Pathogenesis-related proteins are evolutionarily conserved across diploid and octoploid Fragaria species

Pathogenesis-related proteins are evolutionarily conserved across diploid and octoploid Fragaria species | 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 Pathogenesis-related proteins are evolutionarily conserved across diploid and octoploid Fragaria species Mishi V. Vachev, Alicia Sillers, Marta Bjornson, Patrick P. Edger, and 1 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7264946/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted 7 You are reading this latest preprint version Abstract Background: Pathogenesis-related (PR) proteins are induced in response to infection and contribute to immunity through a variety of mechanisms. To date, 19 families of PR proteins with roles in resistance to bacteria, fungi, and insects have been identified across several model and agronomically important plant species. Countless diseases threaten cultivated strawberry (Fragaria × ananassa), and identifying and characterizing PR genes in response to infection can lead to valuable new breeding targets for resistance. Results: In this study, 1060 PR genes across 16 PR families were identified in octoploid F. × ananassa, with approximately 24% of the genes organized in tandem arrays. Members of almost every PR family were found on all four subgenomes; the greatest number was typically found on the A subgenome in keeping with the hypothesis that A is the ’dominant’ subgenome in cultivated strawberry. Some gene loss occurred during polyploidization, but PR gene family size is correlated among diploid and octoploid strawberry (R2 = 0.98) and Arabidopsis thaliana (R2 = 0.95), suggesting conservation of family sizes across plant species. Strawberry PR genes have diverse domain architectures; 62.6% of the identified genes have atypical domain architectures compared to PR type members. During infection by the fungal pathogen Colletrotrichum fructicola, PR genes were dynamically expressed and distinct stages of response to infection were observed at three time points: initial induction, slight repression, and strong induction to combat pathogen spread. PR genes with known roles in response to colonization by fungal pathogens were found to be most significantly induced during the later stages of infection. Conclusions: Characterizing the genome-wide distribution and conservation of PR genes furthers our understanding of the evolution of octoploid strawberry and provides valuable insights into strawberry’s arsenal of defense against pathogens. We found subgenome dominance in octoploid strawberry affected the evolution and expression of PR genes. Strawberry PR genes with atypical domain architectures are expressed during infection, but genes with canonical architectures are the most significantly differentially expressed. Strawberry Strawberry Evolution Pathogens Disease Resistance Pathogenesis-related PR genes PR proteins Colletotrichum Full Text Additional Declarations No competing interests reported. Supplementary Files TableS3Tandemlyarrayedgenes.xlsx TableS2FvescaFxananassaSubgenomeSynteny.xlsx TableS4FxananassaPRgenesKsKaestimates.xlsx TableS6PredictedDomainsSummary.xlsx FigureS1EnlargedphylogenyofPRfamilytypemembersandputativeoctoploidstrawberryPRgenes.pdf TableS1FxananassaFvescaAthalianaPutativePRgenes.xlsx TableS8FxananassaPRgenesMultiinfectionDESeq2.csv TableS10RPKMfornewlyannotatedPRgenes.xlsx TableS5InterproRawOutput.xlsx FigureS3Thaumatindomaintree.pdf FigureS2Barwindomaintree.pdf TableS7PredictedDomainArchitecture.csv TableS9CfructicolainfectionDESeq2results.xlsx TableS11StrawberryandArabidopsisPRfamilysizes.csv Cite Share Download PDF Status: Under Review Version 1 posted Reviews received at journal 11 Sep, 2025 Reviewers agreed at journal 22 Aug, 2025 Reviewers invited by journal 19 Aug, 2025 Editor invited by journal 01 Aug, 2025 Editor assigned by journal 01 Aug, 2025 Submission checks completed at journal 01 Aug, 2025 First submitted to journal 31 Jul, 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-7264946","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":504956231,"identity":"be109048-2b85-47b9-bfaa-8f47e44d6a34","order_by":0,"name":"Mishi V. 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species","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"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":"Strawberry, Strawberry Evolution, Pathogens, Disease Resistance, Pathogenesis-related, PR genes, PR proteins, Colletotrichum","lastPublishedDoi":"10.21203/rs.3.rs-7264946/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-7264946/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eBackground: Pathogenesis-related (PR) proteins are induced in response to infection and contribute to immunity through a variety of mechanisms. To date, 19 families of PR proteins with roles in resistance to bacteria, fungi, and insects have been identified across several model and agronomically important plant species. Countless diseases threaten cultivated strawberry (Fragaria × ananassa), and identifying and characterizing PR genes in response to infection can lead to valuable new breeding targets for resistance.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eResults: In this study, 1060 PR genes across 16 PR families were identified in octoploid F. × ananassa, with approximately 24% of the genes organized in tandem arrays. Members of almost every PR family were found on all four subgenomes; the greatest number was typically found on the A subgenome in keeping with the hypothesis that A is the ’dominant’ subgenome in cultivated strawberry. Some gene loss occurred during polyploidization, but PR gene family size is correlated among diploid and octoploid strawberry (R2 = 0.98) and Arabidopsis thaliana (R2 = 0.95), suggesting conservation of family sizes across plant species. Strawberry PR genes have diverse domain architectures; 62.6% of the identified genes have atypical domain architectures compared to PR type members. During infection by the fungal pathogen Colletrotrichum fructicola, PR genes were dynamically expressed and distinct stages of response to infection were observed at three time points: initial induction, slight repression, and strong induction to combat pathogen spread. PR genes with known roles in response to colonization by fungal pathogens were found to be most significantly induced during the later stages of infection.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eConclusions: Characterizing the genome-wide distribution and conservation of PR genes furthers our understanding of the evolution of octoploid strawberry and provides valuable insights into strawberry’s arsenal of defense against pathogens. We found subgenome dominance in octoploid strawberry affected the evolution and expression of PR genes. Strawberry PR genes with atypical domain architectures are expressed during infection, but genes with canonical architectures are the most significantly differentially expressed.\u003c/p\u003e","manuscriptTitle":"Pathogenesis-related proteins are evolutionarily conserved across diploid and octoploid Fragaria species","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-08-27 08:22:52","doi":"10.21203/rs.3.rs-7264946/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"editorInvitedReview","content":"","date":"2025-09-12T03:51:37+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"115689904349791608295162143818060182587","date":"2025-08-22T05:43:29+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2025-08-19T10:38:16+00:00","index":"","fulltext":""},{"type":"editorInvited","content":"","date":"2025-08-01T07:04:05+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2025-08-01T04:51:03+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2025-08-01T04:50:45+00:00","index":"","fulltext":""},{"type":"submitted","content":"BMC Genomics","date":"2025-07-31T18:11:50+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":"August 27th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"under-review","subjectAreas":[],"tags":[],"updatedAt":"2025-08-27T08:22:52+00:00","versionOfRecord":[],"versionCreatedAt":"2025-08-27 08:22:52","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-7264946","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-7264946","identity":"rs-7264946","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}