Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation

Autores
Willing, Eva Maria; Rawat, Vimal; Mandáková, Terezie; Maumus, Florian; James, Geo Velikkakam; Nordström, Karl J. V.; Becker, Claude; Warthmann, Norman; Chica, Claudia; Szarzynska, Bogna; Zytnicki, Matthias; Albani, Maria C.; Kiefer, Christiane; Bergonzi, Sara; Castaings, Loren; Mateos, Julieta Lisa; Berns, Markus C.; Bujdoso, Nora; Piofczyk, Thomas; Roudier, François; Carbonero, Pilar; Paz Ares, Javier; Davis, Seth J.; Pecinka, Ales; Quesneville, Hadi; Colot, Vincent; Lysak, Martin A.; Weigel, Detlef; Coupland, George; Schneeberger, Korbinian
Año de publicación
2015
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Despite evolutionary conserved mechanisms to silence transposable element activity, there are drastic differences in the abundance of transposable elements even among closely related plant species. We conducted a de novo assembly for the 375 Mb genome of the perennial model plant, Arabis alpina. Analysing this genome revealed long-lasting and recent transposable element activity predominately driven by Gypsy long terminal repeat retrotransposons, which extended the low-recombining pericentromeres and transformed large formerly euchromatic regions into repeat-rich pericentromeric regions. This reduced capacity for long terminal repeat retrotransposon silencing and removal in A. alpina co-occurs with unexpectedly low levels of DNA methylation. Most remarkably, the striking reduction of symmetrical CG and CHG methylation suggests weakened DNA methylation maintenance in A. alpina compared with Arabidopsis thaliana. Phylogenetic analyses indicate a highly dynamic evolution of some components of methylation maintenance machinery that might be related to the unique methylation in A. alpina.
Fil: Willing, Eva Maria. Max Planck Institute for Plant Breeding Research; Alemania
Fil: Rawat, Vimal. Central European Institute of Technology; República Checa
Fil: Mandáková, Terezie. Central European Institute of Technology; República Checa
Fil: Maumus, Florian. INRA. Research Unit in Genomics; Francia
Fil: James, Geo Velikkakam. Max Planck Institute for Plant Breeding Research; Alemania
Fil: Nordström, Karl J. V.. Max Planck Institute for Plant Breeding Research; Alemania
Fil: Becker, Claude. Max Planck Institute for Developmental Biology; Alemania
Fil: Warthmann, Norman. Max Planck Institute for Developmental Biology; Alemania. The Australian National University; Australia
Fil: Chica, Claudia. Centre National de la Recherche Scientifique; Francia
Fil: Szarzynska, Bogna. Centre National de la Recherche Scientifique; Francia
Fil: Zytnicki, Matthias. Max Planck Institute for Developmental Biology; Alemania
Fil: Albani, Maria C.. Max Planck Institute for Plant Breeding Research; Alemania
Fil: Kiefer, Christiane. Max Planck Institute for Plant Breeding Research; Alemania
Fil: Bergonzi, Sara. Max Planck Institute for Plant Breeding Research; Alemania
Fil: Castaings, Loren. Max Planck Institute for Plant Breeding Research; Alemania
Fil: Mateos, Julieta Lisa. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentina. Max Planck Institute for Plant Breeding Research; Alemania
Fil: Berns, Markus C.. Max Planck Institute for Plant Breeding Research; Alemania
Fil: Bujdoso, Nora. Max Planck Institute for Plant Breeding Research; Alemania
Fil: Piofczyk, Thomas. Max Planck Institute for Plant Breeding Research; Alemania
Fil: Roudier, François. Centre National de la Recherche Scientifique; Francia
Fil: Carbonero, Pilar. Universidad Politécnica de Madrid; España
Fil: Paz Ares, Javier. Consejo Superior de Investigaciones Cientificas; España
Fil: Davis, Seth J.. Max Planck Institute for Plant Breeding Research; Alemania
Fil: Pecinka, Ales. Max Planck Institute for Plant Breeding Research; Alemania
Fil: Quesneville, Hadi. INRA. Research Unit in Genomics; Francia
Fil: Colot, Vincent. Centre National de la Recherche Scientifique; Francia
Fil: Lysak, Martin A.. Central European Institute of Technology; República Checa
Fil: Weigel, Detlef. Max Planck Institute for Developmental Biology; Alemania
Fil: Coupland, George. Max Planck Institute for Plant Breeding Research; Alemania
Fil: Schneeberger, Korbinian. Max Planck Institute for Plant Breeding Research; Alemania
Materia
Arabis Alpina
Genome
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:11336/18083

id CONICETDig_4cc2a3746d8b8c84af38453e4fbd7c58
oai_identifier_str oai:ri.conicet.gov.ar:11336/18083
