Whole genome duplication and transposable element proliferation drive genome expansion in corydoradinae catfishes
Autor(a) principal: | |
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Data de Publicação: | 2018 |
Outros Autores: | , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.1098/rspb.2017.2732 http://hdl.handle.net/11449/170776 |
Resumo: | Genome size varies significantly across eukaryotic taxa and the largest changes are typically driven by macro-mutations such as whole genome duplications (WGDs) and proliferation of repetitive elements. These two processes may affect the evolutionary potential of lineages by increasing genetic variation and changing gene expression. Here, we elucidate the evolutionary history and mechanisms underpinning genome size variation in a species-rich group of Neotropical catfishes (Corydoradinae) with extreme variation in genome size—0.6 to 4.4 pg per haploid cell. First, genome size was quantified in 65 species andmapped onto a novel fossil-calibrated phylogeny. Two evolutionaryshifts in genome sizewere identified across the tree—the first between 43 and 49 Ma (95% highest posterior density (HPD) 36.2-68.1 Ma) and the second at approximately 19 Ma (95% HPD 15.3-30.14 Ma). Second, restriction-siteassociated DNA (RAD) sequencing was used to identify potential WGD events and quantify transposable element (TE) abundance in different lineages. Evidence of two lineage-scale WGDs was identified across the phylogeny, the first event occurring between 54 and 66 Ma (95% HPD 42.56-99.5 Ma) and the second at 20-30 Ma (95% HPD 15.3-45 Ma) based on haplotype numbers per contig and between 35 and 44 Ma (95% HPD 30.29-64.51 Ma) and 20-30 Ma (95% HPD 15.3-45 Ma) based on SNP read ratios. TE abundance increased considerably in parallel with genome size, with a single TE-family (TC1-IS630- Pogo) showing several increases across the Corydoradinae, with the most recent at 20-30 Ma (95% HPD 15.3-45 Ma) and an older event at 35-44 Ma (95% HPD 30.29-64.51 Ma). We identified signals congruent with two WGD duplication events, as well as an increase in TE abundance across different lineages, making the Corydoradinae an excellent model system to study the effects ofWGD and TEs on genome and organismal evolution. |
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Whole genome duplication and transposable element proliferation drive genome expansion in corydoradinae catfishesCorydorasGenome size evolutionPolyploidyTransposable elementsWGDGenome size varies significantly across eukaryotic taxa and the largest changes are typically driven by macro-mutations such as whole genome duplications (WGDs) and proliferation of repetitive elements. These two processes may affect the evolutionary potential of lineages by increasing genetic variation and changing gene expression. Here, we elucidate the evolutionary history and mechanisms underpinning genome size variation in a species-rich group of Neotropical catfishes (Corydoradinae) with extreme variation in genome size—0.6 to 4.4 pg per haploid cell. First, genome size was quantified in 65 species andmapped onto a novel fossil-calibrated phylogeny. Two evolutionaryshifts in genome sizewere identified across the tree—the first between 43 and 49 Ma (95% highest posterior density (HPD) 36.2-68.1 Ma) and the second at approximately 19 Ma (95% HPD 15.3-30.14 Ma). Second, restriction-siteassociated DNA (RAD) sequencing was used to identify potential WGD events and quantify transposable element (TE) abundance in different lineages. Evidence of two lineage-scale WGDs was identified across the phylogeny, the first event occurring between 54 and 66 Ma (95% HPD 42.56-99.5 Ma) and the second at 20-30 Ma (95% HPD 15.3-45 Ma) based on haplotype numbers per contig and between 35 and 44 Ma (95% HPD 30.29-64.51 Ma) and 20-30 Ma (95% HPD 15.3-45 Ma) based on SNP read ratios. TE abundance increased considerably in parallel with genome size, with a single TE-family (TC1-IS630- Pogo) showing several increases across the Corydoradinae, with the most recent at 20-30 Ma (95% HPD 15.3-45 Ma) and an older event at 35-44 Ma (95% HPD 30.29-64.51 Ma). We identified signals congruent with two WGD duplication events, as well as an increase in TE abundance across different lineages, making the Corydoradinae an excellent model system to study the effects ofWGD and TEs on genome and organismal evolution.Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Natural Environment Research CouncilInstitute of Aquaculture University of StirlingMolecular Ecology and Fisheries Genetics Laboratory School of Biological Sciences Bangor University, Deiniol RoadDepartamento de Morfologia Instituto de Biociências/UNESP Rua Professor Doutor Antonio Celso Wagner Zanin, s/n818618-689School of Biological Sciences University of East AngliaWildlands Conservation Science, LLC PO Box 1846Department of Cell and Development Biology John Innes Centre Norwich Research Park, Colney LaneDepartamento de Morfologia Instituto de Biociências/UNESP Rua Professor Doutor Antonio Celso Wagner Zanin, s/n818618-689Natural Environment Research Council: NE/C001168/1Natural Environment Research Council: NE/F007205/1Natural Environment Research Council: NE/J500203/1University of StirlingBangor UniversityUniversidade Estadual Paulista (Unesp)University of East AngliaWildlands Conservation ScienceNorwich Research ParkMarburger, SarahAlexandrou, Markos A.Taggart, John B.Creer, SimonCarvalho, GaryOliveira, Claudio [UNESP]Taylor, Martin I.2018-12-11T16:52:22Z2018-12-11T16:52:22Z2018-02-14info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://dx.doi.org/10.1098/rspb.2017.2732Proceedings of the Royal Society B: Biological Sciences, v. 285, n. 1872, 2018.1471-29540962-8452http://hdl.handle.net/11449/17077610.1098/rspb.2017.27322-s2.0-850435866962-s2.0-85043586696.pdfScopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengProceedings of the Royal Society B: Biological Sciences2,8262,826info:eu-repo/semantics/openAccess2023-10-03T06:05:22Zoai:repositorio.unesp.br:11449/170776Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T13:54:45.748447Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Whole genome duplication and transposable element proliferation drive genome expansion in corydoradinae catfishes |
