## 3 Results
### Phylogenetic, Gene Structure, and Promoter Analysis of Terpene Metabolism Genes
_FPPS-1_, _IDI-1_, _DXS-3_, _TPS-6_, _TPS-10_, _TPS-16_, _TPS-26_, _TPS-28_, _TPS-30_ showed high expression levels during the green fruit stage of GLD608, while it was not detected or expressed very low in other varieties and growth stages. _TPS-23_ showed high expression levels in GJ and HDL at the breaking and red stages. Additionally, _HMGS-1_, _FPPS-2_, _GGPPS-6_, _DXS-1_, _TPS-17_, and _TPS-18_ were detected in tiny amounts at different growth stages of the three varieties. Furthermore, we validated the expression levels of 16 differentially expressed genes (_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_, _MECPS-1_, _GPPS-1_, _TPS-5_) at different developmental stages of GLD608, GJ, and HDL fruits using qRT-PCR. (Figure 6). In GLD608, the expression levels of most genes first decreased and then increased. For illustration, compared with the green fruit stage, the expression levels of the _AACT-2_ and _HMGS-3_ genes, respectively, increased  
Figure 5: Heatmap of expression of terpenoid metabolism genes during different fruit developing periods. a, Green fruiting stage. b, Breaking stage. c, Mature stage. Color coded units are FPKM values. Note: Genes with significant differences in expression at different times are labelled with a red star. by 1.5 times and 3 times in the mature stage. It is worth noting that there are also some gene expression levels that show continuous changes over time. Concerning the _IDI-3_ gene, its expression level continues to increase, and the mature stage is about thirteen times that of the green fruit stage. The expression levels of some genes in GJ, such as _FPPS-1_, _CMK-1_, _MECPS-1_, _GGPPS-2_, and _TPS-5_, are significantly higher during the color transformation and mature stages than during the green fruit stage, about 8 to 40 times higher. Also, only the _AACT-1_ gene had the lowest expression level during the mature stage, decreasing by 2.5 times compared to the green stage and 4.5 times compared to the color transition stage. The expression level of  
Figure 6: qRT-PCR analysis of genes in GLD608, GJ, and HDL. Blue: Green fruiting stage. Yellow: Color transform stage. Red: Mature stage. Note: 'ns' denotes \(p>0.05\), '' denotes \(p\leq 0.05\), '' denotes \(p\leq 0.01\), '' denotes \(p\leq 0.001\), '' denotes \(p\leq 0.001\), '' denotes \(p\leq 0.0001\). the _MCT-1_ gene in HDL during the green fruit stage is about 14 times that during the color transition stage and 50 times that during the mature stage. In addition, most genes (such as _AACT-1_, _FPPS-1_, and _IDI-3_) have much higher expression levels during the green fruit stage and color transition stage than during the mature stage. The most noteworthy aspect is that the expression levels of the _TPS-5_ genes in the three stages are the same, indicating that certain aroma substances in HDL may continue to be synthesized and volatilized. By comparing the changes in the gene expression levels of GLD608, GJ, and HDL, it was found that the expression levels of GLD608 showed an opposite trend to those of GJ and HDL. Also, the gene expression levels of GJ and HDL are higher than GLD608, especially the _AACT-1_, _HMGR-2_, _FPPS-1_, _GPPS-1_, and _TPS-5_ genes. This may explain the differences in aroma characteristics among different chili varieties.