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylationWilling, Eva MariaRawat, VimalMandáková, TerezieMaumus, FlorianJames, Geo VelikkakamNordström, Karl J. V.Becker, ClaudeWarthmann, NormanChica, ClaudiaSzarzynska, BognaZytnicki, MatthiasAlbani, Maria C.Kiefer, ChristianeBergonzi, SaraCastaings, LorenMateos, Julieta LisaBerns, Markus C.Bujdoso, NoraPiofczyk, ThomasRoudier, FrançoisCarbonero, PilarPaz Ares, JavierDavis, Seth J.Pecinka, AlesQuesneville, HadiColot, VincentLysak, Martin A.Weigel, DetlefCoupland, GeorgeSchneeberger, KorbinianArabis AlpinaGenomehttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Despite evolutionary conserved mechanisms to silence transposable element activity, there are drastic differences in the abundance of transposable elements even among closely related plant species. We conducted a de novo assembly for the 375 Mb genome of the perennial model plant, Arabis alpina. Analysing this genome revealed long-lasting and recent transposable element activity predominately driven by Gypsy long terminal repeat retrotransposons, which extended the low-recombining pericentromeres and transformed large formerly euchromatic regions into repeat-rich pericentromeric regions. This reduced capacity for long terminal repeat retrotransposon silencing and removal in A. alpina co-occurs with unexpectedly low levels of DNA methylation. Most remarkably, the striking reduction of symmetrical CG and CHG methylation suggests weakened DNA methylation maintenance in A. alpina compared with Arabidopsis thaliana. Phylogenetic analyses indicate a highly dynamic evolution of some components of methylation maintenance machinery that might be related to the unique methylation in A. alpina.Fil: Willing, Eva Maria. Max Planck Institute for Plant Breeding Research; AlemaniaFil: Rawat, Vimal. Central European Institute of Technology; República ChecaFil: Mandáková, Terezie. Central European Institute of Technology; República ChecaFil: Maumus, Florian. INRA. Research Unit in Genomics; FranciaFil: James, Geo Velikkakam. Max Planck Institute for Plant Breeding Research; AlemaniaFil: Nordström, Karl J. V.. Max Planck Institute for Plant Breeding Research; AlemaniaFil: Becker, Claude. Max Planck Institute for Developmental Biology; AlemaniaFil: Warthmann, Norman. Max Planck Institute for Developmental Biology; Alemania. The Australian National University; AustraliaFil: Chica, Claudia. Centre National de la Recherche Scientifique; FranciaFil: Szarzynska, Bogna. Centre National de la Recherche Scientifique; FranciaFil: Zytnicki, Matthias. Max Planck Institute for Developmental Biology; AlemaniaFil: Albani, Maria C.. Max Planck Institute for Plant Breeding Research; AlemaniaFil: Kiefer, Christiane. Max Planck Institute for Plant Breeding Research; AlemaniaFil: Bergonzi, Sara. Max Planck Institute for Plant Breeding Research; AlemaniaFil: Castaings, Loren. Max Planck Institute for Plant Breeding Research; AlemaniaFil: Mateos, Julieta Lisa. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentina. Max Planck Institute for Plant Breeding Research; AlemaniaFil: Berns, Markus C.. Max Planck Institute for Plant Breeding Research; AlemaniaFil: Bujdoso, Nora. Max Planck Institute for Plant Breeding Research; AlemaniaFil: Piofczyk, Thomas. Max Planck Institute for Plant Breeding Research; AlemaniaFil: Roudier, François. Centre National de la Recherche Scientifique; FranciaFil: Carbonero, Pilar. Universidad Politécnica de Madrid; EspañaFil: Paz Ares, Javier. Consejo Superior de Investigaciones Cientificas; EspañaFil: Davis, Seth J.. Max Planck Institute for Plant Breeding Research; AlemaniaFil: Pecinka, Ales. Max Planck Institute for Plant Breeding Research; AlemaniaFil: Quesneville, Hadi. INRA. Research Unit in Genomics; FranciaFil: Colot, Vincent. Centre National de la Recherche Scientifique; FranciaFil: Lysak, Martin A.. Central European Institute of Technology; República ChecaFil: Weigel, Detlef. Max Planck Institute for Developmental Biology; AlemaniaFil: Coupland, George. Max Planck Institute for Plant Breeding Research; AlemaniaFil: Schneeberger, Korbinian. Max Planck Institute for Plant Breeding Research; AlemaniaNature Publishing Group2015-02info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/18083Willing, Eva Maria; Rawat, Vimal; Mandáková, Terezie; Maumus, Florian; James, Geo Velikkakam; et al.; Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation; Nature Publishing Group; Nature Plants; 64; 11; 2-2015; 1879–18912055-0278enginfo:eu-repo/semantics/altIdentifier/url/http://www.nature.com/articles/nplants201423info:eu-repo/semantics/altIdentifier/doi/10.1038/nplants.2014.23info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T09:45:29Zoai:ri.conicet.gov.ar:11336/18083instacron: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:34982025-09-29 09:45:30.088CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation
title Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation
spellingShingle Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation
Willing, Eva Maria
Arabis Alpina
Genome
title_short Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation
title_full Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation
title_fullStr Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation
title_full_unstemmed Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation
title_sort Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation
dc.creator.none.fl_str_mv Willing, Eva Maria
Rawat, Vimal
Mandáková, Terezie
Maumus, Florian
James, Geo Velikkakam
Nordström, Karl J. V.
