Evolutionary trajectories of new duplicated and putative de novo genes

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 gen...

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Autores: Montañés, José Carlos, Huertas, Marta, Messeguer, Xavier, Albà Soler, Mar
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2023
País:España
Institución:Universitat Pompeu Fabra
Repositorio:Repositorio Digital de la UPF
OAI Identifier:oai:repositori.upf.edu:10230/59645
Acceso en línea:http://hdl.handle.net/10230/59645
http://dx.doi.org/10.1093/molbev/msad098
Access Level:acceso abierto
Palabra clave:De novo gene
Gene duplication
Gene family
Phylogeny
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spelling Evolutionary trajectories of new duplicated and putative de novo genesMontañés, José CarlosHuertas, MartaMesseguer, XavierAlbà Soler, MarDe novo geneGene duplicationGene familyPhylogenyThe 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.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.Oxford University Press202420242023info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/59645http://dx.doi.org/10.1093/molbev/msad098reponame:Repositorio Digital de la UPFinstname:Universitat Pompeu FabraInglésMol Biol Evol. 2023 May 2;40(5):msad098info:eu-repo/grantAgreement/EC/HE/101052538info:eu-repo/grantAgreement/ES/2PE/PGC2018-094091-B-I00info:eu-repo/grantAgreement/ES/3PE/PID2021-122726NB-I00info:eu-repo/grantAgreement/ES/3PE/PID2021-122830OB-C43© 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.http://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:repositori.upf.edu:10230/596452026-06-12T07:21:37Z
dc.title.none.fl_str_mv Evolutionary trajectories of new duplicated and putative de novo genes
title Evolutionary trajectories of new duplicated and putative de novo genes
spellingShingle Evolutionary trajectories of new duplicated and putative de novo genes
Montañés, José Carlos
De novo gene
Gene duplication
Gene family
Phylogeny
title_short Evolutionary trajectories of new duplicated and putative de novo genes
title_full Evolutionary trajectories of new duplicated and putative de novo genes
title_fullStr Evolutionary trajectories of new duplicated and putative de novo genes
title_full_unstemmed Evolutionary trajectories of new duplicated and putative de novo genes
title_sort Evolutionary trajectories of new duplicated and putative de novo genes
dc.creator.none.fl_str_mv Montañés, José Carlos
Huertas, Marta
Messeguer, Xavier
Albà Soler, Mar
author Montañés, José Carlos
author_facet Montañés, José Carlos
Huertas, Marta
Messeguer, Xavier
Albà Soler, Mar
author_role author
author2 Huertas, Marta
Messeguer, Xavier
Albà Soler, Mar
author2_role author
author
author
dc.subject.none.fl_str_mv De novo gene
Gene duplication
Gene family
Phylogeny
topic De novo gene
Gene duplication
Gene family
Phylogeny
description 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.
publishDate 2023
dc.date.none.fl_str_mv 2023
2024
2024
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10230/59645
http://dx.doi.org/10.1093/molbev/msad098
url http://hdl.handle.net/10230/59645
http://dx.doi.org/10.1093/molbev/msad098
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Mol Biol Evol. 2023 May 2;40(5):msad098
info:eu-repo/grantAgreement/EC/HE/101052538
info:eu-repo/grantAgreement/ES/2PE/PGC2018-094091-B-I00
info:eu-repo/grantAgreement/ES/3PE/PID2021-122726NB-I00
info:eu-repo/grantAgreement/ES/3PE/PID2021-122830OB-C43
dc.rights.none.fl_str_mv http://creativecommons.org/licenses/by/4.0/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Oxford University Press
publisher.none.fl_str_mv Oxford University Press
dc.source.none.fl_str_mv reponame:Repositorio Digital de la UPF
instname:Universitat Pompeu Fabra
instname_str Universitat Pompeu Fabra
reponame_str Repositorio Digital de la UPF
collection Repositorio Digital de la UPF
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