Comparative repeatome analysis reveals new evidence on genome evolution in wild diploid Arachis (Fabaceae) species

Autores
Samoluk, Sergio Sebastián; Vaio, Magdalena; Ortiz, Alejandra Marcela; Chalup, Laura María Isabel; Robledo Dobladez, Germán Ariel; Bertioli, David J.; Seijo, José Guillermo
Año de publicación
2022
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
The South American genus Arachis (Fabaceae) comprises 83 species organized in nine taxonomic sections. Among them,section Arachis is characterized by species with a wide genome and karyotype diversity. Such diversity is determined mainlyby the amount and composition of repetitive DNA. Here we performed computational analysis on low coverage genomesequencing to infer the dynamics of changes in major repeat families that led to the differentiation of genomes in diploidspecies (x = 10) of genus Arachis, focusing on section Arachis. Estimated repeat content ranged from 62.50 to 71.68% ofthe genomes. Species with different genome composition tended to have different landscapes of repeated sequences. Athilafamily retrotransposons were the most abundant and variable lineage among Arachis repeatomes, with peaks of transpositionalactivity inferred at different times in the evolution of the species. Satellite DNAs (satDNAs) were less abundant, butdifferentially represented among species. High rates of evolution of an AT-rich superfamily of satDNAs led to the differentialaccumulation of heterochromatin in Arachis genomes. The relationship between genome size variation and the repetitivecontent is complex. However, largest genomes presented a higher accumulation of LTR elements and lower contents ofsatDNAs. In contrast, species with lowest genome sizes tended to accumulate satDNAs in detriment of LTR elements. Phylogeneticanalysis based on repetitive DNA supported the genome arrangement of section Arachis. Altogether, our resultsprovide the most comprehensive picture on the repeatome dynamics that led to the genome differentiation of Arachis species.
Fil: Samoluk, Sergio Sebastián. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Botánica del Nordeste. Universidad Nacional del Nordeste. Facultad de Ciencias Agrarias. Instituto de Botánica del Nordeste; Argentina
Fil: Vaio, Magdalena. Universidad de la Republica; Uruguay
Fil: Ortiz, Alejandra Marcela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Botánica del Nordeste. Universidad Nacional del Nordeste. Facultad de Ciencias Agrarias. Instituto de Botánica del Nordeste; Argentina
Fil: Chalup, Laura María Isabel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Botánica del Nordeste. Universidad Nacional del Nordeste. Facultad de Ciencias Agrarias. Instituto de Botánica del Nordeste; Argentina
Fil: Robledo Dobladez, Germán Ariel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Botánica del Nordeste. Universidad Nacional del Nordeste. Facultad de Ciencias Agrarias. Instituto de Botánica del Nordeste; Argentina
Fil: Bertioli, David J.. University of Georgia; Estados Unidos
Fil: Seijo, José Guillermo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Botánica del Nordeste. Universidad Nacional del Nordeste. Facultad de Ciencias Agrarias. Instituto de Botánica del Nordeste; Argentina
Materia
ARACHIS SPECIES
ATHILA RETROELEMENTS
GENOME DIFFERENTIATION
GENOME SIZE VARIATION
SATELLITE DNA
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/215137
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/215137
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Comparative repeatome analysis reveals new evidence on genome evolution in wild diploid Arachis (Fabaceae) speciesSamoluk, Sergio SebastiánVaio, MagdalenaOrtiz, Alejandra MarcelaChalup, Laura María IsabelRobledo Dobladez, Germán ArielBertioli, David J.Seijo, José GuillermoARACHIS SPECIESATHILA RETROELEMENTSGENOME DIFFERENTIATIONGENOME SIZE VARIATIONSATELLITE DNAhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1The South American genus Arachis (Fabaceae) comprises 83 species organized in nine taxonomic sections. Among them,section Arachis is characterized by species with a wide genome and karyotype diversity. Such diversity is determined mainlyby the amount and composition of repetitive DNA. Here we performed computational analysis on low coverage genomesequencing to infer the dynamics of changes in major repeat families that led to the differentiation of genomes in diploidspecies (x = 10) of genus Arachis, focusing on section Arachis. Estimated repeat content ranged from 62.50 to 71.68% ofthe genomes. Species with different genome composition tended to have different landscapes of repeated sequences. Athilafamily retrotransposons