## 3 Results
### Phylogenetic, Gene Structure, and Promoter Analysis of Terpene Metabolism Genes
Further analysis reveals that _CaIDI-2_, _CaPMK-2_, _CaDXS-1_, and _CaTPS-8_ have significantly longer intron lengths than other genes within the same family, suggesting that these genes have more expression regulatory elements. Furthermore, the upstream 2000 bp sequences of the start codons of 67 terpenoid-related genes were analyzed to reveal the expression characteristics of terpenoid genes and explore possible regulatory mechanisms. The results showed that the promoters of terpenoid genes all contain elements related to abiotic stress, biotic stress, light induction, and plant growth and development. Among them, the number of elements related to abiotic stress and plant growth and development accounted for more than 85%. Except for _CaGGPPS-2_, _CaHMGR-2_, and _CaTPS-9_, all other gene promoters contain MYB binding  
Figure 3: Phylogenetic tree, gene structure, and conserved motifs analysis of enzyme genes. (**A**) Interspecies evolutionary relationships. (**B**) Conserved motifs. (**C**) Structural domains. (**D**) Gene structure. components (Figure 4). _CaTPSs_ promoter elements are mainly involved in abiotic and biotic stresses as well as in phytohormone response factors. Stress and hormone response elements were also commonly distributed in the gene promoters. The extracted stress-related _cis_-elements (Myb, Myc, ARE, and STRE) indicated that _CaIDI-3_, _CaTPS-8_, _CaTPS-32_, and _CaHDR_-1 might play a key role in responding to unfavorable conditions. In addition, the drought-inducible element MBS was found among the abiotic stress elements, and this type of response element could be involved in transcriptional regulation in plants in synergy with the MYB element. Among the light-responsive elements, _CaFPS-2_ may play a key role in the light-controlled development of plants. In addition, some promoters are rich in ABRE (involved in ABA response), such as _CaFPS-2_, _CaTPS-2_, and _CaTPS-25_, and these genes may be responsive to ABA hormones. Further analysis of the number of _cis_-acting elements in the promoter region shows that _CaFPS-2_ contains the most _cis_-acting elements, while _CaHDR-1_ contains the most nonbiological stress response elements. _CaMECPS-1_, _CaTPS-1_, _CaTPS-10_, and _CaTPS-20_ do not contain _cis_-acting elements related to photoreaction. Expression Patterns of Enzyme Genes for Terpene Metabolism and Synthesis During Chili Fruit Development  
The expressions of 67 genes were analyzed by transcriptome data at the fruit green, breaking, and red stages in GLD608, GJ, and HDL (Figure 5). The results showed that _AACT-1_, _IDI-2_, _GGPPS-1_, _HDR-1_, and _HDS-1_ exhibited high expression levels at various  
Figure 4: Heatmap matrix of names and numbers of _cis_-acting elements of genes involved in synthesis of terpenoid metabolic pathways. stages of pepper fruit development, indicating that these genes were involved in the biosynthesis of terpenoid flavor compounds throughout the entire development process. _GGPPS-3_, _GGPPS-5_, _TPS-2_, _TPS-4_, _TPS-7_, _TPS-9_, _TPS-11_, _TPS-13_, _TPS-15_, _TPS-16_, _TPS-18_, _TPS-19_, _TPS-22_, _TPS-24_, _TPS-26_, _TPS-27_, _TPS-29_, _TPS-31_, _TPS-32_, and _TPS-33_, a total of 20 genes, were not detected to be expressed. In addition, there are 16 genes with differential expressions, including _AACT-2_, _HMGS-3_, _HMGR-2_, _MVK-1_, _PMK-1_, _MVD-1_, _IDI-3_, _FPPS-1_, _GGPPS-2_, _DXR-1_, _DXS-2_, _MCT-1_, _CMK-1_, _CMK-1_, _MECPS-1_, _GPPS-1_, and _TPS-5_. The remaining twenty-six genes showed differential expressions among varieties or developmental stages. For example, _HMGS-2_ expression was higher at the green fruit stage in GLD608. _TPS-1_ and _TPS-3_ had high expression at the green fruit stage in HDL. _TPS-12_ showed high countenance at the green fruit stage in all three varieties. There are also some genes with differential expressions in a variety of types and developmental stages.