Beyond differential expression: a machine learning approach to identify regulatory hubs in Moniliophthora roreri infection of cacao

Beyond differential expression: a machine learning approach to identify regulatory hubs in Moniliophthora roreri infection of cacao | 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 Beyond differential expression: a machine learning approach to identify regulatory hubs in Moniliophthora roreri infection of cacao Seunghyun Lim, Sunchung Park, Jishnu Bhatt, Jae Hee Jang, Dapeng Zhang, and 2 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-6033283/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 03 Nov, 2025 Read the published version in European Journal of Plant Pathology → Version 1 posted 6 You are reading this latest preprint version Abstract Frosty pod rot (FPR), caused by Moniliophthora roreri, severely impacts global cacao (Theobroma cacao) production. While some cacao genotypes exhibit tolerance, the underlying mechanisms and the pathogen's ability to overcome them remain unclear. This study analyzed M. roreri transcript expression during infection of four cacao genotypes (two susceptible: Pound-7, CATIE-1000; two tolerant: CATIE-R4, CATIE-R7) using publicly available RNA-Seq data. We used t-SNE analysis to reveal a core set of M. roreri genes expressed across all genotypes and highlighted the abundance of transcripts predicted to be secreted. Machine learning models accurately predicted M. roreri transcript expression in most genotypes but were less accurate for the tolerant CATIE-R4, suggesting a more complex pathogen response. Network analysis of 23 differentially expressed genes previously reported to be associated with tolerance identified potential functional modules, including stress response and amino acid metabolism. Furthermore, Bootstrap Forest modeling identified a methyltransferase (evm.model.sctg_0149_0001.18) and a heat shock protein (Hsp20, evm.model.sctg_0022_0002.80) as potential central regulatory hubs influencing the expression of many other M. roreri genes. These findings suggest that M. roreri employs a core transcriptional program for infection, with specific adaptations, potentially regulated by methylation and stress response pathways, to overcome tolerance. This study provides insights into the M. roreri-cacao interaction and identifies key genes and pathways that warrant further investigation as potential targets for novel FPR management strategies. Moniliophthora roreri Theobroma cacao Transcriptomics Tolerance Network Analysis Full Text Cite Share Download PDF Status: Published Journal Publication published 03 Nov, 2025 Read the published version in European Journal of Plant Pathology → Version 1 posted Editorial decision: Major revisions 26 May, 2025 Reviewers agreed at journal 30 Mar, 2025 Reviewers invited by journal 29 Mar, 2025 Editor invited by journal 06 Mar, 2025 Editor assigned by journal 05 Mar, 2025 First submitted to journal 28 Feb, 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. 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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-6033283","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":435824524,"identity":"dcd2b2b8-9929-4cce-9887-f0b307c95df3","order_by":0,"name":"Seunghyun Lim","email":"","orcid":"","institution":"USDA-ARS: USDA Agricultural Research Service","correspondingAuthor":false,"prefix":"","firstName":"Seunghyun","middleName":"","lastName":"Lim","suffix":""},{"id":435824525,"identity":"4c9273e4-fbe6-4722-aafd-a77aae937161","order_by":1,"name":"Sunchung Park","email":"","orcid":"","institution":"USDA-ARS: USDA Agricultural Research Service","correspondingAuthor":false,"prefix":"","firstName":"Sunchung","middleName":"","lastName":"Park","suffix":""},{"id":435824526,"identity":"994d785b-83f4-4561-9e74-d4ae9d6edf22","order_by":2,"name":"Jishnu Bhatt","email":"","orcid":"","institution":"USDA-ARS: USDA Agricultural Research Service","correspondingAuthor":false,"prefix":"","firstName":"Jishnu","middleName":"","lastName":"Bhatt","suffix":""},{"id":435824527,"identity":"13ce6fa7-20fb-4097-8daa-a9c878c9e44f","order_by":3,"name":"Jae Hee Jang","email":"","orcid":"","institution":"USDA-ARS: USDA Agricultural Research Service","correspondingAuthor":false,"prefix":"","firstName":"Jae","middleName":"Hee","lastName":"Jang","suffix":""},{"id":435824528,"identity":"4cc9b026-2529-475e-ad44-83ed78482051","order_by":4,"name":"Dapeng Zhang","email":"","orcid":"","institution":"USDA-ARS: USDA Agricultural Research Service","correspondingAuthor":false,"prefix":"","firstName":"Dapeng","middleName":"","lastName":"Zhang","suffix":""},{"id":435824529,"identity":"99c6d5db-30dd-49ae-af13-2e3e26173ce8","order_by":5,"name":"Lyndel W. 