A barley pan-transcriptome reveals layers of genotype-dependent transcriptional complexity

A barley pan-transcriptome reveals layers of genotype-dependent transcriptional complexity | 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 barley pan-transcriptome reveals layers of genotype-dependent transcriptional complexity Robbie Waugh, Wenbin Guo, Miriam Schreiber, Vanda Marosi, Paolo Bagnaresi, and 43 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-3787876/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 03 Feb, 2025 Read the published version in Nature Genetics → Version 1 posted You are reading this latest preprint version Abstract A pan-transcriptome describes the transcriptional and post-transcriptional consequences of genome diversity from multiple individuals within a species, revealing an assortment of functions that drive biological outcomes. We developed a barley pan-transcriptome using twenty inbred genotypes representing domesticated* barley diversity by generating and analysing extensive short- and long-read RNA sequencing datasets from multiple tissues. To overcome single reference bias and facilitate downstream analyses we constructed genotype-specific reference transcript datasets (RTDs) and integrated these into a linear pan-genome framework to create a single pan-RTD. Categorising transcripts based upon presence or absence across genotypes defined them as core (expressed in all), shell (absent in one or more) or cloud (expressed in only one). Focusing on the core we observed significant transcript abundance variation among tissues and between genotypes. We show that drivers of transcript abundance variation in this category include RNA processing, gene copy number, large structural rearrangements and degree of conservation of promotor motifs. We reveal conserved patterns of co-expression module-tissue correlations encompassing distinct biological functions, as well as frequent functional diversification. We complement the pan-transcriptome by integrating extensive and diverse replicated public RNA-seq datasets from the reference cultivar (cv.) Morex into a comprehensive gene-expression atlas Biological sciences/Plant sciences/Natural variation in plants Biological sciences/Genetics/Gene expression Biological sciences/Molecular biology/Transcriptomics Full Text Additional Declarations Yes there is potential Competing Interest. five of the authors, Christoph Docktor, Qiongxian Lu, Morten Jorgensen, Pai Pedas and Birgitte Skadhauge are employees of the Carlsberg Research Laboratory. All other authors declare no competing interests. Supplementary Files Supplementarydata1.xlsx Basic statistics of the RTDs Supplementarydata2.xlsx Ordering of genotypes incorporated into the linear pan-genome Supplementarydata3.xlsx Gene categories of GsRTD Supplementarydata4.xlsx Alternative splicing events for highly expressed transcripts from core-single-copy genes Supplementarydata5.xlsx Gene copy number variation cluster significantly correlated with the gene expression Supplementarydata6.xlsx C-repeat/DRE-Binding Factor (CBF) genes identifier in GsRTD and their location in the genome Supplementarydata7.xlsx genotypes with the 141Mb 7H inversion and non-inversion Supplementarydata8.xlsx Differentially expressed genes in the 7H inversion Supplementarydata9.xlsx Detailed example of a split pattern in Golden Promise Supplementarydata10.xlsx Barley cv. Morex Expression Atlas Metadata BarleyPanTsAllExtendedData.pdf Extended data figures 1-9 SIGuideBarleyPanTs.docx Supplementary Information Guide Cite Share Download PDF Status: Published Journal Publication published 03 Feb, 2025 Read the published version in Nature Genetics → 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-3787876","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Biological Sciences - Article","associatedPublications":[],"authors":[{"id":265456430,"identity":"4170acb2-da47-49d5-a20a-9b1379f98ec3","order_by":0,"name":"Robbie 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All other authors declare no competing interests.","formattedTitle":"A barley pan-transcriptome reveals layers of genotype-dependent transcriptional complexity","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":true,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":true,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"nature-portfolio","isNatureJournal":true,"hasQc":false,"allowDirectSubmit":false,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"","title":"Nature Portfolio","twitterHandle":"","acdcEnabled":false,"dfaEnabled":false,"editorialSystem":"ejp","reportingPortfolio":"","inReviewEnabled":true,"inReviewRevisionsEnabled":false},"keywords":"","lastPublishedDoi":"10.21203/rs.3.rs-3787876/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-3787876/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"A pan-transcriptome describes the transcriptional and post-transcriptional consequences of genome diversity from multiple individuals within a species, revealing an assortment of functions that drive biological outcomes. 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