Parallel evolution of amphioxus and vertebrate small-scale gene duplications

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• dc.contributor.author Brasó-Vives, Marina, 1990-
• dc.contributor.author Marlétaz, Ferdinand
• dc.contributor.author Echchiki, Amina
• dc.contributor.author Mantica, Federica
• dc.contributor.author Acemel, Rafael D.
• dc.contributor.author Gómez Skarmeta, José Luis
• dc.contributor.author Hartasánchez Frenk, Diego Andrés, 1982-
• dc.contributor.author Le Targa, Lorlane
• dc.contributor.author Pontarotti, Pierre
• dc.contributor.author Tena, Juan J.
• dc.contributor.author Maeso, Ignacio
• dc.contributor.author Escriva, Hector
• dc.contributor.author Irimia Martínez, Manuel
• dc.contributor.author Robinson-Rechavi, Marc
• dc.date.accessioned 2023-01-20T07:48:23Z
• dc.date.available 2023-01-20T07:48:23Z
• dc.date.issued 2022
• dc.description.abstract Background: Amphioxus are non-vertebrate chordates characterized by a slow morphological and molecular evolution. They share the basic chordate body-plan and genome organization with vertebrates but lack their 2R whole-genome duplications and their developmental complexity. For these reasons, amphioxus are frequently used as an outgroup to study vertebrate genome evolution and Evo-Devo. Aside from whole-genome duplications, genes continuously duplicate on a smaller scale. Small-scale duplicated genes can be found in both amphioxus and vertebrate genomes, while only the vertebrate genomes have duplicated genes product of their 2R whole-genome duplications. Here, we explore the history of small-scale gene duplications in the amphioxus lineage and compare it to small- and large-scale gene duplication history in vertebrates. Results: We present a study of the European amphioxus (Branchiostoma lanceolatum) gene duplications thanks to a new, high-quality genome reference. We find that, despite its overall slow molecular evolution, the amphioxus lineage has had a history of small-scale duplications similar to the one observed in vertebrates. We find parallel gene duplication profiles between amphioxus and vertebrates and conserved functional constraints in gene duplication. Moreover, amphioxus gene duplicates show levels of expression and patterns of functional specialization similar to the ones observed in vertebrate duplicated genes. We also find strong conservation of gene synteny between two distant amphioxus species, B. lanceolatum and B. floridae, with two major chromosomal rearrangements. Conclusions: In contrast to their slower molecular and morphological evolution, amphioxus' small-scale gene duplication history resembles that of the vertebrate lineage both in quantitative and in functional terms.
• dc.description.sponsorship MRR acknowledges support from the Swiss National Science Foundation grant 31003A/173048, and from the Etat de Vaud. FMar acknowledges support from the Royal Society grant URF\R1\191161. MI acknowledges support from European Research Council ERC-StG-LS2-637591. HE acknowledges support from the Centre National de la Recherche Scientifique and Agence Nationale de la Recherche (ANR-16-CE12-0008-01 and ANR-19-CE13-0011). PP acknowledges support from the French Government under the “Investissements d’avenir” program managed by the Agence Nationale de la Recherche (Méditerranée Infection 10-IAHU-03). IM acknowledges support from the Spanish Ministry of Science and Innovation and the European Union (RYC-2016-20089 and PGC2018-099392-A-I00). JJT acknowledges support from the ERC (Grant Agreement No. 740041) and the Spanish Ministerio de Ciencia e Innovación (PID2019-103921GB-I00).
• dc.format.mimetype application/pdf
• dc.identifier.citation Brasó-Vives M, Marlétaz F, Echchiki A, Mantica F, Acemel RD, Gómez-Skarmeta JL, Hartasánchez DA, Le Targa L, Pontarotti P, Tena JJ, Maeso I, Escriva H, Irimia M, Robinson-Rechavi M. Parallel evolution of amphioxus and vertebrate small-scale gene duplications. Genome Biol. 2022 Nov 18;23(1):243. DOI: 10.1186/s13059-022-02808-6
• dc.identifier.doi http://dx.doi.org/10.1186/s13059-022-02808-6
• dc.identifier.issn 1474-7596
• dc.identifier.uri http://hdl.handle.net/10230/55350
• dc.language.iso eng
• dc.publisher BioMed Central
• dc.relation.ispartof Genome Biol. 2022 Nov 18;23(1):243
• dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/637591
• dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/PGC2018-099392-A-I00
• dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/740041
• dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/PID2019-103921GB-I00
• dc.rights © The Author(s) 2022. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri http://creativecommons.org/licenses/by/4.0/
• dc.subject.keyword Amphioxus
• dc.subject.keyword Branchiostoma lanceolatum
• dc.subject.keyword Comparative genomics
• dc.subject.keyword Gene duplication
• dc.subject.keyword Genome assembly
• dc.subject.keyword Ohnolog
• dc.subject.keyword Small-scale duplication
• dc.subject.keyword Vertebrate
• dc.title Parallel evolution of amphioxus and vertebrate small-scale gene duplications
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion