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Science 20 November 2009:
Vol. 326. no. 5956, pp. 1112 - 1115
DOI: 10.1126/science.1178534
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Reports

The B73 Maize Genome: Complexity, Diversity, and Dynamics

Patrick S. Schnable,1,2,3,4,* Doreen Ware,5,6,* Robert S. Fulton,7,{dagger} Joshua C. Stein,6,{dagger} Fusheng Wei,8,{dagger} Shiran Pasternak,6 Chengzhi Liang,6 Jianwei Zhang,8 Lucinda Fulton,7 Tina A. Graves,7 Patrick Minx,7 Amy Denise Reily,7 Laura Courtney,7 Scott S. Kruchowski,7 Chad Tomlinson,7 Cindy Strong,7 Kim Delehaunty,7 Catrina Fronick,7 Bill Courtney,7 Susan M. Rock,7 Eddie Belter,7 Feiyu Du,7 Kyung Kim,7 Rachel M. Abbott,7 Marc Cotton,7 Andy Levy,7 Pamela Marchetto,7 Kerri Ochoa,7 Stephanie M. Jackson,7 Barbara Gillam,7 Weizu Chen,7 Le Yan,7 Jamey Higginbotham,7 Marco Cardenas,7 Jason Waligorski,7 Elizabeth Applebaum,7 Lindsey Phelps,7 Jason Falcone,7 Krishna Kanchi,7 Thynn Thane,7 Adam Scimone,7 Nay Thane,7 Jessica Henke,7 Tom Wang,7 Jessica Ruppert,7 Neha Shah,7 Kelsi Rotter,7 Jennifer Hodges,7 Elizabeth Ingenthron,7 Matt Cordes,7 Sara Kohlberg,7 Jennifer Sgro,7 Brandon Delgado,7 Kelly Mead,7 Asif Chinwalla,7 Shawn Leonard,7 Kevin Crouse,7 Kristi Collura,8 Dave Kudrna,8 Jennifer Currie,8 Ruifeng He,8 Angelina Angelova,8 Shanmugam Rajasekar,8 Teri Mueller,8 Rene Lomeli,8 Gabriel Scara,8 Ara Ko,8 Krista Delaney,8 Marina Wissotski,8 Georgina Lopez,8 David Campos,8 Michele Braidotti,8 Elizabeth Ashley,8 Wolfgang Golser,8 HyeRan Kim,8 Seunghee Lee,8 Jinke Lin,8 Zeljko Dujmic,8 Woojin Kim,8 Jayson Talag,8 Andrea Zuccolo,8 Chuanzhu Fan,8 Aswathy Sebastian,8 Melissa Kramer,6 Lori Spiegel,6 Lidia Nascimento,6 Theresa Zutavern,6 Beth Miller,6 Claude Ambroise,6 Stephanie Muller,6 Will Spooner,6 Apurva Narechania,6 Liya Ren,6 Sharon Wei,6 Sunita Kumari,6 Ben Faga,6 Michael J. Levy,6 Linda McMahan,6 Peter Van Buren,6 Matthew W. Vaughn,6 Kai Ying,3 Cheng-Ting Yeh,1,2 Scott J. Emrich,9,10 Yi Jia,3 Ananth Kalyanaraman,9,11 An-Ping Hsia,1,2 W. Brad Barbazuk,12 Regina S. Baucom,13 Thomas P. Brutnell,14 Nicholas C. Carpita,15 Cristian Chaparro,16 Jer-Ming Chia,6 Jean-Marc Deragon,16 James C. Estill,13,17 Yan Fu,2,4 Jeffrey A. Jeddeloh,18 Yujun Han,13,17 Hyeran Lee,19 Pinghua Li,14 Damon R. Lisch,20 Sanzhen Liu,3 Zhijie Liu,6 Dawn Holligan Nagel,13,17 Maureen C. McCann,21 Phillip SanMiguel,22 Alan M. Myers,23 Dan Nettleton,24 John Nguyen,25 Bryan W. Penning,15,21 Lalit Ponnala,26 Kevin L. Schneider,27 David C. Schwartz,28 Anupma Sharma,27 Carol Soderlund,29 Nathan M. Springer,30 Qi Sun,26 Hao Wang,13,17 Michael Waterman,25 Richard Westerman,22 Thomas K. Wolfgruber,27 Lixing Yang,13 Yeisoo Yu,29 Lifang Zhang,6 Shiguo Zhou,28 Qihui Zhu,13,17 Jeffrey L. Bennetzen,13 R. Kelly Dawe,13,17 Jiming Jiang,19 Ning Jiang,31 Gernot G. Presting,27 Susan R. Wessler,13,17 Srinivas Aluru,1,9,32 Robert A. Martienssen,6 Sandra W. Clifton,7 W. Richard McCombie,6 Rod A. Wing,8 Richard K. Wilson7,33,{ddagger}

