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Funding : European Union Seventh Framework Program Network of Excellence EpiGeneSys [HEALTH-F4-2010-257082]; International audience; Background Cytosine methylation is crucial for gene regulation and silencing of transposable elements in mammals and plants. While this epigenetic mark is extensively reprogrammed in the germline and early embryos of mammals, the extent to which DNA methylation is reset between generations in plants remains largely unknown. Results Using Arabidopsis as a model, we uncovered distinct DNA methylation dynamics over transposable element sequences during the early stages of plant development. Specifically, transposable elements and their relics show invariably high methylation at CG sites but increasing methylation at CHG and CHH sites. This non-CG methylation culminates in mature embryos, where it reaches saturation for a large fraction of methylated CHH sites, compared to the typical 10–20% methylation level observed in seedlings or adult plants. Moreover, the increase in CHH methylation during embryogenesis matches the hypomethylated state in the early endosperm. Finally, we show that interfering with the embryo-to-seedling transition results in the persistence of high CHH methylation levels after germination, specifically over sequences that are targeted by the RNA-directed DNA methylation (RdDM) machinery. Conclusion Our findings indicate the absence of extensive resetting of DNA methylation patterns during early plant life and point instead to an important role of RdDM in reinforcing DNA methylation of transposable element sequences in every cell of the mature embryo. Furthermore, we provide evidence that this elevated RdDM activity is a specific property of embryogenesis.

Principal investigators John P. Vogel1, David F. Garvin2, Todd C. Mockler3, Jeremy Schmutz4, Dan Rokhsar5,6, Michael W. Bevan7; DNA sequencing and assembly Kerrie Barry5, Susan Lucas5, Miranda Harmon-Smith5, Kathleen Lail5, Hope Tice5, Jeremy Schmutz4 (Leader), Jane Grimwood4, Neil McKenzie7, Michael W. Bevan7; Pseudomolecule assembly and BACend sequencing Naxin Huo1, Yong Q.Gu1,Gerard R. Lazo1, Olin D.Anderson1, John P. Vogel1 (Leader), Frank M. You8,Ming-Cheng Luo8, Jan Dvorak8, Jonathan Wright7, Melanie Febrer7, Michael W. Bevan7, Dominika Idziak9, Robert Hasterok9, David F. Garvin2; Transcriptome sequencing and analysis Erika Lindquist5, Mei Wang5, Samuel E. Fox3, Henry D. Priest3, Sergei A. Filichkin3, Scott A. Givan3, Douglas W. Bryant3, Jeff H.Chang3, Todd C.Mockler3 (Leader), Haiyan Wu10,24, Wei Wu10, An-Ping Hsia10, Patrick S. Schnable10,24, Anantharaman Kalyanaraman11, Brad Barbazuk12, Todd P.Michael13, Samuel P.Hazen14, Jennifer N. Bragg1, Debbie Laudencia-Chingcuanco1, John P. Vogel1, David F. Garvin2, Yiqun Weng15, Neil McKenzie7, Michael W. Bevan7; Gene analysis and annotation Georg Haberer16, Manuel Spannagl16, Klaus Mayer16 (Leader), Thomas Rattei17, Therese Mitros6, Dan Rokhsar6, Sang-Jik Lee18, Jocelyn K.C. Rose18, Lukas A. Mueller19, Thomas L. York19; Repeats analysis Thomas Wicker20 (Leader), Jan P. Buchmann20, Jaakko Tanskanen21, Alan H. Schulman21 (Leader), Heidrun Gundlach16, Jonathan Wright7, Michael Bevan7, Antonio Costa de Oliveira22, Luciano da C. Maia22, William Belknap1, Yong Q. Gu1, Ning Jiang23, Jinsheng Lai24, Liucun Zhu25, JianxinMa25, Cheng Sun26, Ellen Pritham26; Comparative genomics Jerome Salse27 (Leader), Florent Murat27, Michael Abrouk27, Georg Haberer16, Manuel Spannagl16, Klaus Mayer16, Remy Bruggmann13, Joachim Messing13, Frank M. You8, Ming-Cheng Luo8, Jan Dvorak8; Small RNA analysis Noah Fahlgren3, Samuel E. Fox3, Christopher M. Sullivan3, Todd C. Mockler3, James C. Carrington3, Elisabeth J. Chapman3,28, Greg D.May29, Jixian Zhai30, Matthias Ganssmann30, Sai Guna Ranjan Gurazada30, Marcelo German30, Blake C. Meyers30, Pamela J. Green30 (Leader); Manual annotation and gene family analysis Jennifer N. Bragg1, Ludmila Tyler1,6, Jiajie Wu1,8, Yong Q. Gu1, Gerard R. Lazo1, Debbie Laudencia-Chingcuanco1, James Thomson1, John P. Vogel1 (Leader), Samuel P. Hazen14, Shan Chen14, Henrik V. Scheller31, Jesper Harholt32, Peter Ulvskov32, Samuel E. Fox3, Sergei A. Filichkin3, Noah Fahlgren3, Jeffrey A. Kimbrel3, Jeff H. Chang3, Christopher M. Sullivan3, Elisabeth J. Chapman3,27, James C. Carrington3, Todd C. Mockler3, Laura E. Bartley8,31, Peijian Cao8,31, Ki-Hong Jung8,31, Manoj K Sharma8,31, Miguel Vega-Sanchez8,31, Pamela Ronald8,31, Christopher D.Dardick33, Stefanie De Bodt34,Wim Verelst34, Dirk Inze34, Maren Heese35, Arp Schnittger35, Xiaohan Yang36, Udaya C. Kalluri36, Gerald A. Tuskan36, Zhihua