## 3 Results
### Phylogenetic, Gene Structure, and Promoter Analysis of Terpene Metabolism Genes  
To reveal the potential functions of related proteins in the evolutionary process, we constructed the phylogenetic relationships of enzyme proteins involved in the terpenoid metabolism pathway. The phylogenetic trees of 18 related enzymes are shown in detail in the attached image 1. Most of the genes are more closely related to _Solanum Lyopersicum_, e.g., _CaGPPS-1_ and _CaMECPS-1_. But interestingly, _CaHMGR-2_ is more closely related to _Artemisia ammu_, and _CaFPPS-1_ is more closely related to _Gossypium hirsutum_, which may be related to the retention of relative protein sequences during the evolutionary process. _CaPMK-2_ is more closely related to _Nicotiana tabucum_, and the same is also true for _CaDI-1-3_ and _CaDXS-2_, which is consistent with the fact that chili and tobacco belong to the same family, _Solanaceae_. Moreover, the _CaTPSs_ family was further divided into four subclasses: TPS-a, TPS-b, TPS-e/f, and TPS-g. Among them, the TPS-a subclass contained twenty-two genes, the TPS-e/f subclass contained _CaTPS-5_ and _CaTPS-12_, with the former being more closely related to _Arabidopsis KS1_, and the latter being more closely related to _Arabidopsis TPS4_. The TPS-g subclass contained only the _CaTPS-31_ gene. To further explore the structure, function, characteristics, and conserved motifs of terpene metabolic pathway-related genes and their amino acid sequences, the number and location of introns and exons and conserved motifs of sixty-seven members were analyzed (Figure 3). Of the 67 enzyme genes identified, 53 genes contained conserved motifs, while 14 genes did not retrieve any motifs, such as _CaHDS-1_, _CaDI-1-2-3_, _CaDXR-1_, _CaAACT-1-2_, _CaMVK-1_, _CaMECPS-1_, _CaDXS-1-3_, _CaHDR-1_, and _CaCMK-1_. Genes in the same gene family are highly conservative and share many of the same motifs. _CaTPSs_ all contain motifs 5, 2, 3, and 6. All _CaGGPPS_ genes have motifs 18 and 21 (Figure 3B). Yet, there is still some variation in the type of motifs of different genes within the same family. For example, in the _CaPMK_ family, only _CaPMK-2_ contains motif 23. In the _CaTPS_ family, _CaTPS-12_ and _CaTPS-5_ lack motif 9, _CaTPS-12_ and _CaTPS-24_ lack motif 8, and only _CaTPS-5_ has motif 23. In addition, _CaTPS-2_ has two instances of motif 9. The presence of these unique motifs suggests that these genes may have specific functions in the family. Conservative domain analysis shows that in most cases, the same gene family has the same domain characteristics. Members of _CaTPSs_ include both N-terminal and C-terminal domains (Figure 3C). However, _CaHMRG-4_ differs from other _CaHMRGs_ in that it possesses a unique MARVEL quadruple  
Figure 2: Chromosome mapping and duplication of genes involved in synthesis of terpene metabolic pathway in C. _ammuum_. transmembrane domain. _CaDXS-1_ lacks an N-terminal domain but has an N-terminal gene superfamily domain. These differences may lead to some functional differences in gene expression products. In addition, _CaFPPSS_, _CaGGPPSs_, and _CaGPPS_ all contain polyprenyl-synt structural domains, suggesting that these genes may exercise the same or similar functions. According to the analysis of the gene structure (Figure 3D), the number of introns ranged from 0 to 19, with _CaGGPPS-2_, _CaGGPPS-3_, and _CaGGPPS-4_ containing no introns, whereas _CaHDS-1_ had 19 introns. The number of exons ranged from 1 to 19, with _CaGGPPS-2_, _CaGGPPS-3_, and _CaGGPPS-4_ containing only 1 exon, whereas _CaHDS-1_ had 19 exons. Different gene families showed significant differences in the number of introns and exons. Exon numbers in _CaGGPPSs_ ranged from 1 to 6 predominantly, whereas exon numbers in _CaTPSs_ were clustered between 7 and 8. In addition, members of the same gene family usually have similar numbers of introns and exons. For example, _CaIDI-1-2-3_ all have 6 exons, while 10 introns appear in _CaPMK-1_ and _CaPMK-2_.