A transcriptional atlas of early Arabidopsis seed development suggests mechanisms for inter-tissue coordination

A transcriptional atlas of early Arabidopsis seed development suggests mechanisms for inter-tissue coordination | 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 Article A transcriptional atlas of early Arabidopsis seed development suggests mechanisms for inter-tissue coordination Mary Gehring, Caroline Martin, Kylee Cogdill, Alesandra Pusey This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-6560595/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 Successful seed development is essential for flowering plant reproduction and requires the coordination of three genetically distinct tissues: the embryo and endosperm, which are the products of fertilization, and the maternal seed coat. Our understanding of the transcriptional programs underlying tissue-specific functions and inter-tissue coordination in seeds remains incomplete. To address this, we performed single nucleus RNA-sequencing on Arabidopsis thaliana seeds at 3, 5, and 7 days after pollination. We characterize all major seed cell or nuclei types, further refine transcriptional states in the endosperm, and map signatures of selection on cell type-specific genes. Among other findings, our analyses reveal the compartmentalization of genes involved in brassinosteroid-responsive transcription factor activation, abundant endosperm expression of genes that encode short, secreted peptides (SSPs), and an enrichment of rapidly evolving genes in the chalazal endosperm, illuminating the cell type and species specificity of seed genes. Biological sciences/Plant sciences/Plant reproduction/Seed development Biological sciences/Plant sciences/Plant signalling Full Text Additional Declarations There is NO Competing Interest. Supplementary Files S1markercitations.xlsx Supplementary Table 1 S2HCRprobes.xlsx Supplementary Table 2 S3clustermetadata.xlsx Supplementary Table 3 S4allDE.xlsx Supplementary Table 4 S5pseudotimetxnfactors.xlsx Supplementary Table 5 S6figuresignificance.xlsx Supplementary Table 6 S7M2aM1aCZEanalysis.xlsx Supplementary Table 7 S8mergnerkey.xlsx Supplementary Table 8 S9peptideannotations.xlsx Supplementary Table 9 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. 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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-6560595","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":457073339,"identity":"9bf4dfed-60c4-45f5-a753-8bbb5f0b6c4f","order_by":0,"name":"Mary 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