 & 6.35 & 98.78 & 96.37 & 81.93 \\ NZ1 & 47.35 & 43.01 & 6.45 & 98.68 & 96.07 & 78.49 \\ NZ2 & 47.35 & 43.24 & 6.49 & 98.73 & 96.2 & 81.5 \\ NZ3 & 47.35 & 42.95 & 6.44 & 98.63 & 95.93 & 78.7 \\ YXFZC1 & 47.35 & 42.51 & 6.38 & 98.27 & 94.78 & 76.74 \\ YXFZC2 & 47.35 & 42.5 & 6.38 & 98.29 & 94.82 & 73.63 \\ YXFZC3 & 47.35 & 42.75 & 6.41 & 98.31 & 94.9 & 74.33 \\ summary & 421.26 & 384.31 & 57.65 & / & / & / \\ \hline \multicolumn{7}{c}{AYYS1, AYYS2 and AYYS3 were eucalypt chemotype; NZ1, NZ2 and NZ3 were camphor chemotype; YXFZC1,} \\ \multicolumn{7}{c}{YXFZC2 and YXFZC3 were linalool chemotype.} \\ \end{tabular}
\end{table} 
Table 4: Summary of RNA-seq data from nine RNA libraries of eucalypt chemotype, camphor chemotype and linalool chemotype of _C. porrectum_. Figure 2: Functional annotation and classification of assembled unigenes in _C. porrectum_. (**A**) Annotation information of the Venn diagram. (**B**) KEGG pathway classification of putative proteins. The unigenes were divided into six branches according to the following KEGG metabolic pathways: organism systems A. metabolism B. human diseases C. genetic information processing D. environmental information processing E. and cellular processes F. (**C**) GO classification of unigenes in _C. porrectum_. GO terms are classified into three main categories: biological process (BP), cellular component (CC) and molecular function (MF). unigenes were identified, including 20,270 upregulated genes and 11,238 downregulated genes. A total of 2975 unigenes were unique to the eucalypt chemotype, 5391 unigenes were unique to the linalool chemotype, and 23,142 unigenes were shared by the two chemotypes (Figure 3A). In the camphor chemotype and eucalypt chemotype comparison group, a total of 25,522 unigenes were identified, including 10,834 upregulated genes and 1468 downregulated genes. Of these unigenes, 4969 were unique to the camphor chemotype, 3624 were unique to the eucalypt chemotype, and 16,929 were shared by the two chemotypes (Figure 3B). In the camphor chemotype and linalool chemotype comparison group, a total of 29,691 unigenes were identified, including 17520 upregulated genes and 12,171 downregulated genes. A total of 3011 unigenes were unique to the camphor chemotype, 4160 unigenes were unique to the linalool chemotype, and 22,520 genes were shared by the two chemotypes (Figure 3C). To explore the differences in metabolic pathways between the linalool and eucalypt chemotypes, between the camphor and linalool chemotypes, and between the camphor and eucalypt chemotypes, KEGG enrichment pathways were analyzed using 31,508, 25,522 and 29,691 DEGs, respectively. The top 20 KEGG pathway categories are presented in the form of a dot plot (Figure S2A-C). The pathway with the most significant enrichment of DEGs in the camphor and linalool chemotype comparison group was the \"monoterpene biosynthesis\" pathway. The \"monoterpene biosynthesis\" pathway was also enriched significantly in the camphor and eucalypt chemotype comparison group. Figure 3: (**A**) Number of DEGs in the eucalypt chemotype and linalool chemotype of _C. porrectum_. Red: upregulated genes; green: downregulated genes. Relative expression of DEGs selected at a \(Q\)-value \(<\) 0.05. The fold change (FC) was calculated as the ratio between the linalool chemotype and eucalypt chemotype. The x-axis represents the range of Log2 FC. The y-axis indicates the number of detected DEGs. (**B**) Number of DEGs in camphor chemotype and eucalypt chemotype of _C. porrectum_. The fold change (FC) was calculated as the ratio between the eucalypt chemotype and camphor chemotype.