Intragenomic rDNA variation - the product of concerted evolution, mutation, or something in between?

The classical model of concerted evolution states that hundreds to thousands of ribosomal DNA (rDNA) units undergo homogenization, making the multiple copies of the individual units more uniform across the genome than would be expected given mutation frequencies and gene redundancy. While the univer...

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Autores: Wang, Wencai, Zhang, Xianzhi, Garcia, Sònia, Leitch, Andrew R., Kovařík, Aleš
Formato: artículo
Estado:Versión publicada
Fecha de publicación:2023
País:España
Recursos:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/337143
Acesso em linha:http://hdl.handle.net/10261/337143
Access Level:acceso abierto
Palavra-chave:Evolutionary biology
Evolutionary genetics
Plant evolution
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spelling Intragenomic rDNA variation - the product of concerted evolution, mutation, or something in between?Wang, WencaiZhang, XianzhiGarcia, SòniaLeitch, Andrew R.Kovařík, AlešEvolutionary biologyEvolutionary geneticsPlant evolutionThe classical model of concerted evolution states that hundreds to thousands of ribosomal DNA (rDNA) units undergo homogenization, making the multiple copies of the individual units more uniform across the genome than would be expected given mutation frequencies and gene redundancy. While the universality of this over 50-year-old model has been confirmed in a range of organisms, advanced high throughput sequencing techniques have also revealed that rDNA homogenization in many organisms is partial and, in rare cases, even apparently failing. The potential underpinning processes leading to unexpected intragenomic variation have been discussed in a number of studies, but a comprehensive understanding remains to be determined. In this work, we summarize information on variation or polymorphisms in rDNAs across a wide range of taxa amongst animals, fungi, plants, and protists. We discuss the definition and description of concerted evolution and describe whether incomplete concerted evolution of rDNAs predominantly affects coding or non-coding regions of rDNA units and if it leads to the formation of pseudogenes or not. We also discuss the factors contributing to rDNA variation, such as interspecific hybridization, meiotic cycles, rDNA expression status, genome size, and the activity of effector genes involved in genetic recombination, epigenetic modifications, and DNA editing. Finally, we argue that a combination of approaches is needed to target genetic and epigenetic phenomena influencing incomplete concerted evolution, to give a comprehensive understanding of the evolution and functional consequences of intragenomic variation in rDNA.We thank the Xinglin Fund of Guangzhou University of Chinese Medicine (A1-AFD018191Z0145), Czech Science Foundation (22–16826S), Innovation Project for Forestry Science and Technology in Guangdong (2021KJCX015), as well as the Agencia Estatal de Investigación (PID2020-119163GB-I00 funded by MCIN/AEI/10.13039/501100011033) for support.Abstract Introduction Intragenomic rDNA variations occur in divergent genera across the eukaryote tree-of-life Factors leading to incomplete concerted evolution of rDNAs Genetic and epigenetic barriers interfering with rDNA homogenization processes Conclusions and perspectives Change history References Acknowledgements Author information Ethics declarations Additional information Supplementary information Rights and permissions About this articlePeer reviewedSpringer NatureGuangzhou University of Chinese MedicineCzech Science FoundationMinisterio de Ciencia e Innovación (España)Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]2023202320232023info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionhttp://hdl.handle.net/10261/337143reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Inglés#PLACEHOLDER_PARENT_METADATA_VALUE#info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PID2020-119163GB-I00http://dx.doi.org/10.1038/s41437-023-00634-5Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/3371432026-05-22T06:33:51Z
dc.title.none.fl_str_mv Intragenomic rDNA variation - the product of concerted evolution, mutation, or something in between?
title Intragenomic rDNA variation - the product of concerted evolution, mutation, or something in between?
spellingShingle Intragenomic rDNA variation - the product of concerted evolution, mutation, or something in between?
Wang, Wencai
Evolutionary biology
Evolutionary genetics
Plant evolution
title_short Intragenomic rDNA variation - the product of concerted evolution, mutation, or something in between?
title_full Intragenomic rDNA variation - the product of concerted evolution, mutation, or something in between?
title_fullStr Intragenomic rDNA variation - the product of concerted evolution, mutation, or something in between?
title_full_unstemmed Intragenomic rDNA variation - the product of concerted evolution, mutation, or something in between?
title_sort Intragenomic rDNA variation - the product of concerted evolution, mutation, or something in between?
dc.creator.none.fl_str_mv Wang, Wencai
Zhang, Xianzhi
Garcia, Sònia
Leitch, Andrew R.
Kovařík, Aleš
author Wang, Wencai
author_facet Wang, Wencai
Zhang, Xianzhi
Garcia, Sònia
Leitch, Andrew R.
Kovařík, Aleš
author_role author
author2 Zhang, Xianzhi
Garcia, Sònia
Leitch, Andrew R.
Kovařík, Aleš
author2_role author
author
author
author
dc.contributor.none.fl_str_mv Guangzhou University of Chinese Medicine
Czech Science Foundation
Ministerio de Ciencia e Innovación (España)
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv Evolutionary biology
Evolutionary genetics
Plant evolution
topic Evolutionary biology
Evolutionary genetics
Plant evolution
description The classical model of concerted evolution states that hundreds to thousands of ribosomal DNA (rDNA) units undergo homogenization, making the multiple copies of the individual units more uniform across the genome than would be expected given mutation frequencies and gene redundancy. While the universality of this over 50-year-old model has been confirmed in a range of organisms, advanced high throughput sequencing techniques have also revealed that rDNA homogenization in many organisms is partial and, in rare cases, even apparently failing. The potential underpinning processes leading to unexpected intragenomic variation have been discussed in a number of studies, but a comprehensive understanding remains to be determined. In this work, we summarize information on variation or polymorphisms in rDNAs across a wide range of taxa amongst animals, fungi, plants, and protists. We discuss the definition and description of concerted evolution and describe whether incomplete concerted evolution of rDNAs predominantly affects coding or non-coding regions of rDNA units and if it leads to the formation of pseudogenes or not. We also discuss the factors contributing to rDNA variation, such as interspecific hybridization, meiotic cycles, rDNA expression status, genome size, and the activity of effector genes involved in genetic recombination, epigenetic modifications, and DNA editing. Finally, we argue that a combination of approaches is needed to target genetic and epigenetic phenomena influencing incomplete concerted evolution, to give a comprehensive understanding of the evolution and functional consequences of intragenomic variation in rDNA.
publishDate 2023
dc.date.none.fl_str_mv 2023
2023
2023
2023
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Publisher's version
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/337143
url http://hdl.handle.net/10261/337143
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv #PLACEHOLDER_PARENT_METADATA_VALUE#
info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PID2020-119163GB-I00
http://dx.doi.org/10.1038/s41437-023-00634-5
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Springer Nature
publisher.none.fl_str_mv Springer Nature
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
repository.name.fl_str_mv
repository.mail.fl_str_mv
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