Comprehensive analysis of the mitochondrial genome of Ziziphus mauritiana Lam.: Investigating sequence structure, repeat-mediated recombination, chloroplast-derived transfer, RNA editing, and evolution

•The complete mitochondrial genome of Ziziphus mauritiana Lam. has been successfully assembled for the first time.•Recombination conformations mediated by repeats occurred with varying probabilities in the Z. mauritiana genome.•RNA editing from C to U at the first and second positions of the codon leads to the creation of hydrophilic and hydrophobic amino acids, respectively.•Horizontal gene transfer from chloroplast to mitochondrial is frequent and hard to define the transfer time. Ziziphus mauritiana Lam. is a valuable semi-deciduous tropical fruit tree with economic, medicinal, nutritional, and environmental significance. While the chloroplast genome of Z. mauritiana has been studied, the decoding of its mitochondrial genome (mtGenome) is crucial for various research areas, including molecular phylogeny and functional genomics. In this study, we extracted high-quality genomic DNA from the green leaves of Z. mauritiana and assembled the mtGenome by integrating sequencing data from both long and short reads. The Z. mauritiana mtGenome spans 324,124 bp with a 45.43 % GC content and exhibits six distinct conformations alongside the main circular sequence due to three pairs of repetitive fragments that facilitate recombination. RNA editing events resulted in changes in the physicochemical properties of amino acids, with genes expressed at higher levels showing an increased frequency of editing sites. Chloroplast-to-mitochondria horizontal gene transfers occurred in Z. mauritiana; however, these transferred fragments had few mutations, posing a challenge in determining the exact timing of these transfers. Phylogenetic analysis highlights a slower evolution rate of mitochondrial genes compared to chloroplast genes. These insights greatly enhance our understanding of the dynamics of the Z. mauritiana mtGenome, including recombination, gene expression, evolutionary processes, and more. The data and results of this study will serve as valuable mtGenome data resources within the Rhamnaceae family, thereby facilitating further genomics-based studies on Z. mauritiana.