were the most abundant and variable lineage among Arachis repeatomes, with peaks of transpositionalactivity inferred at different times in the evolution of the species. Satellite DNAs (satDNAs) were less abundant, butdifferentially represented among species. High rates of evolution of an AT-rich superfamily of satDNAs led to the differentialaccumulation of heterochromatin in Arachis genomes. The relationship between genome size variation and the repetitivecontent is complex. However, largest genomes presented a higher accumulation of LTR elements and lower contents ofsatDNAs. In contrast, species with lowest genome sizes tended to accumulate satDNAs in detriment of LTR elements. Phylogeneticanalysis based on repetitive DNA supported the genome arrangement of section Arachis. Altogether, our resultsprovide the most comprehensive picture on the repeatome dynamics that led to the genome differentiation of Arachis species.Fil: Samoluk, Sergio Sebastián. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Botánica del Nordeste. Universidad Nacional del Nordeste. Facultad de Ciencias Agrarias. Instituto de Botánica del Nordeste; ArgentinaFil: Vaio, Magdalena. Universidad de la Republica; UruguayFil: Ortiz, Alejandra Marcela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Botánica del Nordeste. Universidad Nacional del Nordeste. Facultad de Ciencias Agrarias. Instituto de Botánica del Nordeste; ArgentinaFil: Chalup, Laura María Isabel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Botánica del Nordeste. Universidad Nacional del Nordeste. Facultad de Ciencias Agrarias. Instituto de Botánica del Nordeste; ArgentinaFil: Robledo Dobladez, Germán Ariel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Botánica del Nordeste. Universidad Nacional del Nordeste. Facultad de Ciencias Agrarias. Instituto de Botánica del Nordeste; ArgentinaFil: Bertioli, David J.. University of Georgia; Estados UnidosFil: Seijo, José Guillermo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Botánica del Nordeste. Universidad Nacional del Nordeste. Facultad de Ciencias Agrarias. Instituto de Botánica del Nordeste; ArgentinaSpringer2022-07info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfapplication/pdfapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/215137Samoluk, Sergio Sebastián; Vaio, Magdalena; Ortiz, Alejandra Marcela; Chalup, Laura María Isabel; Robledo Dobladez, Germán Ariel; et al.; Comparative repeatome analysis reveals new evidence on genome evolution in wild diploid Arachis (Fabaceae) species; Springer; Planta; 256; 3; 7-2022; 1-180032-0935CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://link.springer.com/article/10.1007/s00425-022-03961-9info:eu-repo/semantics/altIdentifier/doi/10.1007/s00425-022-03961-9info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-10-15T14:24:41Zoai:ri.conicet.gov.ar:11336/215137instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-10-15 14:24:41.502CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Comparative repeatome analysis reveals new evidence on genome evolution in wild diploid Arachis (Fabaceae) species
title Comparative repeatome analysis reveals new evidence on genome evolution in wild diploid Arachis (Fabaceae) species
spellingShingle Comparative repeatome analysis reveals new evidence on genome evolution in wild diploid Arachis (Fabaceae) species
Samoluk, Sergio Sebastián
ARACHIS SPECIES
ATHILA RETROELEMENTS
GENOME DIFFERENTIATION
GENOME SIZE VARIATION
SATELLITE DNA
title_short Comparative repeatome analysis reveals new evidence on genome evolution in wild diploid Arachis (Fabaceae) species
title_full Comparative repeatome analysis reveals new evidence on genome evolution in wild diploid Arachis (Fabaceae) species
title_fullStr Comparative repeatome analysis reveals new evidence on genome evolution in wild diploid Arachis (Fabaceae) species
title_full_unstemmed Comparative repeatome analysis reveals new evidence on genome evolution in wild diploid Arachis (Fabaceae) species
title_sort Comparative repeatome analysis reveals new evidence on genome evolution in wild diploid Arachis (Fabaceae) species
dc.creator.none.fl_str_mv Samoluk, Sergio Sebastián
Vaio, Magdalena
Ortiz, Alejandra Marcela
Chalup, Laura María Isabel
Robledo Dobladez, Germán Ariel
Bertioli, David J.
Seijo, José Guillermo
author Samoluk, Sergio Sebastián
author_facet Samoluk, Sergio Sebastián
Vaio, Magdalena
Ortiz, Alejandra Marcela
Chalup, Laura María Isabel
Robledo Dobladez, Germán Ariel
Bertioli, David J.
Seijo, José Guillermo
author_role author
author2 Vaio, Magdalena
Ortiz, Alejandra Marcela
Chalup, Laura María Isabel
Robledo Dobladez, Germán Ariel
Bertioli, David J.
