Table_4_Evolutionary Dynamics of the Repeatome Explains Contrasting Differences in Genome Sizes and Hybrid and Polyploid Origins of Grass Loliinae Lineages.XLSX

Repeat Explorer 2 comparative analysis. Repeat content data for phylogenetically analyzed clusters (repeat families) in each of the four evolutionary groups of Loliinae: (A) Loliinae; (B) broad-leaved (BL) Loliinae; (C) fine-leaved (FL) Loliinae; (D) Schedonorus.

Detalles Bibliográficos
Autores: Moreno Aguilar, María Fernanda, Inda, Luis A., Sánchez-Rodríguez, Aminael, Arnelas, Itziar, Catalán, Pilar
Tipo de recurso: conjunto de datos
Fecha de publicación:2022
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/331434
Acceso en línea:http://hdl.handle.net/10261/331434
Access Level:acceso abierto
Palabra clave:Diploidized paleo-allopolyploids
Genome size diversification
Festuca
Lolium
Phylogenetic signal
Repeatome
Transposable elements
5S loci
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spelling Table_4_Evolutionary Dynamics of the Repeatome Explains Contrasting Differences in Genome Sizes and Hybrid and Polyploid Origins of Grass Loliinae Lineages.XLSXMoreno Aguilar, María FernandaInda, Luis A.Sánchez-Rodríguez, AminaelArnelas, ItziarCatalán, PilarDiploidized paleo-allopolyploidsGenome size diversificationFestucaLoliumPhylogenetic signalRepeatomeTransposable elements5S lociRepeat Explorer 2 comparative analysis. Repeat content data for phylogenetically analyzed clusters (repeat families) in each of the four evolutionary groups of Loliinae: (A) Loliinae; (B) broad-leaved (BL) Loliinae; (C) fine-leaved (FL) Loliinae; (D) Schedonorus.The repeatome is composed of diverse families of repetitive DNA that keep signatures on the historical events that shaped the evolution of their hosting species. The cold seasonal Loliinae subtribe includes worldwide distributed taxa, some of which are the most important forage and lawn species (fescues and ray-grasses). The Loliinae are prone to hybridization and polyploidization. It has been observed a striking two-fold difference in genome size between the broad-leaved (BL) and fine-leaved (FL) Loliinae diploids and a general trend of genome reduction of some high polyploids. We have used genome skimming data to uncover the composition, abundance, and potential phylogenetic signal of repetitive elements across 47 representatives of the main Loliinae lineages. Independent and comparative analyses of repetitive sequences and of 5S rDNA loci were performed for all taxa under study and for four evolutionary Loliinae groups [Loliinae, Broad-leaved (BL), Fine-leaved (FL), and Schedonorus lineages]. Our data showed that the proportion of the genome covered by the repeatome in the Loliinae species was relatively high (average ∼ 51.8%), ranging from high percentages in some diploids (68.7%) to low percentages in some high-polyploids (30.7%), and that changes in their genome sizes were likely caused by gains or losses in their repeat elements. Ty3-gypsy Retand and Ty1-copia Angela retrotransposons were the most frequent repeat families in the Loliinae although the relatively more conservative Angela repeats presented the highest correlation of repeat content with genome size variation and the highest phylogenetic signal of the whole repeatome. By contrast, Athila retrotransposons presented evidence of recent proliferations almost exclusively in the Lolium clade. The repeatome evolutionary networks showed an overall topological congruence with the nuclear 35S rDNA phylogeny and a geographic-based structure for some lineages. The evolution of the Loliinae repeatome suggests a plausible scenario of recurrent allopolyploidizations followed by diploidizations that generated the large genome sizes of BL diploids as well as large genomic rearrangements in highly hybridogenous lineages that caused massive repeatome and genome contractions in the Schedonorus and Aulaxyper polyploids. Our study has contributed to disentangling the impact of the repeatome dynamics on the genome diversification and evolution of the Loliinae grasses.Peer reviewedFigshareConsejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]202320232022info:eu-repo/semantics/datasethttp://purl.org/coar/resource_type/c_ddb1application/vnd.ms-excelhttp://hdl.handle.net/10261/331434reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)InglésMoreno Aguilar, María Fernanda; Inda, Luis A.; Sánchez-Rodríguez, Aminael; Arnelas, Itziar; Catalán, Pilar. Evolutionary Dynamics of the Repeatome Explains Contrasting Differences in Genome Sizes and Hybrid and Polyploid Origins of Grass Loliinae Lineages. https://doi.org/10.3389/fpls.2022.901733. http://hdl.handle.net/10261/296333https://doi.org/10.3389/fpls.2022.901733.s005Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/3314342026-05-22T06:33:51Z
