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

Eva-Maria Willing; Vimal Rawat; Terezie Mandáková; Florian Maumus; Geo Velikkakam James; Karl J.V. Nordström; Claude Becker; Norman Warthmann; Claudia Chica; Bogna Szarzynska; Matthias Zytnicki; Maria C. Albani; Christiane Kiefer; Sara Bergonzi; Loren Castaings; Julieta L. Mateos; Markus C. Berns; Nora Bujdoso; Thomas Piofczyk; Laura de Lorenzo; Cristina Barrero-Sicilia; Isabel Mateos; Mathieu Piednoël; Jörg Hagmann; Romy Chen-Min-Tao; Raquel Iglesias-Fernández; Stephan C. Schuster; Carlos Alonso-Blanco; François Roudier; Pilar Carbonero; Javier Paz-Ares; Seth J. Davis; Ales Pecinka; Hadi Quesneville; Vincent Colot; Martin A. Lysak; Detlef Weigel; George Coupland; Korbinian Schneeberger

doi:10.1038/nplants.2014.23

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

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

Eva-Maria Willing, Vimal Rawat, Terezie Mandáková, Florian Maumus, Geo Velikkakam James, Karl J.V. Nordström, Claude Becker, Norman Warthmann, Claudia Chica, Bogna Szarzynska, …

Nature plants, Vol.1(2), pp.14023-14028

02/02/2015

DOI: https://doi.org/10.1038/nplants.2014.23

PMID: 27246759

Résumé

Biochemistry, Molecular Biology

Biodiversity

Botanics

Genetics

Genomics

Life Sciences

Plants genetics

Vegetal Biology

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 lowrecombining 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.

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Titre: Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation
Créateurs - sans rôle: Eva-Maria Willing - Department of Plant Developmental Biology
Vimal Rawat - Department of Plant Developmental Biology
Terezie Mandáková - Research group Plant Cytogenomics
Florian Maumus - Unité de Recherche Génomique Info
Geo Velikkakam James - Department of Plant Developmental Biology
Karl J.V. Nordström - Max Planck Institute for Plant Breeding Research
Claude Becker - Department of Molecular Biology
Norman Warthmann - Department of Molecular Biology
Claudia Chica - Institut de biologie de l'ENS Paris
Bogna Szarzynska - Institut de biologie de l'ENS Paris
Matthias Zytnicki - Unité de Biométrie et Intelligence Artificielle (ancêtre de MIAT)
Maria C. Albani - Department of Plant Developmental Biology
Christiane Kiefer - Department of Plant Developmental Biology
Sara Bergonzi - Department of Plant Developmental Biology
Loren Castaings - Department of Plant Developmental Biology
Julieta L. Mateos - Department of Plant Developmental Biology
Markus C. Berns - Department of Plant Developmental Biology
Nora Bujdoso - Department of Plant Developmental Biology
Thomas Piofczyk - Department of Plant Developmental Biology
Laura de Lorenzo - Centro Nacional de Biotecnología [Madrid]
Cristina Barrero-Sicilia - Centro de Biotecnología y Genómica de Plantas
Isabel Mateos - Centro Nacional de Biotecnología [Madrid]
Mathieu Piednoël - Department of Plant Developmental Biology
Jörg Hagmann - Max Planck Institute for Developmental Biology
Romy Chen-Min-Tao - Institut de biologie de l'ENS Paris
Raquel Iglesias-Fernández - Centro de Biotecnología y Genómica de Plantas
Stephan C. Schuster - Center for Comparative Genomics and Bioinformatics
Carlos Alonso-Blanco - Centro Nacional de Biotecnología [Madrid]
François Roudier - Institut de biologie de l'ENS Paris
Pilar Carbonero - Centro de Biotecnología y Genómica de Plantas
Javier Paz-Ares - Centro Nacional de Biotecnología [Madrid]
Seth J. Davis - Department of Plant Developmental Biology
Ales Pecinka - Department of Plant Developmental Biology
Hadi Quesneville - Unité de Recherche Génomique Info
Vincent Colot - Institut de biologie de l'ENS Paris
Martin A. Lysak - Central European Institute of Technology [Brno]
Detlef Weigel - Department of Molecular Biology
George Coupland - Department of Plant Developmental Biology
Korbinian Schneeberger - Department of Plant Developmental Biology
Détails de publication: Nature plants, Vol.1(2), pp.14023-14028
Éditeur: Nature Publishing Group
Nombre de pages: 6
Identifiants: 99155071509311
Unité académique: Institut des Sciences des Plantes de Montpellier - IPSiM
Langue: English
Type de ressource: Journal article