Dataset Information

Characteristics and Comparative Analysis of the Special-Structure (Non-Single-Circle) Mitochondrial Genome of Capsicum pubescens Ruiz & Pav.

ABSTRACT: Chilean peppers, cultivated from Capsicum pubescens, are globally renowned as popular vegetable and spice crops. C. pubescens belongs to the Capsicum L. (pepper) family and is one of the five pepper cultivars grown in China. In this study, we assembled and annotated the complete mt genome of C. pubescens. We investigated several aspects of its genome, including characteristics, codon usage, RNA editing sites, repeat sequences, selective pressure, gene clusters, and phylogenetic relationships. Furthermore, we compared it with other plant mt genomes. The data we obtained will provide valuable information for studying evolutionary processes in the Capsicum genus and will assist in the functional analysis of Capsicum mitogenomes.

SUBMITTER: Wu D

PROVIDER: S-EPMC10888363 | biostudies-literature | 2024 Jan

REPOSITORIES: biostudies-literature

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Characteristics and Comparative Analysis of the Special-Structure (Non-Single-Circle) Mitochondrial Genome of Capsicum pubescens Ruiz & Pav.

Wu Di D Fu Wenting W Fan Gaoling G Huang Dongfu D Wu Kangyun K Zhan Yongfa Y Tu Xiangmin X He Jianwen J

Genes 20240124 2

Chilean peppers, cultivated from Capsicum pubescens, are globally renowned as popular vegetable and spice crops. C. pubescens belongs to the Capsicum L. (pepper) family and is one of the five pepper cultivars grown in China. In this study, we assembled and annotated the complete mt genome of C. pubescens. We investigated several aspects of its genome, including characteristics, codon usage, RNA editing sites, repeat sequences, selective pressure, gene clusters, and ph ...[more]

PMID: 38397142

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Project description:BackgroundPepper (Capsicum pubescens), one of five domesticated pepper species, has unique characteristics, such as numerous hairs on the epidermis of its leaves and stems, black seeds, and vibrant purple flowers. To date, 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.ResultsIn our study, we successfully assembled the first mitogenome of C. pubescens, which was 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 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 exhibited four unique PCGs (atp4, atp8, mttB, and rps1), while two PCGs (rpl10 and rps3) were absent. Notably, each of the three pepper mitogenomes from C. annuum (KJ865409, KJ865410, and MN196478) experienced the loss of four 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. Structural comparison and synteny analysis of the above four pepper mitogenomes revealed that C. pubescens shares high sequence similarity with KJ865409 and that C. pubescens has rearranged with the other three pepper mitogenomes. Interestingly, we observed 72 similar 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 suggested that the nad5 gene underwent obvious positive selection. Furthermore, a single-base mutation in three genes (nad1, nad2, and nad4) resulted in an amino acid change.ConclusionThis study provides a high-quality mitogenome of pepper, providing valuable molecular data for future investigations into the exchange of genetic information between pepper organelle genomes.

Dataset Information

Characteristics and Comparative Analysis of the Special-Structure (Non-Single-Circle) Mitochondrial Genome of Capsicum pubescens Ruiz & Pav.

Publications

Characteristics and Comparative Analysis of the Special-Structure (Non-Single-Circle) Mitochondrial Genome of <i>Capsicum pubescens</i> Ruiz & Pav.

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