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

Nature Plants volume 1, Article number: 14023 (2015) Cite this article

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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.

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Figure 1: Phylogenetic reconstruction and karyotype evolution support a distinct phylogenetic placement of A. alpina.
Figure 2: Genome size variation and differences in transposable element content.
Figure 3: Differences in the distribution of genes, transposable elements and chromatin marks between A. thaliana, A. lyrata and A. alpina.
Figure 4: Species-specific differences in DNA methylation.

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Acknowledgements

We thank José Jiménez-Gómez for helpful discussion throughout the entire project and Marcus Koch, Maarten Koornneef as well as Miltos Tsiantis for critical reading of the manuscript. We apologize to all colleagues whose work has not been cited here because of space constraints. The TRANSNET consortium was initiated based on the funding of PLANT KBBE ‘Transcriptional networks and their evolution in the Brassicaceae (TRANSNET)’. B.S. was supported by a postdoctoral fellowship from the TRANSNET consortium. C.C. was supported by a postdoctoral fellowship first from Investissements d'Avenir ANR-10-LABX-54 MEMO LIFE and then from the European Union EpiGeneSys FP7 Network of Excellence (number 257082). R.C.M.T. was supported by Investissements d'Avenir ANR-10-LABX-54 MEMO LIFE. J.L.M was supported by an Alexander von Humboldt Postdoctoral Fellowship. C.B.S was supported by a postdoctoral fellowship from the TRANSNET consortium. R.I.F. was supported by a post-doctoral Juan de la Cierva contract (JCI-2010-07909) from Ministerio de Ciencia e Innovación (MICINN). A.P. was supported by the research grant PE-1853/2 from German Research Foundation. Work in the Carbonero's group was supported by the Spanish grants BFU2009-11809 and Consolider CSD2007-00057 from Ministerio de Ciencia e Innovación (MICINN). C.A-B. laboratory was funded by grant BIO2013-45407-P from the Ministerio de Economía y Competitividad of Spain. Work in the Colot group was supported by the Agence Nationale de la Recherche (Investissements d'Avenir ANR-10-LABX-54 MEMO LIFE and ANR-11-IDEX-0001-02 PSL* Research University) and the European Union (EpiGeneSys FP7 Network of Excellence number 257082). Work in the Weigel group was supported by an FP7 project AENEAS and the TRANSNET consortium. Work in the Quesneville group was supported by the TRANSNET consortium and by the French national research agency (ANR-08-KBBE-012). Work in the Lysak group was supported by a research grant from the Czech Science Foundation (P501/12/G090) and by the European Social Fund (projects CZ.1.07/2.3.00/30.0037 and CZ.1.07/2.3.00/20.0189). Work on A. alpina in the Coupland laboratory is partly funded by the Cluster of Excellence on Plant Sciences (CEPLAS). Work in the Paz-Ares laboratory has been supported by the French-German-Spanish Trilateral program on Plant Genomics (grant TRANSNET) and Spanish Ministry of Economy competiveness (CONSOLIDER 2007-28317, BIO2011-30546). Schneeberger, Coupland, Weigel and Pecinka groups were supported by the Max Planck Society.

Author information

Author notes

  1. Geo Velikkakam James

    Present address: ‡Present address: Rijk Zwaan R&D Fijnaart, Fijnaart, The Netherlands (G.V.J.),

  2. Karl J.V. Nordström

    Present address: ‡Present address: Laboratory of EpiGenetics, University of Saarland, Saarbrücken, Germany (K.J.V.N.),

  3. Claudia Chica

    Present address: ‡Present address: Departamento de Ciencias Biológicas, Universidad de los Andes, Carrera 1 N° 18A- 12, Bogotá, Colombia (C.C.),

  4. Bogna Szarzynska

    Present address: ‡Present address: Center for Integrative Genomics, University of Lausanne, Genopode Building, CH-1015 Lausanne, Switzerland (B.S-E.),

  5. Matthias Zytnicki

    Present address: ‡Present address: INRA, MIAT UR-875, Castanet-Tolosan 31320, France (M.Z.),

  6. Maria C. Albani

    Present address: ‡Present address: Botanical Institute, University of Cologne, Zülpicher Strasse 47B, D-50674 Cologne, Germany (M.C.A.),

  7. Sara Bergonzi

    Present address: ‡Present address: Laboratory of Plant Breeding, Department of Plant Sciences, Wageningen-UR, PO Box 386, 6700 Wageningen AJ, The Netherlands (S.B.),

  8. Loren Castaings

    Present address: ‡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.),

  9. Julieta L. Mateos

    Present address: ‡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.);,

  10. Nora Bujdoso

    Present address: ‡Present address: Department for Training CUR-BIL-BAN-ELB, Currenta GmbH & Co. OHG, Aprather Weg 18a, 42096 Wuppertal, Germany (N.B.);,

