Comparative analysis of complete mitogenomes of two ornamental plants Chimonanthus salicifolius and Chimonanthus praecox in the family Calycanthaceae

Chimonanthus praecox (Wintersweet) and Chimonanthus salicifolius (Willow-leaf Wintersweet) are species of significant ornamental and medicinal value within the Calycanthaceae family. Although plant mitogenomes are powerful tools for resolving deep evolutionary relationships due to their alternative structures and conserved sequences, mitochondrial genomic studies within the family remain scarce. Here, we determined the mitogenomes of two Chimonanthus species. Both mitogenomes were found to be a combination of linear and circular, with sizes of 816,550 bp and 971,908 bp, respectively. Each mitogenome contains a total of 62 unique mitochondrial genes, including 40 protein-coding genes (PCGs), 19 tRNA genes, and three rRNA genes, exhibiting the gene content characteristic of seed plants. Rearrangement events among the PCGs of mitogenomes were identified, revealing the presence of seven conserved gene clusters in both Chimonanthus mitogenomes. In the comparative genomic analysis, 28 and 38 homologous DNA fragments were detected between the mitochondrial and plastid genomes, and 4,407 and 4,728 homologous DNA fragments were found between the mitogenome and nuclear genomes, in C. salicifolius and C. praecox, respectively, indicating possible gene transferring events in the history. To detect whether natural selection acted in the evolution of mitochondrial genes in Chimonanthus species, we calculated codon usage statistics and nonsynonymous-to-synonymous substitution ratios (Ka/Ks), finding significant differences in biased codon usage in the atp9 and rpl5 genes and positive selection operated in atp4 and rps4 genes. Phylogenetic analyses based on the mitogenome dataset, plastome dataset, and nrDNA dataset, confirm a monophyletic Calycanthaceae comprising nine individuals of Chimonanthus species and two individuals of Calycanthus species. . The study significantly advances our knowledge of Chimonanthus mitogenomes, furnishing high-quality data and novel insights into the evolutionary history and genetic architecture of Calycanthaceae.