A genus-wide pangenome of Hordeum

A genus-wide pangenome of Hordeum | 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 A genus-wide pangenome of Hordeum Martin Mascher, Jia-Wu Feng, Axel Himmelbach, Andreas Houben, and 37 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7766969/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 The genus Hordeum, which includes cultivated barley and its wild relatives, represents a diverse group of grasses with agricultural, ecological, and evolutionary importance. Here, we present a genus-wide pangenome based on 25 chromosome-scale genome sequences encompassing all known diploid Hordeum species and selected tetraploids. Comparative analysis reveals extensive structural variations, including large-scale inversions and chromosomal rearrangements, which disrupt proximal chromosomal collinearity and reflect lineage-specific genome remodeling. Using single-copy gene phylogenies, we identify multiple deep interspecific hybridization events, segmental exchanges, and introgressions, particularly in regions enriched for conserved inversions. We also uncover widespread horizontal gene transfer from Panicoideae grasses into Hordeum, with functional integration of transferred genes. Transposable element dynamics, especially retrotransposon proliferation, account for much of the observed genome size variation and offer insights into polyploid genome evolution. Whole-genome alignments reveal contrasting evolutionary patterns: while coding genes remain highly conserved, regulatory elements show rapid turnover, providing a substrate for phenotypic diversification. Case studies of vernalization and glume development demonstrate how natural variation in regulatory and coding sequences contributes to flowering time and floral morphology. This comprehensive pangenomic framework establishes Hordeum as a model for studying genome evolution, structural variation, and the genetic basis of adaptive traits, offering new avenues for barley improvement. Biological sciences/Genetics/Genomics/Genome evolution Biological sciences/Evolution/Evolutionary genetics Full Text Additional Declarations There is NO Competing Interest. Supplementary Files supplementarytables.xlsx Supplementary Tables 1-20 onlinemethods.pdf Article File extendeddatafigure.pdf Article File 251001Supplementaryfigurescompressed.pdf Article File 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. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. 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-7766969","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Biological Sciences - Article","associatedPublications":[],"authors":[{"id":534899639,"identity":"a71f9e7e-ee79-4dc5-871d-e536b4b04c7e","order_by":0,"name":"Martin 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Here, we present a genus-wide pangenome based on 25 chromosome-scale genome sequences encompassing all known diploid Hordeum species and selected tetraploids. Comparative analysis reveals extensive structural variations, including large-scale inversions and chromosomal rearrangements, which disrupt proximal chromosomal collinearity and reflect lineage-specific genome remodeling. Using single-copy gene phylogenies, we identify multiple deep interspecific hybridization events, segmental exchanges, and introgressions, particularly in regions enriched for conserved inversions. We also uncover widespread horizontal gene transfer from Panicoideae grasses into Hordeum, with functional integration of transferred genes. Transposable element dynamics, especially retrotransposon proliferation, account for much of the observed genome size variation and offer insights into polyploid genome evolution. 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