## 4 Discussion
This information is crucial not only for understanding the roles of terpenoid metabolism genes in peppers and their functions within metabolic pathways but also for gaining insights into the evolution of gene families. Introns are essential components of eukaryotic genes, exhibiting both conservation and diversity in their structure. Among the 67 genes analyzed, intron-free genes were discovered (_CaGGPPS-2_, _CaGGPPS-3_, _CaGGPPS-4_). Introns confer evolutionary advantages by increasing gene length, enhancing intergenic recombination, and contributing to gene expression regulation [32]. Intron less genes, while lacking the recombinational advantages associated with introns, may serve a unique function in rapid response regulation due to their swift transcription into proteins. We hypothesize that _CaGGPPS-2_, _CaGGPPS-3_, and _CaGGPPS-4_ may contribute to faster plant growth and development, potentially shortening breeding cycles. Gene expression patterns correlate significantly with intron length, which tends to be shorter in high-abundance genes compared to low-abundance genes in animalsand Arabidopsis [33]. Thus, quantifying low-abundance genes may require highly sensitive assays for accurate measurement. _Cis_-acting elements are pivotal in gene regulation. These DNA sequences, located in or near gene promoter regions, specifically regulate transcription levels by binding to transcription factors [34]. Understanding these elements and their interactions with promoters is essential for elucidating gene expression mechanisms and regulatory networks. An analysis of the _cis_-acting elements indicated that the more numerous and conserved _CaGGPPSs_ and _CaTPSs_ are critical to terpene metabolism and synthesis, providing a foundation for future research into downstream product mechanisms and functions in pepper terpene pathways. Further analysis revealed that the 34 identified _cis_-regulatory elements were predominantly associated with phytohormone regulatory pathways, especially those involved in methyl jasmone and salicylic acid responses, such as the CGTCA-motif (methyl jasmone response) and TCA-element (salicylic acid response). Methyl jasmone and salicylic acid are two major resistance signaling pathways in plants that play distinct roles in regulating the synthesis and metabolism of flavor compounds. These findings offer new perspectives for investigating the mechanisms underlying chili fruit flavor compound synthesis. Heatmap analysis revealed that some genes exhibited a darker red color, indicating a significant increase in expression and high activation of genes related to the synthesis of chili aroma compounds. This pattern suggests that these conditions may be associated with the initiation or active phase of aroma synthesis pathways. In contrast, other genes displayed lighter-colored or blank regions, suggesting no strong correlation with aroma pathway activation. These differences indicate that specific conditions may favor the activation of flavor compound synthesis pathways, especially those involving _TPSs_, _GGPPSs_, _DXRs_, and _DHSs_. Combined with the heatmap, we can see that certain genes are highly expressed under specific conditions, such as _AACT-1_ and _HDR-1_, which are consistently highly expressed under multiple conditions, suggesting that they may be \"universal\" synthetic genes that are always involved in the synthesis of fragrance substances. And the enhanced expression of other genes (_TPS-5-26_) under specific conditions may be involved in the synthesis of specific compounds, which reflects the complexity and diversity of the synthesis pathway of pepper flavor substances. Volatile terpene components serve as crucial indicators for aroma identification [35]. _C. annuum_ and _C. chinense_ are among the most widely cultivated peppers in China.