  11. Laura de Lorenzo

    Present address: ‡Present address: Department Plant & Soil Sciences, University of Kentucky, 301C Plant Science Building, 1405 Veterans Drive, Lexington, Kentucky 40546-0312, USA (L.d.L.);,

  12. Cristina Barrero-Sicilia

    Present address: ‡Present address: Biological Chemistry and Crop Protection Department, Rothamsted Research, Harpenden AL5 2JQ, UK (C.B-S.);,

  13. Isabel Mateos

    Present address: ‡Present address: Centro Hispano-Luso de Investigaciones Agrarias-CIALE, Salamanca, Spain (I.M.);,

  14. Romy Chen-Min-Tao

    Present address: ‡Present address: Plateforme Bioinformatique, Institut Gustave Roussy, 94805 Villejuif, France (R.C-M-T.);,

  15. Seth J. Davis

    Present address: ‡Present address: Department of Biology, University of York, York, UK (S.J.D.).,

  16. Eva-Maria Willing, Vimal Rawat and Terezie Mandáková: These authors contributed equally to this work

Authors and Affiliations

  1. Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany

    Eva-Maria Willing, Vimal Rawat, Geo Velikkakam James, Karl J.V. Nordström, Maria C. Albani, Christiane Kiefer, Sara Bergonzi, Loren Castaings, Julieta L. Mateos, Markus C. Berns, Nora Bujdoso, Thomas Piofczyk, Mathieu Piednoël, Seth J. Davis, Ales Pecinka, George Coupland & Korbinian Schneeberger

  2. Research group Plant Cytogenomics, CEITEC – Central European Institute of Technology, Masaryk University, Brno, Czech Republic

    Terezie Mandáková & Martin A. Lysak

  3. INRA, UR1164 URGI—Research Unit in Genomics-Info, INRA de Versailles-Grignon, Route de Saint-Cyr, 78026, Versailles, France

    Florian Maumus, Matthias Zytnicki & Hadi Quesneville

  4. Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany

    Claude Becker, Norman Warthmann, Jörg Hagmann & Detlef Weigel

  5. Research School of Biology, The Australian National University, Canberra, 0200, ACT, Australia

    Norman Warthmann

  6. 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

    Claudia Chica, Bogna Szarzynska, Romy Chen-Min-Tao, François Roudier & Vincent Colot

  7. Department of Plant Molecular Genetics, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049 Madrid, Spain

    Laura de Lorenzo, Isabel Mateos, Carlos Alonso-Blanco & Javier Paz-Ares

  8. Centro de Biotecnología y Genómica de Plantas (UPM-INIA). ETSI agrónomos, Universidad Politécnica de Madrid, Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain

    Cristina Barrero-Sicilia, Raquel Iglesias-Fernández & Pilar Carbonero

  9. Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, 16802, Pennsylvania, USA

    Stephan C. Schuster

Authors
  1. Eva-Maria Willing
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  2. Vimal Rawat
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Contributions

E.M.W., S.C.S., C.A-B., F.R., P.C., J.P.A., S.J.D., A.P., H.Q., V.C., M.A.L., D.W., G.C. and K.S. conceived this study and supervised experiments and analyses. L.C., M.C.A., B.S., S.B., L.C., J.L.M., M.C.B., N.B., T.P., L.D.L., I.M. and C.B.S. prepared samples for DNA and RNA sequencing. B.S. prepared samples and performed ChIP and MeDIP experiments. C.B. prepared samples and performed bisulphite experiments. N.W., M.C.A. and C.A-B. constructed genetic maps. T.M. and M.A.L. conducted FISH, chromosome painting and karyotype evolution analysis. K.J.V.N., E.M.W. and N.W. conducted de novo assembly of A. alpina. C.K. conducted de novo assembly of A. montbretiana. G.V.J., E.M.W., C.B.S. and M.Z. performed genome annotations of A. alpina together with all participants of the annotation jamboree held in 2012 in Paris, France. E.M.W. performed genome annotations of A. montbretiana. E.M.W., V.R. and C.C. conducted expression analyses. F.M. performed transposon annotations. E.M.W., F.M., M.P. and K.S. performed transposon analysis. E.M.W., C.C., R.C.M.T. and K.S. performed analysis of ChIP-seq and MeDIP-seq data. E.M.W., C.B., J.H. and K.S. performed BS-seq analysis. E.M.W., V.R. and K.S. conducted comparative genomic analyses. E.M.W. and K.S. wrote the paper with contributions from all authors.

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Correspondence to George Coupland or Korbinian Schneeberger.

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Willing, EM., Rawat, V., Mandáková, T. et al. Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation. Nature Plants 1, 14023 (2015). https://doi.org/10.1038/nplants.2014.23

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