Becker, Claude
Warthmann, Norman
Chica, Claudia
Szarzynska, Bogna
Zytnicki, Matthias
Albani, Maria C.
Kiefer, Christiane
Bergonzi, Sara
Castaings, Loren
Mateos, Julieta Lisa
Berns, Markus C.
Bujdoso, Nora
Piofczyk, Thomas
Roudier, François
Carbonero, Pilar
Paz Ares, Javier
Davis, Seth J.
Pecinka, Ales
Quesneville, Hadi
Colot, Vincent
Lysak, Martin A.
Weigel, Detlef
Coupland, George
Schneeberger, Korbinian
author Willing, Eva Maria
author_facet Willing, Eva Maria
Rawat, Vimal
Mandáková, Terezie
Maumus, Florian
James, Geo Velikkakam
Nordström, Karl J. V.
Becker, Claude
Warthmann, Norman
Chica, Claudia
Szarzynska, Bogna
Zytnicki, Matthias
Albani, Maria C.
Kiefer, Christiane
Bergonzi, Sara
Castaings, Loren
Mateos, Julieta Lisa
Berns, Markus C.
Bujdoso, Nora
Piofczyk, Thomas
Roudier, François
Carbonero, Pilar
Paz Ares, Javier
Davis, Seth J.
Pecinka, Ales
Quesneville, Hadi
Colot, Vincent
Lysak, Martin A.
Weigel, Detlef
Coupland, George
Schneeberger, Korbinian
author_role author
author2 Rawat, Vimal
Mandáková, Terezie
Maumus, Florian
James, Geo Velikkakam
Nordström, Karl J. V.
Becker, Claude
Warthmann, Norman
Chica, Claudia
Szarzynska, Bogna
Zytnicki, Matthias
Albani, Maria C.
Kiefer, Christiane
Bergonzi, Sara
Castaings, Loren
Mateos, Julieta Lisa
Berns, Markus C.
Bujdoso, Nora
Piofczyk, Thomas
Roudier, François
Carbonero, Pilar
Paz Ares, Javier
Davis, Seth J.
Pecinka, Ales
Quesneville, Hadi
Colot, Vincent
Lysak, Martin A.
Weigel, Detlef
Coupland, George
Schneeberger, Korbinian
author2_role author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Arabis Alpina
Genome
topic Arabis Alpina
Genome
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Despite evolutionary conserved mechanisms to silence transposable element activity, there are drastic differences in the abundance of transposable elements even among closely related plant species. We conducted a de novo assembly for the 375 Mb genome of the perennial model plant, Arabis alpina. Analysing this genome revealed long-lasting and recent transposable element activity predominately driven by Gypsy long terminal repeat retrotransposons, which extended the low-recombining pericentromeres and transformed large formerly euchromatic regions into repeat-rich pericentromeric regions. This reduced capacity for long terminal repeat retrotransposon silencing and removal in A. alpina co-occurs with unexpectedly low levels of DNA methylation. Most remarkably, the striking reduction of symmetrical CG and CHG methylation suggests weakened DNA methylation maintenance in A. alpina compared with Arabidopsis thaliana. Phylogenetic analyses indicate a highly dynamic evolution of some components of methylation maintenance machinery that might be related to the unique methylation in A. alpina.
