Insight into the Phylogenetic Relationships and Evolutionary History of Pepper Cultivars (Capsicum annuum L.) through Comparative Analyses of Plastomes

Pepper (Capsicum annuum L.) holds immense global importance, as it is widely cultivated for its economic value in the food industry and its health benefits. Consequently, substantial breeding progress has been made in cultivar development, whole-genome analysis, and transformation techniques aimed at enhancing agricultural traits, including fruit development and capsaicin synthesis. However, research concerning the phylogenetic relationships within C. annuum remains insufficient. In this study, we characterized the plastome sequences of seven C. annuum, including five hot pepper and two bell pepper cultivars, while also elucidating their phylogenetic relationships. Furthermore, we conducted comparative analyses to gain insight into their evolutionary history. The seven plastomes displayed typical quadripartite structures and ranged from 156,821 to 156,922 bp, displaying highly conserved sequences. In contrast to prior studies, our phylogenomic analyses revealed that C. annuum species did not form a monophyletic group. Each subclade was thought to be related to a different evolutionary history, such as hybridization, domestication from wild ancestors, and artificial selection. Therefore, we were able to discern the relationships among cultivars based on their genetic profiles of plastomes. Our findings also revealed that the Korean landraces Younggo 4, 5, 10, and 11 share the most recent common ancestor with Mexican landrace CM334.