Genome-wide analysis of the NLR gene family in strawberry reveals a novel immune receptor architecture in Rosaceae

Genome-wide analysis of the NLR gene family in strawberry reveals a novel immune receptor architecture in Rosaceae | 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 Research Article Genome-wide analysis of the NLR gene family in strawberry reveals a novel immune receptor architecture in Rosaceae Alicia Sillers, Mishi V. Vachev, Marta Bjornson, Patrick P. Edger, and 3 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-8177042/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted 10 You are reading this latest preprint version Abstract Background: Nucleotide-binding leucine-rich-repeat receptors (NLRs) are key components of plant innate immunity. These intracellular proteins specifically recognize pathogen effectors and subsequently activate a defense response. The genes encoding these proteins comprise one of the largest and most diverse gene families in plants. Understanding the various forms and functions of these proteins is imperative to the goal of generating disease resistant crops. This is particularly important for cultivated strawberry, which is heavily impacted by disease. Results: Using conserved motifs and functional domains, we identified 823 NLR-encoding genes (NLRs) in the ( Fragaria \((\times)\) ananassa ) `FaRR1' genome and categorized them according to their association with the anciently diverged RNL, CNL, and TNL classes. Among these, 45 were newly annotated and 149 were predicted to be full-length. 94 genes exhibited a previously unreported architecture, containing both CNL-specific and TNL-specific sequences. This architecture was supported by full-length transcript data and was found to be present in additional Rosaceous species but not in any non-Rosaceous species examined. Expression analyses revealed that 583 NLRs, including nearly all those with the novel mixed architecture, were differentially expressed following inoculation with at least one of five pathogens. Conclusions: Our genome-wide analysis expands the catalog of NLR genes in cultivated strawberry and uncovers a previously undescribed form of domain organization that appears to be unique to the Rosaceae family. The results suggest that recombination or domain swapping among N-terminal regions has contributed to NLR diversification in this lineage, providing insight into the evolutionary and functional basis of pathogen recognition in strawberry. NLR Nucleotide-binding Leucine-rich-repeat Strawberry Rosaceae Resistance genes Effector-triggered immunity Full Text Additional Declarations No competing interests reported. Supplementary Files SupplementalFiles.zip Cite Share Download PDF Status: Under Review Version 1 posted Editorial decision: Revision requested 06 Jan, 2026 Reviews received at journal 22 Dec, 2025 Reviews received at journal 01 Dec, 2025 Reviewers agreed at journal 26 Nov, 2025 Reviewers agreed at journal 26 Nov, 2025 Reviewers invited by journal 26 Nov, 2025 Editor invited by journal 26 Nov, 2025 Editor assigned by journal 24 Nov, 2025 Submission checks completed at journal 24 Nov, 2025 First submitted to journal 21 Nov, 2025 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-8177042","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":565418604,"identity":"e6b07915-8778-4710-9413-623ac40c7d4f","order_by":0,"name":"Alicia Sillers","email":"","orcid":"","institution":"University of California, Davis","correspondingAuthor":false,"prefix":"","firstName":"Alicia","middleName":"","lastName":"Sillers","suffix":""},{"id":565418606,"identity":"b4d23a30-0fdd-48e7-8554-9e73effa9e53","order_by":1,"name":"Mishi V. Vachev","email":"","orcid":"","institution":"University of California, Davis","correspondingAuthor":false,"prefix":"","firstName":"Mishi","middleName":"V.","lastName":"Vachev","suffix":""},{"id":565418608,"identity":"1ee52ece-6e1a-4627-9c5f-12add981065d","order_by":2,"name":"Marta Bjornson","email":"","orcid":"","institution":"University of California, Davis","correspondingAuthor":false,"prefix":"","firstName":"Marta","middleName":"","lastName":"Bjornson","suffix":""},{"id":565418610,"identity":"2598aa02-51e6-4f09-b580-8737e8ebc3c0","order_by":3,"name":"Patrick P. Edger","email":"","orcid":"","institution":"Michigan State University","correspondingAuthor":false,"prefix":"","firstName":"Patrick","middleName":"P.","lastName":"Edger","suffix":""},{"id":565418614,"identity":"776dadd0-03c5-4aa1-bcca-ec393d99f278","order_by":4,"name":"Burkhard Steuernagel","email":"","orcid":"","institution":"John Innes