Evolutionary trajectories of new duplicated and putative de novo genes

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• dc.contributor.author Montañés, José Carlos
• dc.contributor.author Huertas, Marta
• dc.contributor.author Messeguer, Xavier
• dc.contributor.author Albà Soler, Mar
• dc.date.accessioned 2024-04-04T06:26:04Z
• dc.date.available 2024-04-04T06:26:04Z
• dc.date.issued 2023
• dc.description.abstract The formation of new genes during evolution is an important motor of functional innovation, but the rate at which new genes originate and the likelihood that they persist over longer evolutionary periods are still poorly understood questions. Two important mechanisms by which new genes arise are gene duplication and de novo formation from a previously noncoding sequence. Does the mechanism of formation influence the evolutionary trajectories of the genes? Proteins arisen by gene duplication retain the sequence and structural properties of the parental protein, and thus they may be relatively stable. Instead, de novo originated proteins are often species specific and thought to be more evolutionary labile. Despite these differences, here we show that both types of genes share a number of similarities, including low sequence constraints in their initial evolutionary phases, high turnover rates at the species level, and comparable persistence rates in deeper branchers, in both yeast and flies. In addition, we show that putative de novo proteins have an excess of substitutions between charged amino acids compared with the neutral expectation, which is reflected in the rapid loss of their initial highly basic character. The study supports high evolutionary dynamics of different kinds of new genes at the species level, in sharp contrast with the stability observed at later stages.
• dc.description.sponsorship We acknowledge funding from Ministerio de Ciencia e Innovación Agencia Estatal de Investigación grant PGC2018-094091-B-I00 (cofunded by Fondo Europeo de Desarrollo Regional), as well as grants PID2021-122726NB-I00 and PID2021-122830OB-C43 funded by MCIN/AEI/10.13039/501100011033 and by “ERDF: A way of making Europe”, by the “European Union”. We also acknowledge funding from Generalitat de Catalunya, grant 2021SGR00042. The work was also funded by the European Union (ERC, NovoGenePop, project number 101052538). Views and opinions expressed are however those of the authors only and do not necessarily reflect those of the European Union or the European Research Council. Neither the European Union nor the granting authority can be held responsible for them.
• dc.format.mimetype application/pdf
• dc.identifier.citation Montañés JC, Huertas M, Messeguer X, Albà MM. Evolutionary trajectories of new duplicated and putative de novo genes. Mol Biol Evol. 2023 May 2;40(5):msad098. DOI: 10.1093/molbev/msad098
• dc.identifier.doi http://dx.doi.org/10.1093/molbev/msad098
• dc.identifier.issn 0737-4038
• dc.identifier.uri http://hdl.handle.net/10230/59645
• dc.language.iso eng
• dc.publisher Oxford University Press
• dc.relation.ispartof Mol Biol Evol. 2023 May 2;40(5):msad098
• dc.relation.projectID info:eu-repo/grantAgreement/EC/HE/101052538
• dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/PGC2018-094091-B-I00
• dc.relation.projectID info:eu-repo/grantAgreement/ES/3PE/PID2021-122726NB-I00
• dc.relation.projectID info:eu-repo/grantAgreement/ES/3PE/PID2021-122830OB-C43
• dc.rights © The Author(s) 2023. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri http://creativecommons.org/licenses/by/4.0/
• dc.subject.keyword De novo gene
• dc.subject.keyword Gene duplication
• dc.subject.keyword Gene family
• dc.subject.keyword Phylogeny
• dc.title Evolutionary trajectories of new duplicated and putative de novo genes
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion