The chromosome-scale genome assembly of the reef-building coral Platygyra daedalea

The chromosome-scale genome assembly of the reef-building coral Platygyra daedalea | 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 Data Note The chromosome-scale genome assembly of the reef-building coral Platygyra daedalea Craig Michell, Patrick Micke, Shoug Alguthmi, Chloe-Marie Hawley, and 4 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-8967172/v2 This work is licensed under a CC BY 4.0 License Status: Posted Version 2 posted You are reading this latest preprint version Show more versions Abstract The genus Platygyra represents an essential group of reef-building corals in marine ecosystems. Here, we present the first high-quality genome assembly of the brain coral Platygyra daedalea , a widespread species known for its ecological resilience across diverse marine environments. Using long-read sequencing combined with chromosomal-level scaffolding based on a genetic linkage map, we assembled an 878.6 Mb genome with a contig N50 of 34.8 Mb. A total of 99.78% of the assembly was anchored into 16 linkage groups, with only eight contigs remaining unplaced. Annotation identified 27,516 protein-coding genes. This reference genome provides a critical resource for understanding coral biology, aiding conservation efforts, and exploring adaptive potential under climate change. Population Genetics Epigenetics & Genomics Platygyra Chromosome Genome Coral Telomere-2-telomere Full Text Additional Declarations The authors declare no competing interests. Cite Share Download PDF Status: Posted Version 2 posted You are reading this latest preprint version Show more versions 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-8967172","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Data Note","associatedPublications":[],"authors":[{"id":597462458,"identity":"71c57c5a-3e44-4352-abbe-4405e031fd1b","order_by":0,"name":"Craig Michell","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAABEklEQVRIie3RMUvDQBTA8Xcc2OUk6w3FfIXnLNKvknAQl4BOJYODINSl2LVS8TMEhM4vHHQKyXpQh+QbRHDIInihneRaOzrcH7Lc8cu74wB8vn8a2U+ABEZNFu3Xzk4jQFE5EP432TWQeHYCCVa6Lb5gPQ5Wj0TxWxJiXRN0Uw3hE7n/XSWox7AV8mMTUbxOL3OjgC0rDVhGToICUEtLUKZoScZyw4GfzyyBQ2TU7cltR/FrNslrDfzbknDRHCACi243xV7/IY1zUsCZJWDcU2Qp7uwZ7F1MghRtEvViFBbz6kagcU8J5qP3zz7bToKlapvuXl0/10Xb9NOri3DhnjLEBf5aIRge90isP7br8/l8vh8kIGX6UgQjGQAAAABJRU5ErkJggg==","orcid":"https://orcid.org/0000-0003-4706-7256","institution":"Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia","correspondingAuthor":true,"prefix":"","firstName":"Craig","middleName":"","lastName":"Michell","suffix":""},{"id":597462460,"identity":"cb13ae64-d466-413a-ab4b-6186e9a0b1b2","order_by":1,"name":"Patrick Micke","email":"","orcid":"https://orcid.org/0009-0001-8160-2147","institution":"National Marine Science Centre, Faculty of Science and Engineering, Southern Cross University, Coffs Harbour, Australia 2450","correspondingAuthor":false,"prefix":"","firstName":"Patrick","middleName":"","lastName":"Micke","suffix":""},{"id":597462462,"identity":"500c0feb-4d07-4f9b-80b1-74ddfd0e07d2","order_by":2,"name":"Shoug Alguthmi","email":"","orcid":"https://orcid.org/0009-0006-7219-1995","institution":"Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia","correspondingAuthor":false,"prefix":"","firstName":"Shoug","middleName":"","lastName":"Alguthmi","suffix":""},{"id":597462464,"identity":"9c9a9575-173a-4b37-8796-b24e9a9d6fc1","order_by":3,"name":"Chloe-Marie Hawley","email":"","orcid":"","institution":"Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia","correspondingAuthor":false,"prefix":"","firstName":"Chloe-Marie","middleName":"","lastName":"Hawley","suffix":""},{"id":597462466,"identity":"47f370f7-814b-407d-83ae-1df7fbb00b68","order_by":4,"name":"Eli Meyer","email":"","orcid":"","institution":"","correspondingAuthor":false,"prefix":"","firstName":"Eli","middleName":"","lastName":"Meyer","suffix":""},{"id":597462469,"identity":"a602069d-64f8-4027-bf60-1665532125fa","order_by":5,"name":"Holland Elder","email":"","orcid":"https://orcid.org/0000-0001-8432-4632","institution":"James Cook University, Australian Institute of Marine Science, Townsville, Australia 4811.","correspondingAuthor":false,"prefix":"","firstName":"Holland","middleName":"","lastName":"Elder","suffix":""},{"id":597462473,"identity":"30c8bee4-dda2-4325-a157-437a08216e4a","order_by":6,"name":"Emily