Centre","correspondingAuthor":false,"prefix":"","firstName":"Burkhard","middleName":"","lastName":"Steuernagel","suffix":""},{"id":565418621,"identity":"be92c382-8240-4bf8-837e-4084c48209a7","order_by":5,"name":"Steven J. Knapp","email":"","orcid":"","institution":"University of California, Davis","correspondingAuthor":false,"prefix":"","firstName":"Steven","middleName":"J.","lastName":"Knapp","suffix":""},{"id":565418622,"identity":"de9b324b-9834-4427-b413-b6cfcbdb651d","order_by":6,"name":"Mitchell J. Feldmann","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA+klEQVRIiWNgGAWjYFCCgw8YHrCBGMwHGBjYwIiBgQevlsMGDAlgZWwJxGphhmnhMYCqJ6BFt/Ew44OEsm3y5tI93yR+lNkl9vEfYHzwtg23FrMDh5kNEs7dNtw55+w2yZ5zyYltEgnMhnPxajl/TCKx7Tbjhhu526QZ25iN2SQY2KR58dvC/gOoxX7DjZxnQC31xmz8B9h/E9DCxgDUkgjUwgbUcliODRgazAS0MEsA/ZK84UaasWXPueNybBKJzZJzzuHRcuMw44cPZbdtN9xIfnjjR1k1j3z/4YMf3pTh1sIgcQBDiLEBj3og4CcgPwpGwSgYBaOAAQAy/VZi6BLQiwAAAABJRU5ErkJggg==","orcid":"","institution":"University of California, Davis","correspondingAuthor":true,"prefix":"","firstName":"Mitchell","middleName":"J.","lastName":"Feldmann","suffix":""}],"badges":[],"createdAt":"2025-11-22 00:38:10","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-8177042/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-8177042/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":99578754,"identity":"9b5f47fa-e3f1-4c4c-b7ca-8e7830b8bb35","added_by":"auto","created_at":"2026-01-06 05:26:51","extension":"json","order_by":0,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":9915,"visible":true,"origin":"","legend":"","description":"","filename":"b1cd8684eda5447aa9403807184bdb76.json","url":"https://assets-eu.researchsquare.com/files/rs-8177042/v1/347dc0ca9b1819cd44898ffc.json"},{"id":99792493,"identity":"0dee5bcc-f0bd-437a-8905-2a3f07948409","added_by":"auto","created_at":"2026-01-08 13:21:05","extension":"xml","order_by":1,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":116171,"visible":true,"origin":"","legend":"","description":"","filename":"b1cd8684eda5447aa9403807184bdb761enriched.xml","url":"https://assets-eu.researchsquare.com/files/rs-8177042/v1/a37ea3bf50801380d736977c.xml"},{"id":99578761,"identity":"6b472f87-b29d-4257-af90-f30544b4a6f7","added_by":"auto","created_at":"2026-01-06 05:26:51","extension":"png","order_by":4,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":222235,"visible":true,"origin":"","legend":"","description":"","filename":"Fig6dNdSofNLRsubgroupscomparedtoothergenefamiliesinstrawberry.png","url":"https://assets-eu.researchsquare.com/files/rs-8177042/v1/4f6f05625904b21a34b3ed26.png"},{"id":99792287,"identity":"dfe097b3-2fbf-42a3-811a-7c536e5ad934","added_by":"auto","created_at":"2026-01-08 13:17:24","extension":"pdf","order_by":7,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":1871603,"visible":true,"origin":"","legend":"","description":"","filename":"NLRManuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-8177042/v1/121af1fd4fb12953fac06f5b.pdf"},{"id":99793481,"identity":"ddb7d2d3-1f78-4ed1-935e-c076b8f001d8","added_by":"auto","created_at":"2026-01-08 13:31:40","extension":"pdf","order_by":8,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":117850,"visible":true,"origin":"","legend":"","description":"","filename":"SillersNLRStrawberryCoverLetter.pdf","url":"https://assets-eu.researchsquare.com/files/rs-8177042/v1/a26c52bfc0a67a4ef92a5b2b.pdf"},{"id":99578762,"identity":"22a43115-3fe5-4f4e-aef5-46caa5c36107","added_by":"auto","created_at":"2026-01-06 05:26:51","extension":"pdf","order_by":9,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":1874935,"visible":true,"origin":"","legend":"","description":"","filename":"SillersNLRStrawberry20251124.pdf","url":"https://assets-eu.researchsquare.com/files/rs-8177042/v1/192f0ed76d2b7325266cfee2.pdf"},{"id":99578767,"identity":"0623fd85-df1a-47ac-88da-08e263119fa4","added_by":"auto","created_at":"2026-01-06 05:26:51","extension":"zip","order_by":10,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":2493234,"visible":true,"origin":"","legend":"","description":"","filename":"SupplementalFiles.zip","url":"https://assets-eu.researchsquare.com/files/rs-8177042/v1/346061369335db48e1a31646.zip"},{"id":99578757,"identity":"8ca57340-b636-466d-827a-6ecb96a9b2fb","added_by":"auto","created_at":"2026-01-06 05:26:51","extension":"eps","order_by":11,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":2890,"visible":true,"origin":"","legend":"","description":"","filename":"empty.eps","url":"https://assets-eu.researchsquare.com/files/rs-8177042/v1/f5a588af5040c786fbe51dc2.eps"},{"id":99792808,"identity":"3ee5fed4-9f66-48a7-9790-0aaae6b685ec","added_by":"auto","created_at":"2026-01-08 