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


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2015-02-02

AUTHORS

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

ABSTRACT

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. More... »

PAGES

14023

References to SciGraph publications

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  • Journal

    TITLE

    Nature Plants

    ISSUE

    2

    VOLUME

    1

    Author Affiliations

  • Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany
  • Research group Plant Cytogenomics, CEITEC – Central European Institute of Technology, Masaryk University, Brno, Czech Republic
  • INRA, UR1164 URGI—Research Unit in Genomics-Info, INRA de Versailles-Grignon, 78026, Route de Saint-Cyr, Versailles, France
  • ‡Present address: Rijk Zwaan R&D Fijnaart, Fijnaart, The Netherlands (G.V.J.)
  • ‡Present address: Laboratory of EpiGenetics, University of Saarland, Saarbrücken, Germany (K.J.V.N.)
  • Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
  • Research School of Biology, The Australian National University, 0200, Canberra, ACT, Australia
  • ‡Present address: Departamento de Ciencias Biológicas, Universidad de los Andes, Carrera 1 N° 18A- 12, Bogotá, Colombia (C.C.)
  • ‡Present address: Center for Integrative Genomics, University of Lausanne, Genopode Building, CH-1015 Lausanne, Switzerland (B.S-E.)
  • ‡Present address: INRA, MIAT UR-875, Castanet-Tolosan 31320, France (M.Z.)
  • ‡Present address: Botanical Institute, University of Cologne, Zülpicher Strasse 47B, D-50674 Cologne, Germany (M.C.A.)
  • ‡Present address: Laboratory of Plant Breeding, Department of Plant Sciences, Wageningen-UR, PO Box 386, 6700 Wageningen AJ, The Netherlands (S.B.)
  • ‡Present address: Biochimie et Physiologie Moléculaire des Plantes, Centre National de la Recherche Scientifique Unité Mixte de Recherche 5004, Institut de Biologie Intégrative des Plantes, 2 place Pierre Viala, F-34060 Montpellier Cedex 2, France (L.C.)
  • ‡Present address: Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina, C1405BWE Buenos Aires, Argentina (J.M.);
  • ‡Present address: Department for Training CUR-BIL-BAN-ELB, Currenta GmbH & Co. OHG, Aprather Weg 18a, 42096 Wuppertal, Germany (N.B.);
  • ‡Present address: Department Plant & Soil Sciences, University of Kentucky, 301C Plant Science Building, 1405 Veterans Drive, Lexington, Kentucky 40546-0312, USA (L.d.L.);
  • ‡Present address: Biological Chemistry and Crop Protection Department, Rothamsted Research, Harpenden AL5 2JQ, UK (C.B-S.);
  • ‡Present address: Centro Hispano-Luso de Investigaciones Agrarias-CIALE, Salamanca, Spain (I.M.);
  • ‡Present address: Plateforme Bioinformatique, Institut Gustave Roussy, 94805 Villejuif, France (R.C-M-T.);
  • Centro de Biotecnología y Genómica de Plantas (UPM-INIA). ETSI agrónomos, Universidad Politécnica de Madrid, Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain
  • Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, 16802, University Park, Pennsylvania, USA
  • Department of Plant Molecular Genetics, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
  • Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS) UMR 8197 and Institut National de la Santé et de la Recherche Médicale (INSERM) U 1024, Paris, France
  • ‡Present address: Department of Biology, University of York, York, UK (S.J.D.).
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/nplants.2014.23

    DOI

    http://dx.doi.org/10.1038/nplants.2014.23

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1029652574

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/27246759


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