We report an improved draft nucleotide sequence of the 2.3-gigabase genome of maize, an important crop plant and model for biological research. Over 32,000 genes were predicted, of which 99.8% were placed on reference chromosomes. Nearly 85% of the genome is composed of hundreds of families of transposable elements, dispersed nonuniformly across the genome. These were responsible for the capture and amplification of numerous gene fragments and affect the composition, sizes, and positions of centromeres. We also report on the correlation of methylation-poor regions with Mu transposon insertions and recombination, and copy number variants with insertions and/or deletions, as well as how uneven gene losses between duplicated regions were involved in returning an ancient allotetraploid to a genetically diploid state. These analyses inform and set the stage for further investigations to improve our understanding of the domestication and agricultural improvements of maize.

1 Center for Plant Genomics, Iowa State University, Ames, IA 50011, USA.
2 Department of Agronomy, Iowa State University, Ames, IA 50011, USA.
3 Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA.
4 Center for Carbon Capturing Crops, Iowa State University, Ames, IA 50011, USA.
5 U.S. Department of Agriculture (USDA), North Atlantic Area, Robert Holley Center for Agriculture and Health, Ithaca, NY 14853, USA.
6 Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
7 The Genome Center at Washington University, St. Louis, MO 63108, USA.
8 Arizona Genomics Institute, School of Plant Sciences and Department of Ecology and Evolutionary Biology, BIO5 Institute for Collaborative Research, University of Arizona, Tucson, AZ 85721, USA.
9 Department of Electrical and Computer Engineering, Iowa State University, Ames, IA 50011, USA.
10 Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556, USA.
11 School of Electrical Engineering and Computer Science, Washington State University, Pullman, WA 99164, USA.
12 Department of Botany, University of Florida, Gainesville, FL 32611, USA.
13 Department of Genetics, University of Georgia, Athens, GA 30602, USA.
14 Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA.
15 Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA.
16 Université de Perpignan Via Domitia, CNRS, Perpignan, France.
17 Department of Plant Biology, University of Georgia, Athens, GA 30602, USA.
18 NimbleGen, Madison, WI 53711, USA.
19 Department of Horticulture, University of Wisconsin–Madison, Madison, WI 53706, USA.
20 Department of Plant Biology, University of California, Berkeley, CA, 94720, USA.
21 Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA.
22 Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA.
23 Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, 50011, USA.
24 Department of Statistics, Iowa State University, Ames, IA 50011, USA.
25 Departments of Mathematics, Biology, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA.
26 Cornell University Computational Biology Service Unit, Cornell University, Ithaca, NY 14850, USA.
27 Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, HI 96822, USA.
28 Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, University of Wisconsin–Madison, Madison, WI 53706, USA.
29 BIO5 Institute for Collaborative Research, University of Arizona, Tucson, AZ 85721, USA.
30 Department of Plant Biology, University of Minnesota, St. Paul, MN 55108, USA.
31 Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA.
32 Indian Institute of Technology, Bombay, India.
33 Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA.

* These authors contributed equally to this work.

{dagger} These authors contributed equally to data production and analysis.

{ddagger} To whom correspondence should be addressed. E-mail: rwilson{at}wustl.edu

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