FullSynesth: Syntenic Reconciliation of a Set of Consistent Gene Trees

FullSynesth: Syntenic Reconciliation of a Set of Consistent Gene Trees | 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 FullSynesth: Syntenic Reconciliation of a Set of Consistent Gene Trees Mathieu Gascon, Mattéo Delabre, Nadia El-Mabrouk This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-6247846/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 10 Feb, 2026 Read the published version in Theory of Computing Systems → Version 1 posted 9 You are reading this latest preprint version Abstract We present FullSynesth, a tree reconciliation algorithm predicting the evolution of a set of homologous genomic regions or syntenies, inside a species tree. The considered evolutionary model involves segmental events (i.e. acting on multiple genes) including duplications (D), losses (L), synteny fissions and transfers possibly going through unsampled or extinct species. Formally, given a set of syntenies in a set of genomes and a set G of consistent gene trees for the gene families composing the syntenies, the problem is to infer a most parsimonious evolutionary history explaining the observed gene trees and syntenies given a species tree. The problem is known to be NP-hard for the DL distance. FullSynesth is based on Synesth explicating the evolution of a set of syntenies given a single synteny tree, which can be obtained from G by selecting a given supertree. Rather than trying each supertree in turn, FullSynesth is based on a two-in-one approach simultaneously building and reconciling a synteny supertree. This algorithm runs in polynomial time for a fixed number of gene trees. We show on simulated datasets that FullSynesth significantly improves the running time of Synesth applied to each possible supertree. An implementation of the algorithm is available at: https://github.com/UdeM-LBIT/FullSynesth . Phylogenetics Gene Supertree Reconciliation Synteny Duplication Transfer Loss Full Text Additional Declarations No competing interests reported. Cite Share Download PDF Status: Published Journal Publication published 10 Feb, 2026 Read the published version in Theory of Computing Systems → Version 1 posted Editorial decision: Revision requested 23 Jun, 2025 Reviews received at journal 06 Jun, 2025 Reviews received at journal 05 May, 2025 Reviewers agreed at journal 07 Apr, 2025 Reviewers agreed at journal 24 Mar, 2025 Reviewers invited by journal 22 Mar, 2025 Editor assigned by journal 18 Mar, 2025 Submission checks completed at journal 18 Mar, 2025 First submitted to journal 17 Mar, 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-6247846","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":434929770,"identity":"fe1f5dfd-ba43-47cb-aa31-7a57aedc1393","order_by":0,"name":"Mathieu Gascon","email":"","orcid":"","institution":"Université de Montréal","correspondingAuthor":false,"prefix":"","firstName":"Mathieu","middleName":"","lastName":"Gascon","suffix":""},{"id":434929771,"identity":"4ec848eb-5570-41eb-8b3f-df3f594f37ec","order_by":1,"name":"Mattéo Delabre","email":"","orcid":"","institution":"Université de Montréal","correspondingAuthor":false,"prefix":"","firstName":"Mattéo","middleName":"","lastName":"Delabre","suffix":""},{"id":434929772,"identity":"bd1dd48f-b825-4d85-865c-725fdd743bee","order_by":2,"name":"Nadia El-Mabrouk","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA5UlEQVRIiWNgGAWjYFACHhCRIMeGIviACC3GbKh8IrQkNhCtRbf97LEPH9vS0vukDx9g5s2xybOXPnzwQwKDnTwuLWZn8pJnzmzLyW3jS0tg5t2WVszDl5YskcCQbNiAS8uBHGNm3raK3DYeHgOglsOJPUAGUMsBRpxazr8Ba0lnQ2jh//wDqMUep5YbYFtyEpC08LCBbEnEreVdMuOMc2mGbTxsCQfnbktL7DnDZmaRYJCcjNthuYcZPpQly8v3MB988HabTWJ7D/PjGx8q7GxxaUEBBxBMA2LUj4JRMApGwSjABQAB3U+idRntiAAAAABJRU5ErkJggg==","orcid":"","institution":"Université de Montréal","correspondingAuthor":true,"prefix":"","firstName":"Nadia","middleName":"","lastName":"El-Mabrouk","suffix":""}],"badges":[],"createdAt":"2025-03-17 22:23:11","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-6247846/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-6247846/v1","draftVersion":[],"editorialEvents":[{"content":"https://doi.org/10.1007/s00224-025-10259-2","type":"published","date":"2026-02-10T15:58:30+00:00"}],"editorialNote":"","failedWorkflow":false,"files":[{"id":102785378,"identity":"85efcbd6-2422-47c4-974f-19fb0eb305f0","added_by":"auto","created_at":"2026-02-16 16:05:54","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":760295,"visible":true,"origin":"","legend":"","description":"","filename":"FullSynesthSyntenicReconciliationofaSetofConsistentGeneTrees.pdf","url":"https://assets-eu.researchsquare.com/files/rs-6247846/v1_covered_4a821684-992a-422e-ab19-03015cf20cc8.pdf"}],"financialInterests":"No competing interests reported.","formattedTitle":"FullSynesth: Syntenic Reconciliation of a Set of Consistent Gene Trees","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":true,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"theory-of-computing-systems","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"tocs","sideBox":"Learn more about [Theory of Computing Systems](http://link.springer.com/journal/224)","snPcode":"224","submissionUrl":"https://submission.nature.com/new-submission/224/3","title":"Theory of Computing Systems","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"em","reportingPortfolio":"Springer Hybrid","inReviewEnabled":true,"inReviewRevisionsEnabled":false},"keywords":"Phylogenetics, Gene, Supertree, Reconciliation, Synteny, Duplication, Transfer, Loss","lastPublishedDoi":"10.21203/rs.3.rs-6247846/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-6247846/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"We present FullSynesth, a tree reconciliation algorithm predicting the evolution of a set of homologous genomic regions or syntenies, inside a species tree. 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