Mitogenome Architecture and Evolutionary Insights in Origanum vulgare: Comparative Analysis of Structural Diversity and Repeat-Mediated Recombination

Mitogenome Architecture and Evolutionary Insights in Origanum vulgare: Comparative Analysis of Structural Diversity and Repeat-Mediated Recombination | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research Article Mitogenome Architecture and Evolutionary Insights in Origanum vulgare: Comparative Analysis of Structural Diversity and Repeat-Mediated Recombination Meiling Qin, Shaoshuai Yu, Ikram Outissint, Min Tang, Xun Gong This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7070486/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted 7 You are reading this latest preprint version Abstract 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 genome spans 497,243 base pairs and includes 57 protein-coding genes (PCGs), 14 transfer RNA genes, and 4 ribosomal RNA genes. Additionally, we identified 9 simple sequence repeats, 26 tandem repeats, and 607 dispersed repeats, alongside 395 RNA editing sites, predominantly located at the first and second codon positions, suggesting a significant role in gene expression regulation. 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, which may contribute to the plant’s ability to adapt to diverse environmental conditions. The identification of RNA editing events suggests a key role in post-transcriptional regulation, influencing protein diversity and potentially enhancing stress tolerance. 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. Origanum vulgare mitogenome repeat-mediated recombination RNA editing phylogeny Full Text Additional Declarations No competing interests reported. Supplementary Files FigureS1.pdf FigureS2.pdf FigureS3.pdf FigureS4.pdf FigureS5.pdf TableS1.docx TableS2.docx TableS3.docx TableS4.docx TableS5.docx TableS6.docx TableS7.docx TableS8.docx TableS9.docx TableS10.docx TableS11.docx Cite Share Download PDF Status: Under Review Version 1 posted Reviews received at journal 18 Nov, 2025 Reviewers agreed at journal 19 Sep, 2025 Reviewers invited by journal 21 Jul, 2025 Editor assigned by journal 14 Jul, 2025 Editor invited by journal 14 Jul, 2025 Submission checks completed at journal 11 Jul, 2025 First submitted to journal 11 Jul, 2025 You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. 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Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-7070486","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":489359944,"identity":"06c29509-4593-4199-b937-9fe972cb5b6f","order_by":0,"name":"Meiling Qin","email":"","orcid":"","institution":"Affiliated Hospital of Jiangsu University","correspondingAuthor":false,"prefix":"","firstName":"Meiling","middleName":"","lastName":"Qin","suffix":""},{"id":489359945,"identity":"49a6e15e-3f2a-4001-bee9-b0dc6ca5cafc","order_by":1,"name":"Shaoshuai Yu","email":"","orcid":"","institution":"Affiliated People’s Hospital of Jiangsu 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