dc.title.none.fl_str_mv Table_4_Evolutionary Dynamics of the Repeatome Explains Contrasting Differences in Genome Sizes and Hybrid and Polyploid Origins of Grass Loliinae Lineages.XLSX
title Table_4_Evolutionary Dynamics of the Repeatome Explains Contrasting Differences in Genome Sizes and Hybrid and Polyploid Origins of Grass Loliinae Lineages.XLSX
spellingShingle Table_4_Evolutionary Dynamics of the Repeatome Explains Contrasting Differences in Genome Sizes and Hybrid and Polyploid Origins of Grass Loliinae Lineages.XLSX
Moreno Aguilar, María Fernanda
Diploidized paleo-allopolyploids
Genome size diversification
Festuca
Lolium
Phylogenetic signal
Repeatome
Transposable elements
5S loci
title_short Table_4_Evolutionary Dynamics of the Repeatome Explains Contrasting Differences in Genome Sizes and Hybrid and Polyploid Origins of Grass Loliinae Lineages.XLSX
title_full Table_4_Evolutionary Dynamics of the Repeatome Explains Contrasting Differences in Genome Sizes and Hybrid and Polyploid Origins of Grass Loliinae Lineages.XLSX
title_fullStr Table_4_Evolutionary Dynamics of the Repeatome Explains Contrasting Differences in Genome Sizes and Hybrid and Polyploid Origins of Grass Loliinae Lineages.XLSX
title_full_unstemmed Table_4_Evolutionary Dynamics of the Repeatome Explains Contrasting Differences in Genome Sizes and Hybrid and Polyploid Origins of Grass Loliinae Lineages.XLSX
title_sort Table_4_Evolutionary Dynamics of the Repeatome Explains Contrasting Differences in Genome Sizes and Hybrid and Polyploid Origins of Grass Loliinae Lineages.XLSX
dc.creator.none.fl_str_mv Moreno Aguilar, María Fernanda
Inda, Luis A.
Sánchez-Rodríguez, Aminael
Arnelas, Itziar
Catalán, Pilar
author Moreno Aguilar, María Fernanda
author_facet Moreno Aguilar, María Fernanda
Inda, Luis A.
Sánchez-Rodríguez, Aminael
Arnelas, Itziar
Catalán, Pilar
author_role author
author2 Inda, Luis A.
Sánchez-Rodríguez, Aminael
Arnelas, Itziar
Catalán, Pilar
author2_role author
author
author
author
dc.contributor.none.fl_str_mv Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv Diploidized paleo-allopolyploids
Genome size diversification
Festuca
Lolium
Phylogenetic signal
Repeatome
Transposable elements
5S loci
topic Diploidized paleo-allopolyploids
Genome size diversification
Festuca
Lolium
Phylogenetic signal
Repeatome
Transposable elements
5S loci
description Repeat Explorer 2 comparative analysis. Repeat content data for phylogenetically analyzed clusters (repeat families) in each of the four evolutionary groups of Loliinae: (A) Loliinae; (B) broad-leaved (BL) Loliinae; (C) fine-leaved (FL) Loliinae; (D) Schedonorus.
publishDate 2022
dc.date.none.fl_str_mv 2022
2023
2023
dc.type.none.fl_str_mv info:eu-repo/semantics/dataset
http://purl.org/coar/resource_type/c_ddb1
format dataset
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/331434
url http://hdl.handle.net/10261/331434
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Moreno Aguilar, María Fernanda; Inda, Luis A.; Sánchez-Rodríguez, Aminael; Arnelas, Itziar; Catalán, Pilar. Evolutionary Dynamics of the Repeatome Explains Contrasting Differences in Genome Sizes and Hybrid and Polyploid Origins of Grass Loliinae Lineages. https://doi.org/10.3389/fpls.2022.901733. http://hdl.handle.net/10261/296333
https://doi.org/10.3389/fpls.2022.901733.s005
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/vnd.ms-excel
dc.publisher.none.fl_str_mv Figshare
publisher.none.fl_str_mv Figshare
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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score 15,81155

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