Genome-wide identification and expression pattern analysis of the MADS-box gene family in Vaccinium bracteatum

Genome-wide identification and expression pattern analysis of the MADS-box gene family in Vaccinium bracteatum | 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 Genome-wide identification and expression pattern analysis of the MADS-box gene family in Vaccinium bracteatum Jianqiang Zhou, Zhiqiang Cao, Li Cheng, Yufei Chen, Xiaoran Liang, and 6 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7783509/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted 10 You are reading this latest preprint version Abstract Background Vaccinium bracteatum Thunb . is a plant with notable medicinal and economic value and is widely distributed throughout China. The MADS-box gene family is a transcription factor family found across eukaryotes that is involved in many biological processes, including flower development and fruit ripening. However, systematic information on MADS-box genes in V. bracteatum is lacking. Results This study presents the first comprehensive genome-wide identification and functional characterization of the MADS-box transcription factor family in Vaccinium bracteatum . Through bioinformatic analyses, a total of 74 VaMADS genes were identified and classified into two major groups: Type I (44 genes) and Type II (30 genes). The 24 VaMADS genes were defined as 17 pairs of duplication events, including 11 pairs of segmental duplications and 6 pairs of tandem duplications. The collinearity analysis indicated that tandem and segmental duplication contributed to the expansion of MADS-box genes. Gene structure analysis revealed that Type I genes typically have a simple architecture with one exon and no introns, whereas Type II genes have more complex structures with multiple exons and introns, showing high conservation within the subfamilies. Cis-acting element analysis revealed that VaMADS genes participate in growth, development, and stress resistance. Type II genes had higher expression levels than Type I genes during fruit development, indicating that Type II genes play a crucial role in fruit ripening. Conclusions This study identified the MADS gene family in Vaccinium bracteatum for the first time, providing an important reference for further in-depth studies on the function of the MADS-box genes in plant and fruit development. transcription factor Expression pattern cis-elements fruit ripening Full Text Additional Declarations No competing interests reported. Supplementary Files TableS1.csv Additional file 1 File name: Table S1. File format: .csv Title: The categories of 74 MADS-box genes in Vaccinium bracteatum. Description: This table presents the classification of 74 MADS-box genes in Vaccinium bracteatum, including the name of each gene and its assigned category. The genes are divided into two main types. TableS2.csv Additional file 2 File name: Table S2. File format: .csv Title: Data on the locations and statistical significance (p-values) of specific motifs identified within the VaMADS genes. Description: This table provides data on the locations and statistical significance of specific motifs identified within the VaMADS genes. It includes the name of each MADS-box gene, the conserved motif found within the gene, the starting position of the motif in the protein sequence, the length of the motif in amino acids, and the p-value indicating the statistical significance of the motif. The p-value represents the probability that the motif is present by chance. TableS3.csv Additional file 3 File name: Table S3. File format: .csv Title: Ka/Ks ratio of duplicated gene pairs. Description: This table provides the Ka/Ks ratio of duplicated gene pairs in the genome, including the names of the gene pairs, the method used to calculate the Ka/Ks ratio, the number of nonsynonymous (Ka) and synonymous (Ks) substitutions, the Ka/Ks ratio, and the statistical significance (p-value) of the ratio. Additionally, it provides the length of the protein sequence, the number of synonymous and nonsynonymous sites, and the total number of substitutions. The table also includes the divergence distance between the gene pairs and the substitution rate ratios for different types of nucleotide changes. Cite Share Download PDF Status: Under Review Version 1 posted Editorial decision: Revision requested 05 Dec, 2025 Reviews received at journal 21 Oct, 2025 Reviews received at journal 19 Oct, 2025 Reviewers agreed at journal 10 Oct, 2025 Reviewers agreed at journal 09 Oct, 2025 Reviewers invited by