Mitogenome architecture and evolutionary insights in Origanum vulgare: comparative analysis of structural diversity and repeat-mediated recombination

Origanum vulgare is a perennial herb known for its antimicrobial, antioxidant, and anti-inflammatory properties, valued in both traditional medicine and modern phytopharmacology. Despite substantial research on its chemical and pharmacological properties, genomic studies have been limited. In this study, we present the first comprehensive assembly and annotation of the mitochondrial genome (mitogenome) of O. vulgare using HiFi long-read sequencing technology. The assembled mitogenome spans 497,243 bp and contains 57 annotated genes, including 39 PCGs, 14 tRNA genes, and four rRNA genes. Additionally, we identified 9 simple sequence repeats, 26 tandem repeats, and 607 dispersed repeats, alongside 395 candidate RNA editing sites, predominantly located at the first and second codon positions. Phylogenetic analysis of mitochondrial PCGs from 25 representative species confirmed O. vulgare ‘s close evolutionary relationship with other species within the Lamiales order, highlighting significant genomic rearrangements and adaptive evolution. We also completed the assembly, annotation, and comprehensive analysis of the chloroplast genome of O. vulgare , providing further insights into its organellar genomes. Our findings further indicate that the mitogenome exhibits high levels of structural variability. The computational prediction of candidate RNA-editing sites provides a basis for future transcriptome-based validation of mitochondrial post-transcriptional modification in O. vulgare . This research establishes a genomic foundation for O. vulgare , advancing our understanding of its mitogenome structure, molecular evolution, and adaptive mechanisms, with important implications for phytopharmacological research and biotechnological applications in plant breeding.