13:26:43","extension":"eps","order_by":12,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":91593,"visible":true,"origin":"","legend":"","description":"","filename":"fig.eps","url":"https://assets-eu.researchsquare.com/files/rs-8177042/v1/8b2a4cacd4585b896f1fb97a.eps"},{"id":99578763,"identity":"35eb14f6-fd10-4f3e-8eb3-62b55d3574cd","added_by":"auto","created_at":"2026-01-06 05:26:51","extension":"bbl","order_by":15,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":44289,"visible":true,"origin":"","legend":"","description":"","filename":"snarticle.bbl","url":"https://assets-eu.researchsquare.com/files/rs-8177042/v1/884dd7175b3ebd072ac9cec4.bbl"},{"id":99578764,"identity":"b000b356-12db-4cda-a814-c9fbebd38688","added_by":"auto","created_at":"2026-01-06 05:26:51","extension":"bst","order_by":16,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":35733,"visible":true,"origin":"","legend":"","description":"","filename":"snbasic.bst","url":"https://assets-eu.researchsquare.com/files/rs-8177042/v1/947b85e6f3530be3cd8af2ea.bst"},{"id":99578768,"identity":"a3550b4e-5d98-4331-a78b-d706cfb224c7","added_by":"auto","created_at":"2026-01-06 05:26:51","extension":"cls","order_by":17,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":55331,"visible":true,"origin":"","legend":"","description":"","filename":"snjnl.cls","url":"https://assets-eu.researchsquare.com/files/rs-8177042/v1/efe2bc8b5648daca94615ab6.cls"},{"id":99578769,"identity":"82016ab2-57f1-41dc-a8a2-8155a9fc7332","added_by":"auto","created_at":"2026-01-06 05:26:51","extension":"bst","order_by":18,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":64141,"visible":true,"origin":"","legend":"","description":"","filename":"snmathphysnum.bst","url":"https://assets-eu.researchsquare.com/files/rs-8177042/v1/22d302eda3633f11e3c63d2d.bst"},{"id":99578760,"identity":"1eac89dd-42c9-4a39-ae6f-a00334e91282","added_by":"auto","created_at":"2026-01-06 05:26:51","extension":"bst","order_by":19,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":38349,"visible":true,"origin":"","legend":"","description":"","filename":"snnature.bst","url":"https://assets-eu.researchsquare.com/files/rs-8177042/v1/cfc3b53e89592a1981a9aa4d.bst"},{"id":99578770,"identity":"43143300-e186-48a4-82b2-19b1dfdcac2e","added_by":"auto","created_at":"2026-01-06 05:26:51","extension":"xml","order_by":21,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":123013,"visible":true,"origin":"","legend":"","description":"","filename":"b1cd8684eda5447aa9403807184bdb761structuring.xml","url":"https://assets-eu.researchsquare.com/files/rs-8177042/v1/da3ebec3dff75a300614eea9.xml"},{"id":99578766,"identity":"c665b16c-212f-4625-a9b6-a80d0a4dd6bd","added_by":"auto","created_at":"2026-01-06 05:26:51","extension":"html","order_by":22,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":135785,"visible":true,"origin":"","legend":"","description":"","filename":"earlyproof.html","url":"https://assets-eu.researchsquare.com/files/rs-8177042/v1/46d9c53cbd7a989f49f22b5e.html"},{"id":99804196,"identity":"68af6215-4594-4011-8a55-4bac0ca6b97c","added_by":"auto","created_at":"2026-01-08 14:12:20","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":2379828,"visible":true,"origin":"","legend":"","description":"","filename":"SillersNLRStrawberry20251124.pdf","url":"https://assets-eu.researchsquare.com/files/rs-8177042/v1_covered_f901f61f-3b7b-4c3c-882a-ae90e78d6c98.pdf"},{"id":99578756,"identity":"51ed6543-79ce-4abd-892c-7aeba9169c8a","added_by":"auto","created_at":"2026-01-06 05:26:51","extension":"zip","order_by":0,"title":"","display":"","copyAsset":false,"role":"supplement","size":2493234,"visible":true,"origin":"","legend":"","description":"","filename":"SupplementalFiles.zip","url":"https://assets-eu.researchsquare.com/files/rs-8177042/v1/d9cf2365a799824b05cc6910.zip"}],"financialInterests":"No competing interests reported.","formattedTitle":"Genome-wide analysis of the NLR gene family in strawberry reveals a novel immune receptor architecture in Rosaceae","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":true,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"bmc-genomics","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"gics","sideBox":"Learn more about [BMC Genomics](http://bmcgenomics.biomedcentral.com/)","snPcode":"","submissionUrl":"https://www.editorialmanager.com/gics","title":"BMC Genomics","twitterHandle":"#BMCGenomics","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"em","reportingPortfolio":"BMC Series","inReviewEnabled":true,"inReviewRevisionsEnabled":true},"keywords":"NLR, Nucleotide-binding Leucine-rich-repeat, Strawberry, Rosaceae, Resistance