The International Brachypodium Initiative

The International Brachypodium Initiative

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

NaxinHuo1, Yong Q.Gu1,GerardR. Lazo1, OlinD.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, JeffH.Chang3, ToddC.Mockler3 (Leader), HaiyanWu10,24, Wei Wu10, An-Ping Hsia10, Patrick S. Schnable10,24, Ananth Kalyanaraman11, Brad Barbazuk12, Todd P.Michael13, Samuel P.Hazen14, JenniferN. 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, ThereseMitros6, 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, JesperHarholt32, 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, StefanieDe Bodt34,Wim Verelst34, Dirk Inze´34, Maren Heese35, Arp Schnittger35, Xiaohan Yang36, Udaya C. Kalluri36, GeraldA. Tuskan36, ZhihuaHua37, 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 Ho¨fte39, Todd Michael13, Je´rome Pelloux40, Devin O’Connor41, James Schnable41, Scott Rowe41, Frank Harmon41, Cynthia L. Cass42, John C. Sedbrook42, Mary E. Byrne7, SeanWalsh7, Janet Higgins7, Michael Bevan7, PinghuaLi19, ThomasBrutnell19, TurgayUnver43,Hikmet Budak43, Harry Belcram44, Mathieu Charles44, Boulos Chalhoub44, Ivan Baxter45

1USDA-ARS Western Regional Research Center, Albany, California 94710, USA.
2USDA-ARS Plant Science Research Unit and University of Minnesota, St Paul, Minnesota 55108, USA.
3Oregon State University, Corvallis, Oregon 97331-4501, USA.
4HudsonAlpha Institute, Huntsville, Alabama 35806, USA.
5US DOE Joint Genome Institute, Walnut Creek, California 94598, USA.
6University of California Berkeley, Berkeley, California 94720, USA.
7John Innes Centre, Norwich NR4 7UJ, UK.
8University of California Davis, Davis, California 95616, USA.
9University of Silesia, 40-032 Katowice, Poland.
10Iowa State University, Ames, Iowa 50011, USA.
11Washington State University, Pullman, Washington 99164, USA.
12University of Florida, Gainsville, Florida 32611, USA.
13Rutgers University, Piscataway, New Jersey 08855-0759, USA.
14University of Massachusetts, Amherst, Massachusetts 01003-9292, USA.
15USDA-ARS Vegetable Crops Research Unit, Horticulture Department, University of Wisconsin, Madison, Wisconsin 53706, USA.
16Helmholtz Zentrum Mu¨nchen, D-85764 Neuherberg, Germany.
17Technical University Mu¨nchen, 80333 Mu¨nchen, Germany.
18Cornell University, Ithaca, New York 14853, USA.
19Boyce Thompson Institute for Plant Research, Ithaca, New York 14853-1801, USA.
20University of Zurich, 8008 Zurich, Switzerland.
21MTT Agrifood Research and University of Helsinki, FIN-00014 Helsinki, Finland.
22Federal University of Pelotas, Pelotas, 96001-970, RS, Brazil.
23Michigan State University, East Lansing, Michigan 48824, USA.
24China Agricultural University, Beijing 10094, China.
25Purdue University, West Lafayette, Indiana 47907, USA.
26The University of Texas, Arlington, Arlington, Texas 76019, USA.
27Institut National de la Recherche´ Agronomique UMR 1095, 63100 Clermont-Ferrand, France.
28University of California San Diego, La Jolla, California 92093, USA.
29National Centre for Genome Resources, Santa Fe, New Mexico 87505, USA.
30University of Delaware, Newark, Delaware 19716, USA.
31Joint Bioenergy Institute, Emeryville, California 94720, USA.
32University of Copenhagen, Frederiksberg DK-1871, Denmark.
33USDA-ARS Appalachian Fruit Research Station, Kearneysville, West Virginia 25430, USA.
34VIB Department of Plant Systems Biology, VIB and Department of Plant Biotechnology and Genetics, Ghent University, Technologiepark 927, 9052 Gent, Belgium.
35Institut de Biologie Mole´culaire des Plantes du CNRS, Strasbourg 67084, France.
36BioEnergy Science Center and Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6422, USA.
37University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.
38The Ohio State University, Columbus, Ohio 43210, USA.
39Institut Jean-Pierre Bourgin, UMR1318, Institut National de la Recherche Agronomique, 78026 Versailles cedex, France.
40Universite´ de Picardie, Amiens 80039, France.
41Plant Gene Expression Center, University of California Berkeley, Albany, California 94710, USA.
42Illinois State University and DOE Great Lakes Bioenergy Research Center, Normal, Illinois 61790, USA.
43Sabanci University, Istanbul 34956, Turkey.
44Unite´ de Recherche en Ge´nomique Ve´ge´tale: URGV (INRA-CNRS-UEVE), Evry 91057, France.
45USDA-ARS/Donald Danforth Plant Science Center, St Louis, Missouri 63130, USA. {Present address: The School of Plant Molecular Systems Biotechnology, Kyung Hee University, Yongin 446-701, Korea.