Fil: Willing, Eva Maria. Max Planck Institute for Plant Breeding Research; Alemania
Fil: Rawat, Vimal. Central European Institute of Technology; República Checa
Fil: Mandáková, Terezie. Central European Institute of Technology; República Checa
Fil: Maumus, Florian. INRA. Research Unit in Genomics; Francia
Fil: James, Geo Velikkakam. Max Planck Institute for Plant Breeding Research; Alemania
Fil: Nordström, Karl J. V.. Max Planck Institute for Plant Breeding Research; Alemania
Fil: Becker, Claude. Max Planck Institute for Developmental Biology; Alemania
Fil: Warthmann, Norman. Max Planck Institute for Developmental Biology; Alemania. The Australian National University; Australia
Fil: Chica, Claudia. Centre National de la Recherche Scientifique; Francia
Fil: Szarzynska, Bogna. Centre National de la Recherche Scientifique; Francia
Fil: Zytnicki, Matthias. Max Planck Institute for Developmental Biology; Alemania
Fil: Albani, Maria C.. Max Planck Institute for Plant Breeding Research; Alemania
Fil: Kiefer, Christiane. Max Planck Institute for Plant Breeding Research; Alemania
Fil: Bergonzi, Sara. Max Planck Institute for Plant Breeding Research; Alemania
Fil: Castaings, Loren. Max Planck Institute for Plant Breeding Research; Alemania
Fil: Mateos, Julieta Lisa. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentina. Max Planck Institute for Plant Breeding Research; Alemania
Fil: Berns, Markus C.. Max Planck Institute for Plant Breeding Research; Alemania
Fil: Bujdoso, Nora. Max Planck Institute for Plant Breeding Research; Alemania
Fil: Piofczyk, Thomas. Max Planck Institute for Plant Breeding Research; Alemania
Fil: Roudier, François. Centre National de la Recherche Scientifique; Francia
Fil: Carbonero, Pilar. Universidad Politécnica de Madrid; España
Fil: Paz Ares, Javier. Consejo Superior de Investigaciones Cientificas; España
Fil: Davis, Seth J.. Max Planck Institute for Plant Breeding Research; Alemania
Fil: Pecinka, Ales. Max Planck Institute for Plant Breeding Research; Alemania
Fil: Quesneville, Hadi. INRA. Research Unit in Genomics; Francia
Fil: Colot, Vincent. Centre National de la Recherche Scientifique; Francia
Fil: Lysak, Martin A.. Central European Institute of Technology; República Checa
Fil: Weigel, Detlef. Max Planck Institute for Developmental Biology; Alemania
Fil: Coupland, George. Max Planck Institute for Plant Breeding Research; Alemania
Fil: Schneeberger, Korbinian. Max Planck Institute for Plant Breeding Research; Alemania
description Despite evolutionary conserved mechanisms to silence transposable element activity, there are drastic differences in the abundance of transposable elements even among closely related plant species. We conducted a de novo assembly for the 375 Mb genome of the perennial model plant, Arabis alpina. Analysing this genome revealed long-lasting and recent transposable element activity predominately driven by Gypsy long terminal repeat retrotransposons, which extended the low-recombining pericentromeres and transformed large formerly euchromatic regions into repeat-rich pericentromeric regions. This reduced capacity for long terminal repeat retrotransposon silencing and removal in A. alpina co-occurs with unexpectedly low levels of DNA methylation. Most remarkably, the striking reduction of symmetrical CG and CHG methylation suggests weakened DNA methylation maintenance in A. alpina compared with Arabidopsis thaliana. Phylogenetic analyses indicate a highly dynamic evolution of some components of methylation maintenance machinery that might be related to the unique methylation in A. alpina.
publishDate 2015
dc.date.none.fl_str_mv 2015-02
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/11336/18083
Willing, Eva Maria; Rawat, Vimal; Mandáková, Terezie; Maumus, Florian; James, Geo Velikkakam; et al.; Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation; Nature Publishing Group; Nature Plants; 64; 11; 2-2015; 1879–1891
2055-0278
url http://hdl.handle.net/11336/18083
identifier_str_mv Willing, Eva Maria; Rawat, Vimal; Mandáková, Terezie; Maumus, Florian; James, Geo Velikkakam; et al.; Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation; Nature Publishing Group; Nature Plants; 64; 11; 2-2015; 1879–1891
2055-0278
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/http://www.nature.com/articles/nplants201423
info:eu-repo/semantics/altIdentifier/doi/10.1038/nplants.2014.23
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
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
dc.publisher.none.fl_str_mv Nature Publishing Group
publisher.none.fl_str_mv Nature Publishing Group
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
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
_version_ 1844613426763005952
score 13.070432