Hua37, Richard D. Vierstra37, David F. Garvin3, Yu Cui24, Shuhong Ouyang24, Qixin Sun24, Zhiyong Liu24, Alper Yilmaz38, Erich Grotewold38, Richard Sibout39, Kian Hematy39, Gregory Mouille39, Herman Höfte39, Todd Michael13, Jérome Pelloux40, Devin O'Connor41, James Schnable41, Scott Rowe41, Frank Harmon41, Cynthia L. Cass42, John C. Sedbrook42, Mary E. Byrne7, Sean Walsh7, Janet Higgins7, Michael Bevan7, Pinghua Li19, Thomas Brutnell19, Turgay Unver43,Hikmet Budak43, Harry Belcram44, Mathieu Charles44, Boulos Chalhoub44, Ivan Baxter45 1 USDA-ARS Western Regional Research Center, Albany, California 94710, USA. 2 USDA-ARS Plant Science Research Unit and University of Minnesota, St Paul, Minnesota 55108, USA. 3 Oregon State University, Corvallis, Oregon 97331-4501, USA. 4 HudsonAlpha Institute, Huntsville, Alabama 35806, USA. 5 US DOE Joint Genome Institute, Walnut Creek, California 94598, USA. 6 University of California Berkeley, Berkeley, California 94720, USA. 7 John Innes Centre, Norwich NR4 7UJ, UK. 8 University of California Davis, Davis, California 95616, USA. 9 University of Silesia, 40-032 Katowice, Poland. 10 Iowa State University, Ames, Iowa 50011, USA. 11 Washington State University, Pullman, Washington 99163, USA. 12 University of Florida, Gainsville, Florida 32611, USA. 13 Rutgers University, Piscataway, New Jersey 08855-0759, USA. 14 University of Massachusetts, Amherst, Massachusetts 01003-9292, USA. 15 USDA-ARS Vegetable Crops Research Unit, Horticulture Department, University of Wisconsin, Madison, Wisconsin 53706, USA. 16 Helmholtz Zentrum München, D-85764 Neuherberg, Germany. 17 Technical University München, 80333 München, Germany. 18 Cornell University, Ithaca, New York 14853, USA. 19 Boyce Thompson Institute for Plant Research, Ithaca, New York 14853-1801, USA. 20 University of Zurich, 8008 Zurich, Switzerland. 21 MTT Agrifood Research and University of Helsinki, FIN-00014 Helsinki, Finland. 22 Federal University of Pelotas, Pelotas, 96001-970, RS, Brazil. 23 Michigan State University, East Lansing, Michigan 48824, USA. 24 China Agricultural University, Beijing 10094, China. 25 Purdue University, West Lafayette, Indiana 47907, USA. 26 The University of Texas, Arlington, Arlington, Texas 76019, USA. 27 Institut National de la Recherche Agronomique UMR 1095, 63100 Clermont-Ferrand, France. 28 University of California San Diego, La Jolla, California 92093, USA. 29 National Centre for Genome Resources, Santa Fe, New Mexico 87505, USA. 30 University of Delaware, Newark, Delaware 19716, USA. 31 Joint Bioenergy Institute, Emeryville, California 94720, USA. 32 University of Copenhagen, Frederiksberg DK-1871, Denmark. 33 USDA-ARS Appalachian Fruit Research Station, Kearneysville, West Virginia 25430, USA. 34 VIB Department of Plant Systems Biology, VIB and Department of Plant Biotechnology and Genetics, Ghent University, Technologiepark 927, 9052 Gent, Belgium. 35 Institut de Biologie Moléculaire des Plantes du CNRS, Strasbourg 67084, France. 36 BioEnergy Science Center and Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6422, USA. 37 University of Wisconsin-Madison, Madison, Wisconsin 53706, USA. 38 The Ohio State University, Columbus, Ohio 43210, USA. 39 Institut Jean-Pierre Bourgin, UMR1318, Institut National de la Recherche Agronomique, 78026 Versailles cedex, France. 40 Université de Picardie, Amiens 80039, France. 41 Plant Gene Expression Center, University of California Berkeley, Albany, California 94710, USA. 42 Illinois State University and DOE Great Lakes Bioenergy Research Center, Normal, Illinois 61790, USA. 43 Sabanci University, Istanbul 34956, Turkey. 44 Unité de Recherche en Génomique Végétale: URGV (INRA-CNRS-UEVE), Evry 91057, France. 45 USDA-ARS/Donald Danforth Plant Science Center, St Louis, Missouri 63130, USA.; Three subfamilies of grasses, the Ehrhartoideae, Panicoideae and Pooideae, provide the bulk of human nutrition and are poised to become major sources of renewable energy. Here we describe the genome sequence of the wild grass Brachypodium distachyon (Brachypodium), which is, to our knowledge, the first member of the Pooideae subfamily to be sequenced. Comparison of the Brachypodium, rice and sorghum genomes shows a precise history of genome evolution across a broad diversity of the grasses, and establishes a template for analysis of the large genomes of economically important pooid grasses such as wheat. The high-quality genome sequence, coupled with ease of cultivation and transformation, small size and rapid life cycle, will help Brachypodium reach its potential as an important model system for developing new energy and food crops.