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While some cacao genotypes exhibit tolerance, the underlying mechanisms and the pathogen's ability to overcome them remain unclear. This study analyzed M. roreri transcript expression during infection of four cacao genotypes (two susceptible: Pound-7, CATIE-1000; two tolerant: CATIE-R4, CATIE-R7) using publicly available RNA-Seq data. We used t-SNE analysis to reveal a core set of M. roreri genes expressed across all genotypes and highlighted the abundance of transcripts predicted to be secreted. Machine learning models accurately predicted M. roreri transcript expression in most genotypes but were less accurate for the tolerant CATIE-R4, suggesting a more complex pathogen response. Network analysis of 23 differentially expressed genes previously reported to be associated with tolerance identified potential functional modules, including stress response and amino acid metabolism. Furthermore, Bootstrap Forest modeling identified a methyltransferase (evm.model.sctg_0149_0001.18) and a heat shock protein (Hsp20, evm.model.sctg_0022_0002.80) as potential central regulatory hubs influencing the expression of many other M. roreri genes. These findings suggest that M. roreri employs a core transcriptional program for infection, with specific adaptations, potentially regulated by methylation and stress response pathways, to overcome tolerance. This study provides insights into the M. roreri-cacao interaction and identifies key genes and pathways that warrant further investigation as potential targets for novel FPR management strategies.","manuscriptTitle":"Beyond differential expression: a machine learning approach to identify regulatory hubs in Moniliophthora roreri infection of cacao","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-04-18 04:56:59","doi":"10.21203/rs.3.rs-6033283/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Major revisions","date":"2025-05-26T14:55:53+00:00","index":"","fulltext":""},{"type":"reviewerAgreed","content":"","date":"2025-03-30T10:20:55+00:00","index":0,"fulltext":""},{"type":"reviewersInvited","content":"","date":"2025-03-30T01:59:06+00:00","index":"","fulltext":""},{"type":"editorInvited","content":"European Journal of Plant Pathology","date":"2025-03-07T02:34:04+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2025-03-05T21:55:33+00:00","index":"","fulltext":""},{"type":"submitted","content":"European Journal of Plant Pathology","date":"2025-02-28T07:17:34+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"european-journal-of-plant-pathology","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"ejpp","sideBox":"Learn more about [European Journal of Plant Pathology](http://link.springer.com/journal/10658)","snPcode":"10658","submissionUrl":"https://www.editorialmanager.com/ejpp/default2.aspx","title":"European Journal of Plant Pathology","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"em","reportingPortfolio":"Springer Hybrid","inReviewEnabled":true,"inReviewRevisionsEnabled":false}}],"origin":"","ownerIdentity":"3dec9219-ecaf-44c9-afab-8abaecf13726","owner":[],"postedDate":"April 18th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"published-in-journal","subjectAreas":[],"tags":[],"updatedAt":"2025-11-10T16:01:49+00:00","versionOfRecord":{"articleIdentity":"rs-6033283","link":"https://doi.org/10.1007/s10658-025-03154-6","journal":{"identity":"european-journal-of-plant-pathology","isVorOnly":false,"title":"European Journal of Plant Pathology"},"publishedOn":"2025-11-03 15:56:54","publishedOnDateReadable":"November 3rd, 2025"},"versionCreatedAt":"2025-04-18 04:56:59","video":"","vorDoi":"10.1007/s10658-025-03154-6","vorDoiUrl":"https://doi.org/10.1007/s10658-025-03154-6","workflowStages":[]},"version":"v1","identity":"rs-6033283","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-6033283","identity":"rs-6033283","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}