Exploratory analysis of salicylic acid responsive long non coding RNAs linked to abiotic stress-related pathways in Datura metel

Exploratory analysis of salicylic acid responsive long non coding RNAs linked to abiotic stress-related pathways in Datura metel | 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 Exploratory analysis of salicylic acid responsive long non coding RNAs linked to abiotic stress-related pathways in Datura metel Irushi Imaduwage¹, Gayan Perera, Madhavi Hewadikaram² This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-8849535/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: Long non-coding RNAs (lncRNAs) act as key regulators of plant responses to abiotic stresses, such as drought, cold, heat, and salinity. In parallel, the exogenous application of certain chemical compounds has been shown to enhance plant stress tolerance, potentially through lncRNA-mediated regulatory pathways. Salicylic acid (SA) is a phytohormone involved in the regulation of plant responses to both biotic and abiotic stresses. This study reanalysed publicly available RNA-seq data to identify and characterize SA-responsive lncRNAs associated with abiotic stress tolerance in Datura metel , a medicinally important plant with limited genomic resources. Results: A total of 65,469 transcripts were classified as putative lncRNAs from control and SA-treated leaf transcriptomes. Comparative expression analysis identified subsets of lncRNAs and protein-coding genes showing distinct expression patterns between treatments. Functional annotation of protein-coding genes associated with these expression changes showed significant enrichment in stress-related processes, including responses to drought, salt, osmotic stress, and oxidative stress. Cis - and trans -target prediction analyses suggested potential regulatory associations between SA-responsive lncRNAs and these genes, many of which were involved in glutathione metabolism, abscisic acid signalling pathways, protein serine/threonine kinase activity, inositol metabolism, and antioxidant biosynthesis. Conclusions: This study provides a genome-wide catalogue of lncRNAs and their associated expression patterns in Datura metel in response to SA treatment. The findings offer an exploratory view of the potential role of lncRNAs in enhancing the plant’s tolerance to abiotic stresses. Although based on computational predictions and expression trends, these results highlight candidate stress-related lncRNAs that may serve as a valuable resource for future functional and experimental validation studies. abiotic stress chemical treatment defense response long non-coding RNA stress tolerance Full Text Additional Declarations No competing interests reported. Supplementary Files AdditionalFile1.xlsx Cite Share Download PDF Status: Under Review Version 1 posted Reviewers agreed at journal 07 May, 2026 Reviewers agreed at journal 05 May, 2026 Reviewers invited by journal 24 Feb, 2026 Editor invited by journal 24 Feb, 2026 Editor assigned by journal 12 Feb, 2026 Submission checks completed at journal 12 Feb, 2026 First submitted to journal 11 Feb, 2026 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-8849535","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":596113548,"identity":"2213f764-e7a7-40f1-9ebb-30579347d179","order_by":0,"name":"Irushi Imaduwage¹","email":"","orcid":"","institution":"NSBM Green University","correspondingAuthor":false,"prefix":"","firstName":"Irushi","middleName":"","lastName":"Imaduwage¹","suffix":""},{"id":596113549,"identity":"4b68fa15-85d4-425a-9a6f-3e67e62a85cd","order_by":1,"name":"Gayan Perera","email":"","orcid":"","institution":"NSBM Green University","correspondingAuthor":false,"prefix":"","firstName":"Gayan","middleName":"","lastName":"Perera","suffix":""},{"id":596113550,"identity":"3d7db0bb-b865-4698-85be-86adcc247907","order_by":2,"name":"Madhavi Hewadikaram²","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA3klEQVRIiWNgGAWjYHACMyCWYDBgb2BghggwNxOphecATAsjUVoYGAwkEojUott+eNuDn20WDOaSbw9/LsxhkOdvYGw2wGvFmbRyw942CQbL2Xlp0jO3MRjOOMDYnIBXy4EcMwmeM0C/3M4xY+bdxsC4AeiwA3i1nH9jJvkHpOXmGePPQC32hLXcyDGT5qkAarnBYyAN1JII0oLfYTeelUnLVEjwGJwB6p25TSJ5xmFC3j+fvE3yjUGdnMFxoMMKt9nY9rc3H5bApwUGeKA0UDEzMepHwSgYBaNgFOAFAEuxQu51rRV3AAAAAElFTkSuQmCC","orcid":"","institution":"NSBM Green University","correspondingAuthor":true,"prefix":"","firstName":"Madhavi","middleName":"","lastName":"Hewadikaram²","suffix":""}],"badges":[],"createdAt":"2026-02-11 09:09:38","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-8849535/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-8849535/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":104397350,"identity":"676506c2-8855-4ae8-b8e9-9c119e0cf331","added_by":"auto","created_at":"2026-03-11 11:47:01","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":1181324,"visible":true,"origin":"","legend":"","description":"","filename":"researchpaper2.pdf","url":"https://assets-eu.researchsquare.com/files/rs-8849535/v1_covered_4d07600a-1108-4c62-a07b-188c9a366ebe.pdf"},{"id":103456505,"identity":"2cada975-b2d7-4038-b236-3be6701cb9fb","added_by":"auto","created_at":"2026-02-26 00:39:07","extension":"xlsx","order_by":0,"title":"","display":"","copyAsset":false,"role":"supplement","size":23895666,"visible":true,"origin":"","legend":"","description":"","filename":"AdditionalFile1.