Directional magnitude and intricacy of minimal repeat-mediated recombination across mouse and primates

Directional magnitude and intricacy of minimal repeat-mediated recombination across mouse and primates | 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 Directional magnitude and intricacy of minimal repeat-mediated recombination across mouse and primates Masoud Arabfard, Alireza Nikkhah, Hadi Bayat, Ali M.A. Maddi, and 3 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7977169/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 Background Crossover and recombination may be crucially linked to evolution and speciation, because they create genetic diversity in a large spectrum of genomes. We recently reported that minimal repeats (MRs), such as dinucleotide two- and three-repeat units (D2Us and D3Us, respectively) are ubiquitous sites of unequal crossover and recombination and consequent colonization across the human genome. However, this phenomenon remains largely unexplored at the cross-species level. Methods On a genome-wide scale, we mapped and compared the magnitude and intricacy of AT/TA and CG/GC D3U recombination and colonization in seven species of common ancestry, including mouse (rodent), marmoset (New World monkeys), macaque (Old World monkeys), gibbon (lesser apes), and gorilla, chimpanzee, and human (great apes). Moreover, we studied the largest colony of each species as a prototype for MR-mediated intricacy comparison across the seven species. Results The AT/TA D3U colonies were significantly more abundant, larger, and more intricate than CG/GC colonies across all selected species. In these colonies, D2Us and D3Us were the sites of unequal crossover and recombination, which resulted in primary and secondary recombinants. The primary recombinants overlapped, and subsequent non-overlapping recombination of these recombinants created secondary recombinants. In a positive slope, the AT/TA D3U colony counts were in increasing order in primates in comparison to mouse, and the great apes had the highest counts. With respect to intricacy, the largest D3U colony in mouse consisted of primary recombinants only. Primary recombinants were longer in marmoset, and secondary recombinants were also rare in these monkeys. In macaque, the largest colony predominantly consisted of periodic secondary recombinants. The intricacy of recombinants increased in gibbon, and reached its maximum in the great apes. Conclusions The magnitude and intricacy of AT/TA MR-mediated recombination are directional, bearing positive slope from mouse to great apes. These directional events may link to natural selection and adaptivity across these species. Human Primate Mouse Minimal repeat Crossover Recombination hotspot Directional Full Text Additional Declarations No competing interests reported. Supplementary Files Suppl.Counts.docx 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-7977169","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":544339479,"identity":"38cb36a6-654e-48d7-9471-0124ecf469fc","order_by":0,"name":"Masoud Arabfard","email":"","orcid":"","institution":"Baqiyatallah University of Medical Sciences","correspondingAuthor":false,"prefix":"","firstName":"Masoud","middleName":"","lastName":"Arabfard","suffix":""},{"id":544339482,"identity":"ce097031-b8e8-4c10-bc11-506ee60e1cdc","order_by":1,"name":"Alireza Nikkhah","email":"","orcid":"","institution":"Baqiyatallah University of Medical 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primates","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":"Human, Primate, Mouse, Minimal repeat, Crossover, Recombination hotspot, Directional","lastPublishedDoi":"10.21203/rs.3.rs-7977169/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-7977169/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003ch2\u003eBackground\u003c/h2\u003e\u003cp\u003eCrossover and recombination may be crucially linked to evolution and speciation, because they create genetic diversity in a large spectrum of genomes. We recently reported that minimal repeats (MRs), such as dinucleotide two- and three-repeat units (D2Us and D3Us, respectively) are ubiquitous sites of unequal crossover and recombination and consequent colonization across the human genome. However, this phenomenon remains largely unexplored at the cross-species level.\u003c/p\u003e\u003ch2\u003eMethods\u003c/h2\u003e\u003cp\u003eOn a genome-wide scale, we mapped and compared the magnitude and intricacy of AT/TA and CG/GC D3U recombination and colonization in seven species of common ancestry, including mouse (rodent), marmoset (New World monkeys), macaque (Old World monkeys), gibbon (lesser apes), and gorilla, chimpanzee, and human (great apes). Moreover, we studied the largest colony of each species as a prototype for MR-mediated intricacy comparison across the seven species.\u003c/p\u003e\u003ch2\u003eResults\u003c/h2\u003e\u003cp\u003eThe AT/TA D3U colonies were significantly more abundant, larger, and more intricate than CG/GC colonies across all selected species. In these colonies, D2Us and D3Us were the sites of unequal crossover and recombination, which resulted in primary and secondary recombinants. The primary recombinants overlapped, and subsequent non-overlapping recombination of these recombinants created secondary recombinants. In a positive slope, the AT/TA D3U colony counts were in increasing order in primates in comparison to mouse, and the great apes had the highest counts. With respect to intricacy, the largest D3U colony in mouse consisted of primary recombinants only. Primary recombinants were longer in marmoset, and secondary recombinants were also rare in these monkeys. In macaque, the largest colony predominantly consisted of periodic secondary recombinants. The intricacy of recombinants increased in gibbon, and reached its maximum in the great apes.\u003c/p\u003e\u003ch2\u003eConclusions\u003c/h2\u003e\u003cp\u003eThe magnitude and intricacy of AT/TA MR-mediated recombination are directional, bearing positive slope from mouse to great apes. These directional events may link to natural selection and adaptivity across these species.\u003c/p\u003e","manuscriptTitle":"Directional magnitude and intricacy of minimal repeat-mediated recombination across mouse and primates","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-11-14 15:16:39","doi":"10.21203/rs.3.rs-7977169/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":"d0515c5e-2759-41ce-9f73-a099a84c2107","owner":[],"postedDate":"November 14th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[],"tags":[],"updatedAt":"2025-12-11T16:23:45+00:00","versionOfRecord":[],"versionCreatedAt":"2025-11-14 15:16:39","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-7977169","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-7977169","identity":"rs-7977169","version":["v1"]},"buildId":"XKTyCvWXoU3ODBz1xrDgd","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}