journal 09 Oct, 2025 Editor assigned by journal 09 Oct, 2025 Editor invited by journal 09 Oct, 2025 Submission checks completed at journal 09 Oct, 2025 First submitted to journal 09 Oct, 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-7783509","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":532754245,"identity":"b43bb175-6425-476b-beb3-4f8c03529cbb","order_by":0,"name":"Jianqiang Zhou","email":"","orcid":"","institution":"Anhui Provincial Key Laboratory of Biodiversity Conservation and Ecological Security in the Yangtze River Basin","correspondingAuthor":false,"prefix":"","firstName":"Jianqiang","middleName":"","lastName":"Zhou","suffix":""},{"id":532754246,"identity":"94f25539-d2a5-4757-adc8-779947e2fdce","order_by":1,"name":"Zhiqiang 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11:14:46","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":1959274,"visible":true,"origin":"","legend":"","description":"","filename":"Paper.pdf","url":"https://assets-eu.researchsquare.com/files/rs-7783509/v1_covered_4a1b8a48-9131-450d-b39e-a9c3aeb59adc.pdf"},{"id":94110658,"identity":"abcddb69-2db3-46c0-aa97-89fd852cffff","added_by":"auto","created_at":"2025-10-22 13:19:52","extension":"csv","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":1276,"visible":true,"origin":"","legend":"\u003cp\u003eAdditional file 1\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eFile name\u003c/strong\u003e: Table S1.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eFile format\u003c/strong\u003e: .csv\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eTitle\u003c/strong\u003e: The categories of 74 MADS-box genes in Vaccinium bracteatum.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eDescription\u003c/strong\u003e: This table presents the classification of 74 MADS-box genes in Vaccinium bracteatum, including the name of each gene and its assigned category. The genes are divided into two main types.\u003c/p\u003e","description":"","filename":"TableS1.csv","url":"https://assets-eu.researchsquare.com/files/rs-7783509/v1/99f6ad128baacef68e690048.csv"},{"id":94109434,"identity":"a117fa9e-6c46-4546-9cc2-678263bc5fd9","added_by":"auto","created_at":"2025-10-22 13:03:51","extension":"csv","order_by":2,"title":"","display":"","copyAsset":false,"role":"supplement","size":3868,"visible":true,"origin":"","legend":"\u003cp\u003eAdditional file 2\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eFile name\u003c/strong\u003e: Table S2.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eFile format\u003c/strong\u003e: .csv\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eTitle\u003c/strong\u003e: Data on the locations and statistical significance (p-values) of specific motifs identified within the VaMADS genes.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eDescription\u003c/strong\u003e: This table provides data on the locations and statistical significance of specific motifs identified within the VaMADS genes. It includes the name of each MADS-box gene, the conserved motif found within the gene, the starting position of the motif in the protein sequence, the length of the motif in amino acids, and the p-value indicating the statistical significance of the motif. The p-value represents the probability that the motif is present by chance.\u003c/p\u003e","description":"","filename":"TableS2.csv","url":"https://assets-eu.researchsquare.com/files/rs-7783509/v1/2a276bc2cb49864259e14584.csv"},{"id":94109435,"identity":"23027c91-f5b6-43a8-aed8-b17a9acd8f8c","added_by":"auto","created_at":"2025-10-22 13:03:52","extension":"csv","order_by":3,"title":"","display":"","copyAsset":false,"role":"supplement","size":8361,"visible":true,"origin":"","legend":"\u003cp\u003eAdditional file 3\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eFile name\u003c/strong\u003e: Table S3.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eFile format\u003c/strong\u003e: .csv\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eTitle\u003c/strong\u003e: Ka/Ks ratio of duplicated gene pairs.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eDescription\u003c/strong\u003e: This table provides the Ka/Ks ratio of duplicated gene pairs in the genome, including the names of the gene pairs, the method used to calculate the Ka/Ks ratio, the number of nonsynonymous (Ka) and synonymous (Ks) substitutions, the Ka/Ks ratio, and the statistical significance (p-value) of the ratio. Additionally, it provides the length of the protein sequence, the number of synonymous and nonsynonymous sites, and the total number of substitutions. The table also includes the divergence distance between the gene pairs and the substitution rate ratios for different types of nucleotide changes.