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-8849535/v1/1da7735cd3575593cf279f71.xlsx"}],"financialInterests":"No competing interests reported.","formattedTitle":"Exploratory analysis of salicylic acid responsive long non coding RNAs linked to abiotic stress-related pathways in Datura metel","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-genomic-data","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"gtic","sideBox":"Learn more about [BMC Genomic Data](http://bmcgenet.biomedcentral.com/)","snPcode":"","submissionUrl":"https://www.editorialmanager.com/gtic/default.aspx","title":"BMC Genomic Data","twitterHandle":"BMC_series","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"em","reportingPortfolio":"BMC Series","inReviewEnabled":true,"inReviewRevisionsEnabled":true},"keywords":"abiotic stress, chemical treatment, defense response, long non-coding RNA, stress tolerance","lastPublishedDoi":"10.21203/rs.3.rs-8849535/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-8849535/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003e\u003cb\u003eBackground:\u003c/b\u003e\u003c/p\u003e \u003cp\u003eLong non-coding RNAs (lncRNAs) act as key regulators of plant responses to abiotic stresses, such as drought, cold, heat, and salinity. In parallel, the exogenous application of certain chemical compounds has been shown to enhance plant stress tolerance, potentially through lncRNA-mediated regulatory pathways. Salicylic acid (SA) is a phytohormone involved in the regulation of plant responses to both biotic and abiotic stresses. This study reanalysed publicly available RNA-seq data to identify and characterize SA-responsive lncRNAs associated with abiotic stress tolerance in \u003cem\u003eDatura metel\u003c/em\u003e, a medicinally important plant with limited genomic resources.\u003c/p\u003e\u003cp\u003e\u003cb\u003eResults:\u003c/b\u003e\u003c/p\u003e \u003cp\u003eA total of 65,469 transcripts were classified as putative lncRNAs from control and SA-treated leaf transcriptomes. Comparative expression analysis identified subsets of lncRNAs and protein-coding genes showing distinct expression patterns between treatments. Functional annotation of protein-coding genes associated with these expression changes showed significant enrichment in stress-related processes, including responses to drought, salt, osmotic stress, and oxidative stress. \u003cem\u003eCis\u003c/em\u003e- and \u003cem\u003etrans\u003c/em\u003e-target prediction analyses suggested potential regulatory associations between SA-responsive lncRNAs and these genes, many of which were involved in glutathione metabolism, abscisic acid signalling pathways, protein serine/threonine kinase activity, inositol metabolism, and antioxidant biosynthesis.\u003c/p\u003e\u003cp\u003e\u003cb\u003eConclusions:\u003c/b\u003e\u003c/p\u003e \u003cp\u003eThis study provides a genome-wide catalogue of lncRNAs and their associated expression patterns in \u003cem\u003eDatura metel\u003c/em\u003e in response to SA treatment. The findings offer an exploratory view of the potential role of lncRNAs in enhancing the plant\u0026rsquo;s tolerance to abiotic stresses. Although based on computational predictions and expression trends, these results highlight candidate stress-related lncRNAs that may serve as a valuable resource for future functional and experimental validation studies.\u003c/p\u003e","manuscriptTitle":"Exploratory analysis of salicylic acid responsive long non coding RNAs linked to abiotic stress-related pathways in Datura metel","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2026-02-26 00:38:57","doi":"10.21203/rs.3.rs-8849535/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"reviewerAgreed","content":"122145911992731801582478109287791934138","date":"2026-05-07T09:45:26+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"163751567587913128513499694047256706731","date":"2026-05-05T12:51:06+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2026-02-24T07:33:50+00:00","index":"","fulltext":""},{"type":"editorInvited","content":"","date":"2026-02-24T07:00:18+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2026-02-12T09:06:28+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2026-02-12T09:00:27+00:00","index":"","fulltext":""},{"type":"submitted","content":"BMC Genomic Data","date":"2026-02-11T08:41:06+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"bmc-genomic-data","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"gtic","sideBox":"Learn more about [BMC Genomic Data](http://bmcgenet.biomedcentral.com/)","snPcode":"","submissionUrl":"https://www.editorialmanager.com/gtic/default.aspx","title":"BMC Genomic Data","twitterHandle":"BMC_series","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"em","reportingPortfolio":"BMC Series","inReviewEnabled":true,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"760d7c62-67a1-4c8d-891a-eef160bb50a1","owner":[],"postedDate":"February 26th, 2026","published":true,"recentEditorialEvents":[{"type":"reviewerAgreed","content":"122145911992731801582478109287791934138","date":"2026-05-07T09:45:26+00:00","index":30,"fulltext":""},{"type":"reviewerAgreed","content":"163751567587913128513499694047256706731","date":"2026-05-05T12:51:06+00:00","index":28,"fulltext":""}],"rejectedJournal":[],"revision":"","amendment":"","status":"under-review","subjectAreas":[],"tags":[],"updatedAt":"2026-02-26T00:38:58+00:00","versionOfRecord":[],"versionCreatedAt":"2026-02-26 00:38:57","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-8849535","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-8849535","identity":"rs-8849535","version":["v1"]},"buildId":"XKTyCvWXoU3ODBz1xrDgd","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}