genes, Effector-triggered immunity","lastPublishedDoi":"10.21203/rs.3.rs-8177042/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-8177042/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003ch2\u003eBackground:\u003c/h2\u003e\u003cp\u003eNucleotide-binding leucine-rich-repeat receptors (NLRs) are key components of plant innate immunity. These intracellular proteins specifically recognize pathogen effectors and subsequently activate a defense response. The genes encoding these proteins comprise one of the largest and most diverse gene families in plants. Understanding the various forms and functions of these proteins is imperative to the goal of generating disease resistant crops. This is particularly important for cultivated strawberry, which is heavily impacted by disease.\u003c/p\u003e\u003ch2\u003eResults:\u003c/h2\u003e\u003cp\u003eUsing conserved motifs and functional domains, we identified 823 NLR-encoding genes (NLRs) in the (\u003c/p\u003e\u003ch2\u003eFragaria\u003c/h2\u003e\u003cp\u003e\u003cspan class=\"InlineEquation\"\u003e\u003cspan class=\"mathinline\"\u003e\\((\\times)\\)\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\u003ch2\u003eananassa\u003c/h2\u003e\u003cp\u003e) `FaRR1' genome and categorized them according to their association with the anciently diverged RNL, CNL, and TNL classes. Among these, 45 were newly annotated and 149 were predicted to be full-length. 94 genes exhibited a previously unreported architecture, containing both CNL-specific and TNL-specific sequences. This architecture was supported by full-length transcript data and was found to be present in additional Rosaceous species but not in any non-Rosaceous species examined. Expression analyses revealed that 583 NLRs, including nearly all those with the novel mixed architecture, were differentially expressed following inoculation with at least one of five pathogens.\u003c/p\u003e\u003ch2\u003eConclusions:\u003c/h2\u003e\u003cp\u003eOur genome-wide analysis expands the catalog of NLR genes in cultivated strawberry and uncovers a previously undescribed form of domain organization that appears to be unique to the Rosaceae family. The results suggest that recombination or domain swapping among N-terminal regions has contributed to NLR diversification in this lineage, providing insight into the evolutionary and functional basis of pathogen recognition in strawberry.\u003c/p\u003e","manuscriptTitle":"Genome-wide analysis of the NLR gene family in strawberry reveals a novel immune receptor architecture in Rosaceae","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2026-01-06 05:26:46","doi":"10.21203/rs.3.rs-8177042/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Revision requested","date":"2026-01-06T14:47:51+00:00","index":"","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-12-22T11:15:34+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-12-01T07:05:34+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"12706561279936032249234553569575432085","date":"2025-11-27T01:41:19+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"208958566475364226308865221108833883776","date":"2025-11-26T23:50:49+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2025-11-26T21:02:10+00:00","index":"","fulltext":""},{"type":"editorInvited","content":"","date":"2025-11-26T17:24:39+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2025-11-25T00:36:46+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2025-11-25T00:36:04+00:00","index":"","fulltext":""},{"type":"submitted","content":"BMC Genomics","date":"2025-11-22T00:29:30+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"bmc-genomics","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"gics","sideBox":"Learn more about [BMC Genomics](http://bmcgenomics.biomedcentral.com/)","snPcode":"","submissionUrl":"https://www.editorialmanager.com/gics","title":"BMC Genomics","twitterHandle":"#BMCGenomics","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"em","reportingPortfolio":"BMC Series","inReviewEnabled":true,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"4dded516-61cc-4f29-a6ba-26ede9a3bed8","owner":[],"postedDate":"January 6th, 2026","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"under-review","subjectAreas":[],"tags":[],"updatedAt":"2026-03-30T17:09:35+00:00","versionOfRecord":[],"versionCreatedAt":"2026-01-06 05:26:46","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-8177042","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-8177042","identity":"rs-8177042","version":["v1"]},"buildId":"XKTyCvWXoU3ODBz1xrDgd","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}