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
.jpg)
- Institución
- Consejo Nacional de Investigaciones Científicas y Técnicas
- OAI Identificador
- oai:ri.conicet.gov.ar:11336/18083
Ver los metadatos del registro completo
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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 Técnicas2025-10-15T14:39:04Zoai: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:34982025-10-15 14:39:05.088CONICET 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 |
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article |
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publishedVersion |
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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 |
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eng |
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eng |
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info:eu-repo/semantics/altIdentifier/url/http://www.nature.com/articles/nplants201423 info:eu-repo/semantics/altIdentifier/doi/10.1038/nplants.2014.23 |
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Nature Publishing Group |
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Nature Publishing Group |
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