T2T Assembly of Oryza australiensis Reveals Centromere Repositioning Mechanisms and Identifies the EE Genome as Direct Donor of the Extinct DD Lineage

T2T Assembly of Oryza australiensis Reveals Centromere Repositioning Mechanisms and Identifies the EE Genome as Direct Donor of the Extinct DD Lineage | 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 Biological Sciences - Article T2T Assembly of Oryza australiensis Reveals Centromere Repositioning Mechanisms and Identifies the EE Genome as Direct Donor of the Extinct DD Lineage Tao Zhang, Yu Bao, Hanli You, Shuo Liu, Guanqing Liu, Yuechao Wu, and 6 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7517070/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted You are reading this latest preprint version Abstract Oryza australiensis (EE genome), as the sole representative of the EE genome in the genus Oryza, holds significant research value due to its extreme environmental adaptability, unique grain pigmentation and starch properties, and making it a critical resource for deciphering polyploid evolution and mining stress-resistance genes for crop breeding. Here, a telomere-to-telomere (T2T) assembly of O. australiensis has been generated, yielding a 901 Mb chromosome-scale genome with 12 complete chromosomes (BUSCO:99.2%; LAI:22.67). This enabled comprehensive annotation of centromeres, telomeres, and 36,753 genes, revealing non-canonical telomeric repeats and three distinct centromere repositioning mechanisms in Oryza: inversion-driven shifts, segmental duplication-mediated neocentromeres, and transposon burst-induced neocentromere formation to the EE genome. Crucially, transposon dynamics revealed synchronized amplification of Angela LTR retrotransposons in EE genome and the DD subgenome of allotetraploid O. alta (CCDD) prior to 1.7 million years ago (Mya). Phylogenetic and synteny analyses of conserved Angela LTR integrase domains, alongside a unique 275-bp repeat marker exclusive to EE and DD, demonstrate that the pre-1.7 Mya EE lineage served as the direct donor of the extinct DD genome. This resolves a major controversy in Oryza evolution and establishes transposon-centric approaches for reconstructing paleogenomic histories. Biological sciences/Genetics/Genomics/Genome evolution Biological sciences/Evolution/Evolutionary genetics Genome assembly O. australiensis Centromere Transposon Evolutionary Full Text Additional Declarations There is NO Competing Interest. Supplementary Files SupplementaryInformation.docx Supplementary Figs and Supplementary Tables Cite Share Download PDF Status: Under Review Version 1 posted 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. We do this by developing innovative software and high quality services for the global research community. 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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-7517070","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Biological Sciences - Article","associatedPublications":[],"authors":[{"id":511806327,"identity":"42d2c103-3f1f-455e-b786-a8276a69d95e","order_by":0,"name":"Tao 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