Organellar genome analysis of Stephania epigaea: a medicinal plant endemic to Southwest China

Mitochondria and chloroplast are central organelles in plant metabolism, playing crucial roles at various developmental stages. Stephania epigaea is a traditional medicinal plant utilized by minority ethnic groups, widely employed for treating malaria and stomach pain. Understanding the organelle genomes of S. epigaea —specifically its mitochondrial and chloroplast genomes—is essential for elucidating the molecular strategies underlying this species’ evolutionary adaptation. The complete mitochondrial genome of this species is 476,231 bp in length and comprises three discrete circular chromosomes together with one additional complex structure. In contrast, the chloroplast genome is 158,139 bp and exhibits the canonical circular quadripartite architecture. A homologous segment of 9,723 bp was found to be shared with the chloroplast, involving the transfer of 24 homologous sequences. Relative Synonymous Codon Usage (RSCU) analysis indicates that the codon preference in the chloroplast genome of S. epigaea is generally higher than that in the mitochondria. Phylogenetic analysis indicates that S. epigaea shares a close genetic relationship with the congeneric plant S. japonica , and a substantial number of homologous blocks have been identified in the synteny analysis. Selection pressure analysis shows that the most of protein-coding genes (PCGs) exhibit a Ka/Ks ratio of less than 1, suggesting that these genes tend to maintain their original functions and avoid deleterious mutations. This study has significant implications for understanding the evolutionary relationships within the genus Stephania , laying a foundation for genetic research on the traditional medicine S. epigaea .