J. Howells","email":"","orcid":"https://orcid.org/0000-0001-7732-2372","institution":"National Marine Science Centre, Faculty of Science and Engineering, Southern Cross University, Coffs Harbour, Australia 2450. Lizard Island Research Station, Australian Museum, Sydney, New South Wales, Australia","correspondingAuthor":false,"prefix":"","firstName":"Emily","middleName":"J.","lastName":"Howells","suffix":""},{"id":597462478,"identity":"575add3a-9842-40dd-a620-0a72f53cd0e9","order_by":7,"name":"Manuel Aranda","email":"","orcid":"https://orcid.org/0000-0001-6673-016X","institution":"Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia","correspondingAuthor":false,"prefix":"","firstName":"Manuel","middleName":"","lastName":"Aranda","suffix":""}],"badges":[],"createdAt":"2026-02-25 11:27:31","currentVersionCode":2,"declarations":{"humanSubjects":false,"vertebrateSubjects":false,"conflictsOfInterestStatement":false,"humanSubjectEthicalGuidelines":false,"humanSubjectConsent":false,"humanSubjectClinicalTrial":false,"humanSubjectCaseReport":false,"vertebrateSubjectEthicalGuidelines":false},"doi":"10.21203/rs.3.rs-8967172/v2","doiUrl":"https://doi.org/10.21203/rs.3.rs-8967172/v2","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":106404772,"identity":"55a4489a-cd79-406a-94a9-a14bc57f68f9","added_by":"auto","created_at":"2026-04-08 09:17:00","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":1456423,"visible":true,"origin":"","legend":"","description":"","filename":"PlatygyraGenomev4.pdf","url":"https://assets-eu.researchsquare.com/files/rs-8967172/v2_covered_4fc3012f-25d6-49cf-9c68-dd702ee91bfc.pdf"}],"financialInterests":"The authors declare no competing interests.","formattedTitle":"\u003cp\u003eThe chromosome-scale genome assembly of the reef-building coral \u003cem\u003ePlatygyra daedalea\u003c/em\u003e\u003c/p\u003e","fulltext":[],"fulltextSource":"","fullText":"","funders":[{"identity":"4a492772-2c39-44c1-8422-dd783d75f4b3","identifier":"10.13039/501100004052","name":"King Abdullah University of Science and Technology","awardNumber":"URF/1/4697-01-01","order_by":0}],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":true,"hideJournal":true,"highlight":"","institution":"King Abdullah University of Science and Technology","isAcceptedByJournal":false,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true},"keywords":"Platygyra, Chromosome, Genome, Coral, Telomere-2-telomere","lastPublishedDoi":"10.21203/rs.3.rs-8967172/v2","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-8967172/v2","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eThe genus \u003cem\u003ePlatygyra\u003c/em\u003e represents an essential group of reef-building corals in marine ecosystems. Here, we present the first high-quality genome assembly of the brain coral \u003cem\u003ePlatygyra daedalea\u003c/em\u003e, a widespread species known for its ecological resilience across diverse marine environments. Using long-read sequencing combined with chromosomal-level scaffolding based on a genetic linkage map, we assembled an 878.6 Mb genome with a contig N50 of 34.8 Mb. A total of 99.78% of the assembly was anchored into 16 linkage groups, with only eight contigs remaining unplaced. Annotation identified 27,516 protein-coding genes. This reference genome provides a critical resource for understanding coral biology, aiding conservation efforts, and exploring adaptive potential under climate change.\u003c/p\u003e","manuscriptTitle":"The chromosome-scale genome assembly of the reef-building coral Platygyra daedalea","msid":"","msnumber":"","nonDraftVersions":[{"code":2,"date":"2026-04-07 19:57:24","doi":"10.21203/rs.3.rs-8967172/v2","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true}},{"code":1,"date":"2026-02-26 10:09:07","doi":"10.21203/rs.3.rs-8967172/v1","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"4d9566e3-7322-4b98-9c86-68bf23bef060","owner":[],"postedDate":"April 7th, 2026","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[{"id":65888772,"name":"Population Genetics"},{"id":65888773,"name":"Epigenetics \u0026 Genomics"}],"tags":[],"updatedAt":"2026-02-26T10:09:07+00:00","versionOfRecord":[],"versionCreatedAt":"2026-04-07 19:57:24","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v2","identity":"rs-8967172","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-8967172","identity":"rs-8967172","version":["v2"]},"buildId":"XKTyCvWXoU3ODBz1xrDgd","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}