Mitochondrial genome assembly and analysis of Cercis chinensis: insights into an economically valuable ornamental species

Cercis chinensis is a leguminous species with notable ornamental value and considerable economic potential, and is primarily distributed in southern China. Among species in the genus Cercis, only the complete mitochondrial genome of Cercis canadensis has been publicly available. This lack of mitochondrial genomic data constrains our understanding of the evolutionary history, genetic diversity, and environmental adaptability of Cercis chinensis and its closely related species. In this study, we successfully completed the de novo assembly and annotation of Cercis chinensis mitochondrial genome. The mitochondrial genome of Cercis chinensis consists of two putative circular chromosomes, totaling 393,546 bp in length with a GC content of 45.29%. A total of 61 genes were annotated, including 39 protein-coding genes (PCGs), 20 transfer RNA (tRNA) genes, and 2 ribosomal RNA (rRNA) genes. Functional analysis predicted 546 C-to-U RNA editing sites, the majority of which result in nonsynonymous amino acid substitutions. A total of 155 repeat elements were identified, comprising simple sequence repeats (SSRs), tandem repeats, and dispersed repeats, highlighting the structural complexity of the mitochondrial genome. Furthermore, 18 mitochondrial plastid DNA transfer events (MTPTs) were detected, encompassing six complete genes, including 5 tRNA genes and 1 rRNA gene, originating from the chloroplast genome. The presence of intact tRNA and rRNA fragments among MTPTs suggests that such transfers may not only add to structural diversity but could also provide functional redundancy or influence RNA processing within the mitochondrial genome. Ka/Ks analysis indicated that most core PCGs are subject to purifying selection, reflecting high functional conservation across species. Notably, atp4 and nad4 exhibited signs of positive selection, suggesting their potential involvement in the adaptive evolution of Cercis chinensis. Phylogenetic analysis based on shared mitochondrial and chloroplast protein-coding genes placed Cercis chinensis in close relation to Bauhinia purpurea, thereby supporting its current taxonomic classification within the Fabaceae. This study provides the first characterization of the mitochondrial genome of Cercis chinensis, detailing its structural organization, functional elements, and evolutionary dynamics. The assembled genome and associated analyses provide valuable insights into the mitochondrial architecture of Cercis chinensis and enrich the genomic resources for the Fabaceae family, enhancing our understanding of mitochondrial genome evolution in legumes and serving as a foundational reference for future research in species identification, molecular breeding, and phylogenetic studies of C. chinensis and related taxa. • The complete mitochondrial genome of Cercis chinensis was de novo assembled using third-generation sequencing technology. • The genome of Cercis chinensis consists of two circular chromosomes, in contrast to the single-chromosome structure reported in Cercis canadensis, but two species exhibit slight differences in genome size and GC content. • Comparative analysis revealed that some genes (rpl2, rps19) are lost in both Cercis chinensis and Cercis canadensis, while the cox2 is retained in C. chinensis, suggesting a lineage-specific gene retention mechanism within the genus Cercis. • Phylogenetic trees constructed based on 22 mitochondrial protein-coding genes and 68 chloroplast protein-coding genes confirmed the monophyly of Fabaceae, with both trees exhibiting highly congruent topologies.