Assembly and characterization of the first complete mitochondrial genome of Epimedium sagittatum (Sieb. et Zucc.) Maxim (Berberidaceae):an invaluable traditional Chinese medicine

BACKGROUND: Epimedium sagittatum (Sieb. et Zucc.) Maxim is an invaluable traditional Chinese medicine plant known for its properties of tonifying kidney yang, strengthening bones and muscles, and dispelling rheumatism. The chloroplast (cp) genome of E. sagittatum have been sequenced, offering critical insights for breeding and phylogenetic research. However, the mitochondrial (mt) genome of E. sagittatum remains uncharacterized, limiting comprehensive insights into its genomic evolution. RESULTS: In this study, we assembled the first complete mt genome of E. sagittatum employing Illumina and Nanopore sequencing technology and subsequently investigated comparative analysis with its closely related species. The mt genome of E. sagittatum was assembled as a multi-branched structure with a length of 339,191 bp, within a GC content of 46.91%. Our annotation results have shown 39 protein-coding genes (PCGs), 22 tRNA genes, three rRNA genes and four pseudogenes in the E. sagittatum mt genome. The analysis of sequence repeats has detected 79 simple sequence repeats (SSRs), 10 tandem repeats and 255 dispersed repeats in the E. sagittatum mt genome. A total of 720 C to U RNA editing sites of the 34 PCGs was predicted in E. sagittatum. The codons exhibited a strong preference for A or U bases in the E. sagittatum mt genome. The analysis of nucleotide diversity (Pi) highlighted differences in genetic variability across the tested genes, with atp9 gene exhibiting the highest genetic variation. Selection pressure analysis showed that most genes were affected by negative selection during evolution, whereas ccmB, rps10, and rps12 underwent positive selection in different plants. Additionally, a Bayesian phylogenetic tree showed that E. sagittatum was closely related to E. wushanense and E. pubescens. In total of 14 homologous fragments totaling 8,954 bp were identified between the cp and mt genomes of E. sagittatum. CONCLUSIONS: This study presents the first assembled and annotated mt genome of E. sagittatum, which provides a valuable genetic resource for the Epimedium genus and lays the foundation for investigating the phylogenetic relationship and genetic variation of this invaluable medicinal plant.