title |
Whole genome duplication and transposable element proliferation drive genome expansion in corydoradinae catfishes |
spellingShingle |
Whole genome duplication and transposable element proliferation drive genome expansion in corydoradinae catfishes Marburger, Sarah Corydoras Genome size evolution Polyploidy Transposable elements WGD |
title_short |
Whole genome duplication and transposable element proliferation drive genome expansion in corydoradinae catfishes |
title_full |
Whole genome duplication and transposable element proliferation drive genome expansion in corydoradinae catfishes |
title_fullStr |
Whole genome duplication and transposable element proliferation drive genome expansion in corydoradinae catfishes |
title_full_unstemmed |
Whole genome duplication and transposable element proliferation drive genome expansion in corydoradinae catfishes |
title_sort |
Whole genome duplication and transposable element proliferation drive genome expansion in corydoradinae catfishes |
author |
Marburger, Sarah |
author_facet |
Marburger, Sarah Alexandrou, Markos A. Taggart, John B. Creer, Simon Carvalho, Gary Oliveira, Claudio [UNESP] Taylor, Martin I. |
author_role |
author |
author2 |
Alexandrou, Markos A. Taggart, John B. Creer, Simon Carvalho, Gary Oliveira, Claudio [UNESP] Taylor, Martin I. |
author2_role |
author author author author author author |
dc.contributor.none.fl_str_mv |
University of Stirling Bangor University Universidade Estadual Paulista (Unesp) University of East Anglia Wildlands Conservation Science Norwich Research Park |
dc.contributor.author.fl_str_mv |
Marburger, Sarah Alexandrou, Markos A. Taggart, John B. Creer, Simon Carvalho, Gary Oliveira, Claudio [UNESP] Taylor, Martin I. |
dc.subject.por.fl_str_mv |
Corydoras Genome size evolution Polyploidy Transposable elements WGD |
topic |
Corydoras Genome size evolution Polyploidy Transposable elements WGD |
description |
Genome size varies significantly across eukaryotic taxa and the largest changes are typically driven by macro-mutations such as whole genome duplications (WGDs) and proliferation of repetitive elements. These two processes may affect the evolutionary potential of lineages by increasing genetic variation and changing gene expression. Here, we elucidate the evolutionary history and mechanisms underpinning genome size variation in a species-rich group of Neotropical catfishes (Corydoradinae) with extreme variation in genome size—0.6 to 4.4 pg per haploid cell. First, genome size was quantified in 65 species andmapped onto a novel fossil-calibrated phylogeny. Two evolutionaryshifts in genome sizewere identified across the tree—the first between 43 and 49 Ma (95% highest posterior density (HPD) 36.2-68.1 Ma) and the second at approximately 19 Ma (95% HPD 15.3-30.14 Ma). Second, restriction-siteassociated DNA (RAD) sequencing was used to identify potential WGD events and quantify transposable element (TE) abundance in different lineages. Evidence of two lineage-scale WGDs was identified across the phylogeny, the first event occurring between 54 and 66 Ma (95% HPD 42.56-99.5 Ma) and the second at 20-30 Ma (95% HPD 15.3-45 Ma) based on haplotype numbers per contig and between 35 and 44 Ma (95% HPD 30.29-64.51 Ma) and 20-30 Ma (95% HPD 15.3-45 Ma) based on SNP read ratios. TE abundance increased considerably in parallel with genome size, with a single TE-family (TC1-IS630- Pogo) showing several increases across the Corydoradinae, with the most recent at 20-30 Ma (95% HPD 15.3-45 Ma) and an older event at 35-44 Ma (95% HPD 30.29-64.51 Ma). We identified signals congruent with two WGD duplication events, as well as an increase in TE abundance across different lineages, making the Corydoradinae an excellent model system to study the effects ofWGD and TEs on genome and organismal evolution. |
publishDate |
2018 |
dc.date.none.fl_str_mv |
2018-12-11T16:52:22Z 2018-12-11T16:52:22Z 2018-02-14 |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://dx.doi.org/10.1098/rspb.2017.2732 Proceedings of the Royal Society B: Biological Sciences, v. 285, n. 1872, 2018. 1471-2954 0962-8452 http://hdl.handle.net/11449/170776 10.1098/rspb.2017.2732 2-s2.0-85043586696 2-s2.0-85043586696.pdf |
url |
http://dx.doi.org/10.1098/rspb.2017.2732 http://hdl.handle.net/11449/170776 |
identifier_str_mv |
Proceedings of the Royal Society B: Biological Sciences, v. 285, n. 1872, 2018. 1471-2954 0962-8452 10.1098/rspb.2017.2732 2-s2.0-85043586696 2-s2.0-85043586696.pdf |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Proceedings of the Royal Society B: Biological Sciences 2,826 2,826 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
application/pdf |
dc.source.none.fl_str_mv |
Scopus reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
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Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
institution |
UNESP |
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Repositório Institucional da UNESP |
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Repositório Institucional da UNESP |
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Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
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1808128289246543872 |