Comparative genomics and proteomics analysis on Capsicum species reveals insights about the capsaicin biosynthesis

Capsaicin is the primary capsaicinoid compound responsible for the spiciness of chilli peppers. Several known and unknown genes synthesize capsaicin through various metabolic pathways, such as the phenylpropanoid or the L-valine metabolism pathways. We conducted comprehensive comparative genomics and proteomics analyses to identify genes and proteins associated with the capsaicin pathway in Capsicum chinense, Capsicum baccatum and the two C.annuum cultivars, CM334 and ECW. A BLAST search against the NCBI database identified 26 and 58 enzyme genes and proteins, respectively. These enzyme genes displayed distinct expression patterns, indicating diverse regulatory functions in capsaicin biosynthesis. Several enzymes were crucial for capsaicin accumulation, including 13 important genes. We identified unique proteins in C. chinense, with the highest pungency level, and others missing in C. annuum cultivar ECW, with the lowest pungency level. Our study increases our understanding of the genetics underlying the capsaicin biosynthesis pathway and influencing pungency variation in chilli pepper cultivars, further contributing to the broader knowledge of capsaicin production. Studying the functional properties of these enzyme genes is highly needed to explore their potential applications in biotechnology, food science, and medicine. © 2023 IEEE.