\u003c/p\u003e","description":"","filename":"TableS3.csv","url":"https://assets-eu.researchsquare.com/files/rs-7783509/v1/732262b36d53ad12d99778ba.csv"}],"financialInterests":"No competing interests reported.","formattedTitle":"Genome-wide identification and expression pattern analysis of the MADS-box gene family in Vaccinium bracteatum","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":"transcription factor, Expression pattern, cis-elements, fruit ripening","lastPublishedDoi":"10.21203/rs.3.rs-7783509/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-7783509/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003ch2\u003eBackground\u003c/h2\u003e\u003cp\u003e\u003cem\u003eVaccinium bracteatum Thunb\u003c/em\u003e. is a plant with notable medicinal and economic value and is widely distributed throughout China. The MADS-box gene family is a transcription factor family found across eukaryotes that is involved in many biological processes, including flower development and fruit ripening. However, systematic information on MADS-box genes in \u003cem\u003eV. bracteatum\u003c/em\u003e is lacking.\u003c/p\u003e\u003ch2\u003eResults\u003c/h2\u003e\u003cp\u003eThis study presents the first comprehensive genome-wide identification and functional characterization of the MADS-box transcription factor family in \u003cem\u003eVaccinium bracteatum\u003c/em\u003e. Through bioinformatic analyses, a total of 74 VaMADS genes were identified and classified into two major groups: Type I (44 genes) and Type II (30 genes). The 24 VaMADS genes were defined as 17 pairs of duplication events, including 11 pairs of segmental duplications and 6 pairs of tandem duplications. The collinearity analysis indicated that tandem and segmental duplication contributed to the expansion of MADS-box genes. Gene structure analysis revealed that Type I genes typically have a simple architecture with one exon and no introns, whereas Type II genes have more complex structures with multiple exons and introns, showing high conservation within the subfamilies. Cis-acting element analysis revealed that VaMADS genes participate in growth, development, and stress resistance. Type II genes had higher expression levels than Type I genes during fruit development, indicating that Type II genes play a crucial role in fruit ripening.\u003c/p\u003e\u003ch2\u003eConclusions\u003c/h2\u003e\u003cp\u003eThis study identified the MADS gene family in \u003cem\u003eVaccinium bracteatum\u003c/em\u003e for the first time, providing an important reference for further in-depth studies on the function of the MADS-box genes in plant and fruit development.\u003c/p\u003e","manuscriptTitle":"Genome-wide identification and expression pattern analysis of the MADS-box gene family in Vaccinium bracteatum","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-10-22 13:03:47","doi":"10.21203/rs.3.rs-7783509/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Revision requested","date":"2025-12-05T05:39:50+00:00","index":"","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-10-21T09:20:30+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-10-20T02:34:20+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"308644339683681143077891798627161582993","date":"2025-10-10T05:23:37+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"147195872809041916454847191012903190008","date":"2025-10-10T00:35:30+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2025-10-09T06:41:40+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2025-10-09T06:36:49+00:00","index":"","fulltext":""},{"type":"editorInvited","content":"","date":"2025-10-09T06:30:39+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2025-10-09T04:47:09+00:00","index":"","fulltext":""},{"type":"submitted","content":"BMC Genomics","date":"2025-10-09T04:43:28+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":"d737283a-c72e-46d8-afdf-0cbfed97bca5","owner":[],"postedDate":"October 22nd, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"under-review","subjectAreas":[],"tags":[],"updatedAt":"2026-03-16T02:39:11+00:00","versionOfRecord":[],"versionCreatedAt":"2025-10-22 13:03:47","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-7783509","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-7783509","identity":"rs-7783509","version":["v1"]},"buildId":"XKTyCvWXoU3ODBz1xrDgd","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}