Analysis of Synonymous Codon Usage Bias in the Chloroplast Genome of Rhododendron farrerae

Analysis of Synonymous Codon Usage Bias in the Chloroplast Genome of Rhododendron farrerae | 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 Analysis of Synonymous Codon Usage Bias in the Chloroplast Genome of Rhododendron farrerae Xianlin Rong, Lu Huang, Jianshuang Shen This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-4615402/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract In this study, the codon usage patterns of the chloroplast genome of Rhododendron farrerae were analyzed to provide genetic information for the conservation and innovation of Rhododendron germplasm resources. Codon usage and preferences of 54 protein coding sequences (CDS) from R. farrerae were analyzed using software such as Codon, R package, and EMBOSS. The results showed that the average GC content of the 54 CDS in the chloroplast genome of R. farrerae was 38.10%, with GC 1 (46.11%), GC 2 (39.68%), and GC 3 (28.51%) representing the GC contents at different positions, indicating that the third base of codons in the chloroplast genome of R. farrerae is predominantly composed of A and T. ENC-plot, PR2-plot, and neutral plotting analysis revealed that natural selection pressure was the most significant factor influencing the synonymous codon usage preference in the chloroplast genome of R. farrerae , leading to the identification of 16 optimal codons. This study provides genetic information for the chloroplast genome of R. farrerae and serves as a reference for genetic improvement and germplasm innovation. Rhododendron farrerae Chloroplast genome Codon Synonymous codon usage Full Text Additional Declarations No competing interests reported. Cite Share Download PDF Status: Posted Version 1 posted 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. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. 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-4615402","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":320576905,"identity":"aa94cc81-92c4-4d4e-b82d-0cb3a98e0b92","order_by":0,"name":"Xianlin Rong","email":"","orcid":"","institution":"Hangzhou Vocational and Technical College","correspondingAuthor":false,"prefix":"","firstName":"Xianlin","middleName":"","lastName":"Rong","suffix":""},{"id":320576907,"identity":"84073b43-ddd7-4f0a-989c-4ed7819202ce","order_by":1,"name":"Lu Huang","email":"","orcid":"","institution":"Hangzhou Vocational and Technical College","correspondingAuthor":false,"prefix":"","firstName":"Lu","middleName":"","lastName":"Huang","suffix":""},{"id":320576909,"identity":"1c9f3d7a-a056-49b7-81cd-86db19d34df1","order_by":2,"name":"Jianshuang Shen","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAABDklEQVRIiWNgGAWjYDACCRA2gDKApBw/M/PhB6RosTCWbGdLMyCoBYlRkbjhPI+CBE7lQCA/u/nYA4sCuzz52T2Gnwt+SRgbH+ZhMGCosYnGpcXgzrF0AwmD5GKDO2eMpWf2SciZHeY98IDhWFpuAy4tEjlmEhIGzIkbJHIMpHl7JIzNDvMlGDA2HMapRX5G/jeglvrE+TNyjH8DtSRubuYxkMCnheFGDhtQy+HEhhs5ZtI8PyQSNzAT0GJwIw3ksOOJG26klVnzNkgYSxwGBnICHr/Iz0h+Ji3xpxrosOTNt3n+1Mnx9x8+/OBDjQ1uhwEBMzwaGNugjAQ8ysEKP8CZfwgoHQWjYBSMghEJALYEVhMKw+k5AAAAAElFTkSuQmCC","orcid":"","institution":"Hangzhou Vocational and Technical College","correspondingAuthor":true,"prefix":"","firstName":"Jianshuang","middleName":"","lastName":"Shen","suffix":""}],"badges":[],"createdAt":"2024-06-21 06:51:06","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-4615402/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-4615402/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":62140320,"identity":"a388fc4a-72a1-4a40-9eaa-3565d54df259","added_by":"auto","created_at":"2024-08-09 17:03:49","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":421036,"visible":true,"origin":"","legend":"","description":"","filename":"AnalysisofSynonymousCodonUsageBiasintheChloroplastGenomeofRhododendronfarrerae.pdf","url":"https://assets-eu.researchsquare.com/files/rs-4615402/v1_covered_029e5370-4aeb-417c-87b6-b101be9f1177.pdf"}],"financialInterests":"No competing interests reported.","formattedTitle":"Analysis of Synonymous Codon Usage Bias in the Chloroplast Genome of Rhododendron farrerae","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":true,"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":"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},"keywords":"Rhododendron farrerae, Chloroplast genome, Codon, Synonymous codon usage","lastPublishedDoi":"10.21203/rs.3.rs-4615402/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-4615402/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eIn this study, the codon usage patterns of the chloroplast genome of \u003cem\u003eRhododendron farrerae\u003c/em\u003e were analyzed to provide genetic information for the conservation and innovation of \u003cem\u003eRhododendron\u003c/em\u003e germplasm resources. Codon usage and preferences of 54 protein coding sequences (CDS) from \u003cem\u003eR. farrerae\u003c/em\u003e were analyzed using software such as Codon, R package, and EMBOSS. The results showed that the average GC content of the 54 CDS in the chloroplast genome of \u003cem\u003eR. farrerae\u003c/em\u003e was 38.10%, with GC\u003csub\u003e1\u003c/sub\u003e (46.11%), GC\u003csub\u003e2\u003c/sub\u003e (39.68%), and GC\u003csub\u003e3\u003c/sub\u003e (28.51%) representing the GC contents at different positions, indicating that the third base of codons in the chloroplast genome of \u003cem\u003eR. farrerae\u003c/em\u003e is predominantly composed of A and T. ENC-plot, PR2-plot, and neutral plotting analysis revealed that natural selection pressure was the most significant factor influencing the synonymous codon usage preference in the chloroplast genome of \u003cem\u003eR. farrerae\u003c/em\u003e, leading to the identification of 16 optimal codons. 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