Assembly and analysis of stephania japonica mitochondrial genome provides new insights into its identification and energy metabolism.

Stephania japonica, a popular indoor ornamental and medicinal plant widely found in southern China, contains many natural compounds with potential medicinal value. S. japonica is also favored by researchers for its ability to produce catharanthine. Energy metabolism functions in plant development, and the composition of mitochondrial genome is regarded as the foundation for understanding energy metabolism and getting insights into plant environmental adaptation. In present investigation, the whole mitochondrial genome of S. japonica was assembled from both second- and third-generation sequencing data. The mitochondrial genome size of S. japonica is 555,117 bp. It is depicted as a complex polycyclic structure. In addition, we conducted an in-depth study of the cytochrome c oxidase (cox) gene, of which expression levels in different tissues of S. japonica were measured by real-time quantification PCR. Two phylogenetic trees were established in the light of sequences concerning 19 conserved mitochondrial protein-coding genes and cox gene, respectively. Both phylogenetic trees show that S. japonica is more closely related to Aconitum kusnezoffii. The result showed that the cox genes were the most highly expressed in the roots. A high-quality mitochondrial genome exhibits potential application value for the progress of molecular markers, identification of species as super DNA barcoding, and resolve mitochondrial energy metabolism mechanisms in response to the environment using genomic information. With the recognition of the medicinal value of Stephania plants, the genomic information of S. japonica has been thoroughly studied and the comprehensive analysis of its mitochondrial genome in this investigation can offer valuable insights for the breeding of new plant varieties.