Integrative Transcriptomic and Metabolomics Reveal Dynamic Differences in Pathogen Resistance Between Resistant and Susceptible Cultivars of Myrica rubra

Integrative Transcriptomic and Metabolomics Reveal Dynamic Differences in Pathogen Resistance Between Resistant and Susceptible Cultivars of Myrica rubra | 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 Integrative Transcriptomic and Metabolomics Reveal Dynamic Differences in Pathogen Resistance Between Resistant and Susceptible Cultivars of Myrica rubra Yingyao Liu, Yang Song, Peian Zhang, Quan Zhao, Hui Li, Jun Chen, and 3 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7090173/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 05 Dec, 2025 Read the published version in BMC Plant Biology → Version 1 posted 13 You are reading this latest preprint version Abstract Background: Twig blight (TB), caused by Pestalotiopsis -like species, induces twig dieback in Myrica rubra, leading to substantial economic losses in its production across China and posing a significant threat to M. rubra cultivation. To date, the immune response of M. rubra to Pestalotiopsis -like infections remains poorly understood. Results: In this study, full-length transcriptomics and untargeted metabolomics were employed to investigate the immune responses of resistant “Dingao” (DA) and susceptible “Dongkui” (DK) M. rubra cultivars to Pestalotiopsis pathogen infection at early (1DPI) and later (5DPI) stage. The main findings revealed that the resistant DA triggered a rapid and robust immune response at 1DPI, with 1,111 differentially expressed genes (DEGs), including 583 increased and 528 decreased. As the immune response progressed to 5DPI, the number of DEGs in DA was reduced to with 324 DEGs (114 upregulated and 210 downregulated). In contrast, the susceptible DK cultivar exhibited a weak and delayed defense response. At 1DPI only 99 DEGs (26 upregulated and 73 downregulated) in DK leaves; by 5DPI, a substantial shift occurred in DK samples, with 3,414 DEGs (2,141 upregulated and 1,273 downregulated), showing a late but massive defense response. In DA samples, WRKY, AP2/ERF transcription factors (TFs) were the most up-regulated TFs at the early immune response stage; by 5DPI, NAC and WRKY families became the most prominently expressed TFs. In DK, notable TF upregulation (including WRKY, MYB and AP2/ERF ) was only observed at 5DPI and there were not significantly expression changes at the early immune response stage. Untargeted metabolomics further revealed that DK exhibited 280 upregulated and 12 downregulated differentially accumulated metabolites (DMs) at 1DPI; 503 DMs upregulated and 166 downregulated DMs at 5DPI. In DA plants, 472 DMs were upregulated and 110 downregulated at 1DPI, whereas at 5DPI, 387 DMs were upregulated and 219 downregulated. Conclusions: Through a combined analysis of full-length transcriptomics and untargeted metabolomics, we revealed distinct molecular and metabolic responses between resistant “Dingao” (DA) and susceptible “Dongkui” (DK) M. rubra cultivars under TB stress. M. rubra Pestalotiopsis Immune response Transcriptomics Metabolomics Full Text Additional Declarations No competing interests reported. Supplemental figures S1-S4 are not available with this version. Supplementary Files Supplementarytables.xlsx Cite Share Download PDF Status: Published Journal Publication published 05 Dec, 2025 Read the published version in BMC Plant Biology → Version 1 posted Editorial decision: Revision requested 06 Aug, 2025 Reviews received at journal 05 Aug, 2025 Reviews received at journal 02 Aug, 2025 Reviews received at journal 22 Jul, 2025 Reviewers agreed at journal 21 Jul, 2025 Reviewers agreed at journal 21 Jul, 2025 Reviewers agreed at journal 20 Jul, 2025 Reviewers agreed at journal 18 Jul, 2025 Reviewers invited by journal 17 Jul, 2025 Editor invited by journal 17 Jul, 2025 Editor assigned by journal 17 Jul, 2025 Submission checks completed at journal 17 Jul, 2025 First submitted to journal 17 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. 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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-7090173","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":488646363,"identity":"4668d28b-59b5-47c3-a4d7-6834853d19a7","order_by":0,"name":"Yingyao Liu","email":"","orcid":"","institution":"Zhejiang Institute of Subtropical Crops","correspondingAuthor":false,"prefix":"","firstName":"Yingyao","middleName":"","lastName":"Liu","suffix":""},{"id":488646364,"identity":"6eebcf9e-cea9-4116-b398-d932a7a5f8ba","order_by":1,"name":"Yang Song","email":"","orcid":"","institution":"Zhejiang Institute of Subtropical 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rubra","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"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":"bmc-plant-biology","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"pbio","sideBox":"Learn more about [BMC Plant Biology](http://bmcplantbiol.biomedcentral.com/)","snPcode":"","submissionUrl":"https://www.editorialmanager.com/pbio/default.aspx","title":"BMC Plant Biology","twitterHandle":"BMC_series","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"em","reportingPortfolio":"BMC Series","inReviewEnabled":true,"inReviewRevisionsEnabled":true},"keywords":"M. rubra, Pestalotiopsis, Immune response, Transcriptomics, Metabolomics","lastPublishedDoi":"10.21203/rs.3.rs-7090173/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-7090173/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003e\u003cstrong\u003eBackground:\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eTwig blight (TB), caused by \u003cem\u003ePestalotiopsis\u003c/em\u003e-like species, induces twig dieback in Myrica rubra, leading to substantial economic losses in its production across China and posing a significant threat to \u003cem\u003eM. rubra\u003c/em\u003e cultivation. To date, the immune response of \u003cem\u003eM. rubra\u003c/em\u003e to \u003cem\u003ePestalotiopsis\u003c/em\u003e-like infections remains poorly understood.