Seijo, José Guillermo
author2_role author
author
author
author
author
author
dc.subject.none.fl_str_mv ARACHIS SPECIES
ATHILA RETROELEMENTS
GENOME DIFFERENTIATION
GENOME SIZE VARIATION
SATELLITE DNA
topic ARACHIS SPECIES
ATHILA RETROELEMENTS
GENOME DIFFERENTIATION
GENOME SIZE VARIATION
SATELLITE DNA
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv The South American genus Arachis (Fabaceae) comprises 83 species organized in nine taxonomic sections. Among them,section Arachis is characterized by species with a wide genome and karyotype diversity. Such diversity is determined mainlyby the amount and composition of repetitive DNA. Here we performed computational analysis on low coverage genomesequencing to infer the dynamics of changes in major repeat families that led to the differentiation of genomes in diploidspecies (x = 10) of genus Arachis, focusing on section Arachis. Estimated repeat content ranged from 62.50 to 71.68% ofthe genomes. Species with different genome composition tended to have different landscapes of repeated sequences. Athilafamily retrotransposons were the most abundant and variable lineage among Arachis repeatomes, with peaks of transpositionalactivity inferred at different times in the evolution of the species. Satellite DNAs (satDNAs) were less abundant, butdifferentially represented among species. High rates of evolution of an AT-rich superfamily of satDNAs led to the differentialaccumulation of heterochromatin in Arachis genomes. The relationship between genome size variation and the repetitivecontent is complex. However, largest genomes presented a higher accumulation of LTR elements and lower contents ofsatDNAs. In contrast, species with lowest genome sizes tended to accumulate satDNAs in detriment of LTR elements. Phylogeneticanalysis based on repetitive DNA supported the genome arrangement of section Arachis. Altogether, our resultsprovide the most comprehensive picture on the repeatome dynamics that led to the genome differentiation of Arachis species.
Fil: Samoluk, Sergio Sebastián. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Botánica del Nordeste. Universidad Nacional del Nordeste. Facultad de Ciencias Agrarias. Instituto de Botánica del Nordeste; Argentina
Fil: Vaio, Magdalena. Universidad de la Republica; Uruguay
Fil: Ortiz, Alejandra Marcela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Botánica del Nordeste. Universidad Nacional del Nordeste. Facultad de Ciencias Agrarias. Instituto de Botánica del Nordeste; Argentina
Fil: Chalup, Laura María Isabel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Botánica del Nordeste. Universidad Nacional del Nordeste. Facultad de Ciencias Agrarias. Instituto de Botánica del Nordeste; Argentina
Fil: Robledo Dobladez, Germán Ariel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Botánica del Nordeste. Universidad Nacional del Nordeste. Facultad de Ciencias Agrarias. Instituto de Botánica del Nordeste; Argentina
Fil: Bertioli, David J.. University of Georgia; Estados Unidos
Fil: Seijo, José Guillermo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Botánica del Nordeste. Universidad Nacional del Nordeste. Facultad de Ciencias Agrarias. Instituto de Botánica del Nordeste; Argentina
description The South American genus Arachis (Fabaceae) comprises 83 species organized in nine taxonomic sections. Among them,section Arachis is characterized by species with a wide genome and karyotype diversity. Such diversity is determined mainlyby the amount and composition of repetitive DNA. Here we performed computational analysis on low coverage genomesequencing to infer the dynamics of changes in major repeat families that led to the differentiation of genomes in diploidspecies (x = 10) of genus Arachis, focusing on section Arachis. Estimated repeat content ranged from 62.50 to 71.68% ofthe genomes. Species with different genome composition tended to have different landscapes of repeated sequences. Athilafamily retrotransposons were the most abundant and variable lineage among Arachis repeatomes, with peaks of transpositionalactivity inferred at different times in the evolution of the species. Satellite DNAs (satDNAs) were less abundant, butdifferentially represented among species. High rates of evolution of an AT-rich superfamily of satDNAs led to the differentialaccumulation of heterochromatin in Arachis genomes. The relationship between genome size variation and the repetitivecontent is complex. However, largest genomes presented a higher accumulation of LTR elements and lower contents ofsatDNAs. In contrast, species with lowest genome sizes tended to accumulate satDNAs in detriment of LTR elements. Phylogeneticanalysis based on repetitive DNA supported the genome arrangement of section Arachis. Altogether, our resultsprovide the most comprehensive picture on the repeatome dynamics that led to the genome differentiation of Arachis species.
publishDate 2022
dc.date.none.fl_str_mv 2022-07
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/215137
Samoluk, Sergio Sebastián; Vaio, Magdalena; Ortiz, Alejandra Marcela; Chalup, Laura María Isabel; Robledo Dobladez, Germán Ariel; et al.; Comparative repeatome analysis reveals new evidence on genome evolution in wild diploid Arachis (Fabaceae) species; Springer; Planta; 256; 3; 7-2022; 1-18
0032-0935
CONICET Digital
CONICET
url http://hdl.handle.net/11336/215137
identifier_str_mv Samoluk, Sergio Sebastián; Vaio, Magdalena; Ortiz, Alejandra Marcela; Chalup, Laura María Isabel; Robledo Dobladez, Germán Ariel; et al.; Comparative repeatome analysis reveals new evidence on genome evolution in wild diploid Arachis (Fabaceae) species; Springer; Planta; 256; 3; 7-2022; 1-18
0032-0935
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
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info:eu-repo/semantics/altIdentifier/doi/10.1007/s00425-022-03961-9
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
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eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
application/pdf
application/pdf
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dc.publisher.none.fl_str_mv Springer
publisher.none.fl_str_mv Springer
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
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instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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