The complete mitochondrial genome assembly of Capsicum pubescens reveals key evolutionary characteristics of mitochondrial genes of two Capsicum subspecies

Abstract

Abstract Pepper (Capsicum pubescens), one of the five domesticated pepper species, boasts unique characteristics such as numerous hairs on the epidermis of its leaves and stems, black seeds, and vibrant purple flowers. Previously, no studies have reported on the complete assembly of the mitochondrial genome (mitogenome) of C. pubescens. Understanding the mitogenome is crucial for further research on C. pubescens. In our study, we successfully assembled the first mitogenome of C. pubescens, which has been assigned the GenBank accession number OP957066. This mitogenome has a length of 454,165 bp and exhibits the typical circular structure observed in most mitogenomes. We have annotated a total of 70 genes, including 35 protein-coding genes (PCGs), 30 tRNA genes, 3 rRNA genes, and 2 pseudogenes. Compared to the other three pepper mitogenomes (KJ865409, KJ865410, and MN196478), C. pubescens OP957066 exhibits 4 unique PCGs (atp4, atp8, mttB, and rps1), while 2 PCGs (rpl10 and rps3) are absent. It's worth mentioning that each of the three pepper mitogenomes (KJ865409, KJ865410, and MN196478) experienced the loss of 4 PCGs (atp4, atp8, mttB, and rps1). To further explore the evolutionary relationships, we reconstructed a phylogenetic tree using the mitogenomes of C. pubescens and fourteen other species. The structural comparison and synteny analysis of the above four pepper mitogenomes showed that C. pubescens has a higher sequence similarity with KJ865409, and C. pubescens experienced rearrangements with the other three pepper mitogenomes. Interestingly, we observed 72 homologous sequences between the mitochondrial and chloroplast genomes, which accounted for 12.60% of the mitogenome, with a total length of 57,207 bp. These sequences encompassed 12 tRNA genes and the rRNA gene (rrn18). Remarkably, selective pressure analysis suggests that the nad5 gene underwent obvious positive selection. Furthermore, the single base mutation in three genes (nad1, nad2, and nad4) resulted in amino acid change. This study has provided a high-quality mitogenome of pepper, offering valuable molecular data for future investigations into the genetic information exchange between organelle genomes in pepper.