Comparative genomics of strains of varying virulence of the Gram-positive bacterial pathogen of maize, Clavibacter nebraskensis

Comparative genomics of strains of varying virulence of the Gram-positive bacterial pathogen of maize, Clavibacter nebraskensis | 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 Comparative genomics of strains of varying virulence of the Gram-positive bacterial pathogen of maize, Clavibacter nebraskensis Molly Veregge, Luis Fernando Flores-Lopez, Thomas Kono, Veronica Roman-Reyna, and 1 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7860969/v2 This work is licensed under a CC BY 4.0 License Status: Posted Version 2 posted You are reading this latest preprint version Show more versions Abstract Background Clavibacter nebraskensis ( Cn ) is a Gram-positive bacterial plant pathogen that infects the vascular tissue of maize, causing Goss’s Wilt and Leaf Blight. Detection of highly virulent strains since the mid-2000s suggests that genetic divergence has contributed to the re-emergence of the disease following its effective management and subsequent disappearance in the 1980s. However, few genomic resources exist for this pathogen, and little is known about genomic variation in the species. Our study aimed to characterize genomic diversity across a set of differentially virulent strains isolated from both historic epidemics and recent outbreaks. Results We sequenced 17 Cn strains of varying virulence isolated from epidemics spanning their earliest detection to subsequent outbreaks in the mid-2010s across various US states and Manitoba, Canada. Contrary to previous studies, we found no strong population structure associated with geographic origin or year of isolation based on haplotype analysis. We detected five heterogeneous plasmids in strains CDK032, CDK039, CDK044, CDK045, and CDK046, whereas to date, only one plasmid has been sequenced in a single Cn strain. Genomic islands were detected in all strains, and the putative virulence gene celA was found to be encoded in one such island. Secreted CAZymes, hypothesized to be involved in pathogenicity, are well conserved across all Cn genomes, indicating that allelic or expression diversity, and not gene copy number, might be implicated in virulence diversity. Importantly, we identified deletions in a secreted cellulase within the linker peptide region between the carbohydrate-binding domain and the cellulase domain that have not been reported in the literature previously. Conclusion Our analyses provide insight into genomic diversity within the species, revealing five novel plasmids and genomic islands harboring CAzymes, including the celA gene. Genes encoding cell wall degrading enzymes are well-conserved across strains of all virulence phenotypes. Deletions within a secreted cellulase not previously reported have been described for future functional analysis. Clavibacter nebraskensis Goss’s Wilt and Leaf Blight microbial genomics pathogenicity cellulase activity Full Text Additional Declarations The authors declare no competing interests. Cite Share Download PDF Status: Posted Version 2 posted You are reading this latest preprint version Show more versions 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-7860969","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":532634797,"identity":"15a283d9-82d1-4e19-ad28-c4b601be7bb1","order_by":0,"name":"Molly Veregge","email":"","orcid":"","institution":"University of Minnesota – Twin Cities","correspondingAuthor":false,"prefix":"","firstName":"Molly","middleName":"","lastName":"Veregge","suffix":""},{"id":532634798,"identity":"ac91126a-4b50-4929-b26c-838d3cc0efe3","order_by":1,"name":"Luis Fernando Flores-Lopez","email":"","orcid":"","institution":"Pennsylvania State 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Blight, microbial genomics, pathogenicity, cellulase activity","lastPublishedDoi":"10.21203/rs.3.rs-7860969/v2","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-7860969/v2","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eBackground\u003c/p\u003e\n\u003cp\u003e\u003cem\u003eClavibacter nebraskensis \u003c/em\u003e(\u003cem\u003eCn\u003c/em\u003e) is a Gram-positive bacterial plant pathogen that infects the vascular tissue of maize, causing Goss’s Wilt and Leaf Blight. Detection of highly virulent strains since the mid-2000s suggests that genetic divergence has contributed to the re-emergence of the disease following its effective management and subsequent disappearance in the 1980s. However, few genomic resources exist for this pathogen, and little is known about genomic variation in the species. Our study aimed to characterize genomic diversity across a set of differentially virulent strains isolated from both historic epidemics and recent outbreaks.\u003c/p\u003e\n\u003cp\u003eResults\u003c/p\u003e\n\u003cp\u003eWe sequenced 17 \u003cem\u003eCn \u003c/em\u003estrains of varying virulence isolated from epidemics spanning their earliest detection to subsequent outbreaks in the mid-2010s across various US states and Manitoba, Canada. Contrary to previous studies, we found no strong population structure associated with geographic origin or year of isolation based on haplotype analysis. We detected five heterogeneous plasmids in strains CDK032, CDK039, CDK044, CDK045, and CDK046, whereas to date, only one plasmid has been sequenced in a single \u003cem\u003eCn \u003c/em\u003estrain. Genomic islands were detected in all strains, and the putative virulence gene \u003cem\u003ecelA \u003c/em\u003ewas found to be encoded in one such island. Secreted CAZymes, hypothesized to be involved in pathogenicity, are well conserved across all \u003cem\u003eCn\u003c/em\u003e genomes, indicating that allelic or expression diversity, and not gene copy number, might be implicated in virulence diversity. Importantly, we identified deletions in a secreted cellulase within the linker peptide region between the carbohydrate-binding domain and the cellulase domain that have not been reported in the literature previously.\u003c/p\u003e\n\u003cp\u003eConclusion\u003c/p\u003e\n\u003cp\u003eOur analyses provide insight into genomic diversity within the species, revealing five novel plasmids and genomic islands harboring CAzymes, including the \u003cem\u003ecelA\u003c/em\u003e gene. Genes encoding cell wall degrading enzymes are well-conserved across strains of all virulence phenotypes. Deletions within a secreted cellulase not previously reported have been described for future functional analysis.\u003c/p\u003e","manuscriptTitle":"Comparative genomics of strains of varying virulence of the Gram-positive bacterial pathogen of maize, Clavibacter nebraskensis","msid":"","msnumber":"","nonDraftVersions":[{"code":2,"date":"2026-01-26 15:21:30","doi":"10.21203/rs.3.rs-7860969/v2","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true}},{"code":1,"date":"2025-10-21 05:43:50","doi":"10.21203/rs.3.rs-7860969/v1","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"7d351616-732d-4861-a7af-ea010f587a6b","owner":[],"postedDate":"January 26th, 2026","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[],"tags":[],"updatedAt":"2025-11-20T12:53:37+00:00","versionOfRecord":[],"versionCreatedAt":"2026-01-26 15:21:30","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v2","identity":"rs-7860969","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-7860969","identity":"rs-7860969","version":["v2"]},"buildId":"XKTyCvWXoU3ODBz1xrDgd","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}