Comparative analysis of complete chloroplast genome of the Peruvian landrace of Capsicum chinense, arnaucho chili pepper, and related species of the Capsiceae tribe

Although many complete chloroplast (cp) genomes of different types of peppers have already been published, there has been no comprehensive study that summarizes all the characteristics of the Peruvian landrace “arnaucho” chili pepper (ACP) comparing it with other types of genomes in its Capsiceae tribe. In this study, a comprehensive analysis was conducted using data from cp genomes obtained from NCBI GenBank. These 14 genomes were annotated using Geseq, followed by genomic comparisons, chloroplast structure analysis, phylogeny, and repetitive sequence analysis, employing a variety of bioinformatics tools. The findings revealed length variations among the cp genomes, ranging from 156,583 bp in C. lycianthoides to 157,390 bp in C. pubescens, with a GC content of 37% across all genomes. The comparative genome analysis revealed that the greatest variation among the 14 genomes occurred in the non-coding regions. Arnaucho chili pepper exhibited greater divergence in coding regions with C. lycianthoides, specifically in the genes accD, rpl20, rps12, clpP, ycf2, ndhF, ndhA, ycf1, and rpl2. The results of the phylogeny and pairwise distance analysis in this study support that the arnaucho chili pepper clusters with C. galapagoense, with an average distance value of 0.00002733. Additionally, the repetitive sequence analysis determined that ACP maintains a number of repetitive sequences similar to other Capsicum species but possesses a lower number of SSRs (33). Finally, it was determined that the junction regions of ACP have a total length of 156,931 bp, similar to C. galapagoense with 156,959 bp. The four boundary regions exhibited consistent gene patterns, except for the JSB region, where the ycf1 gene in ACP was located only in the IRb region, whereas it was absent in other Capsicum species. This research provides additional effective evidence for characterizing the entire cp genome and classifying species and genera within the Capsiceae tribe.