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eResults:\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eIn this study, full-length transcriptomics and untargeted metabolomics were employed to investigate the immune responses of resistant “Dingao” (DA) and susceptible “Dongkui” (DK) M. rubra cultivars to Pestalotiopsis pathogen infection at early (1DPI) and later (5DPI) stage. The main findings revealed that the resistant DA triggered a rapid and robust immune response at 1DPI, with 1,111 differentially expressed genes (DEGs), including 583 increased and 528 decreased. As the immune response progressed to 5DPI, the number of DEGs in DA was reduced to with 324 DEGs (114 upregulated and 210 downregulated). In contrast, the susceptible DK cultivar exhibited a weak and delayed defense response. At 1DPI only 99 DEGs (26 upregulated and 73 downregulated) in DK leaves; by 5DPI, a substantial shift occurred in DK samples, with 3,414 DEGs (2,141 upregulated and 1,273 downregulated), showing a late but massive defense response. In DA samples, WRKY, AP2/ERF transcription factors (TFs) were the most up-regulated TFs at the early immune response stage; by 5DPI, NAC and WRKY families became the most prominently expressed TFs. In DK, notable TF upregulation (including WRKY, MYB and AP2/ERF ) was only observed at 5DPI and there were not significantly expression changes at the early immune response stage. Untargeted metabolomics further revealed that DK exhibited 280 upregulated and 12 downregulated differentially accumulated metabolites (DMs) at 1DPI; 503 DMs upregulated and 166 downregulated DMs at 5DPI. In DA plants, 472 DMs were upregulated and 110 downregulated at 1DPI, whereas at 5DPI, 387 DMs were upregulated and 219 downregulated.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eConclusions:\u003c/strong\u003e\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eThrough a combined analysis of full-length transcriptomics and untargeted metabolomics, we revealed distinct molecular and metabolic responses between resistant “Dingao” (DA) and susceptible “Dongkui” (DK)\u003cem\u003e M. rubra\u003c/em\u003e cultivars under TB stress.\u003c/p\u003e","manuscriptTitle":"Integrative Transcriptomic and Metabolomics Reveal Dynamic Differences in Pathogen Resistance Between Resistant and Susceptible Cultivars of Myrica rubra","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-07-22 05:36:28","doi":"10.21203/rs.3.rs-7090173/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Revision requested","date":"2025-08-06T07:34:57+00:00","index":"","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-08-05T14:24:18+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-08-02T15:56:58+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-07-22T04:58:34+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"86914729221134118543619564248964796781","date":"2025-07-21T10:54:29+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"252212366821020449672529127353916051410","date":"2025-07-21T07:16:45+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"160851300703305006570081006314391733821","date":"2025-07-21T02:06:17+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"51241022267274676680098396281002813930","date":"2025-07-18T07:24:28+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2025-07-18T02:20:20+00:00","index":"","fulltext":""},{"type":"editorInvited","content":"","date":"2025-07-17T09:35:53+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2025-07-17T09:17:45+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2025-07-17T06:54:10+00:00","index":"","fulltext":""},{"type":"submitted","content":"BMC Plant Biology","date":"2025-07-17T06:52:50+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"bmc-plant-biology","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"pbio","sideBox":"Learn more about [BMC Plant Biology](http://bmcplantbiol.biomedcentral.com/)","snPcode":"","submissionUrl":"https://www.editorialmanager.com/pbio/default.aspx","title":"BMC Plant Biology","twitterHandle":"BMC_series","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"em","reportingPortfolio":"BMC Series","inReviewEnabled":true,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"888e9680-d328-4b3e-8d04-9b41b536938e","owner":[],"postedDate":"July 22nd, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"published-in-journal","subjectAreas":[],"tags":[],"updatedAt":"2025-12-08T16:12:05+00:00","versionOfRecord":{"articleIdentity":"rs-7090173","link":"https://doi.org/10.1186/s12870-025-07543-1","journal":{"identity":"bmc-plant-biology","isVorOnly":false,"title":"BMC Plant Biology"},"publishedOn":"2025-12-05 15:58:22","publishedOnDateReadable":"December 5th, 2025"},"versionCreatedAt":"2025-07-22 05:36:28","video":"","vorDoi":"10.1186/s12870-025-07543-1","vorDoiUrl":"https://doi.org/10.1186/s12870-025-07543-1","workflowStages":[]},"version":"v1","identity":"rs-7090173","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-7090173","identity":"rs-7090173","version":["v1"]},"buildId":"XKTyCvWXoU3ODBz1xrDgd","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}