The B73 Maize Genome: Complexity, Diversity, and Dynamics
- Patrick S. Schnable1,2,3,4,*,
- Doreen Ware5,6,*,
- Robert S. Fulton7,†,
- Joshua C. Stein6,†,
- Fusheng Wei8,†,
- Shiran Pasternak6,
- Chengzhi Liang6,
- Jianwei Zhang8,
- Lucinda Fulton7,
- Tina A. Graves7,
- Patrick Minx7,
- Amy Denise Reily7,
- Laura Courtney7,
- Scott S. Kruchowski7,
- Chad Tomlinson7,
- Cindy Strong7,
- Kim Delehaunty7,
- Catrina Fronick7,
- Bill Courtney7,
- Susan M. Rock7,
- Eddie Belter7,
- Feiyu Du7,
- Kyung Kim7,
- Rachel M. Abbott7,
- Marc Cotton7,
- Andy Levy7,
- Pamela Marchetto7,
- Kerri Ochoa7,
- Stephanie M. Jackson7,
- Barbara Gillam7,
- Weizu Chen7,
- Le Yan7,
- Jamey Higginbotham7,
- Marco Cardenas7,
- Jason Waligorski7,
- Elizabeth Applebaum7,
- Lindsey Phelps7,
- Jason Falcone7,
- Krishna Kanchi7,
- Thynn Thane7,
- Adam Scimone7,
- Nay Thane7,
- Jessica Henke7,
- Tom Wang7,
- Jessica Ruppert7,
- Neha Shah7,
- Kelsi Rotter7,
- Jennifer Hodges7,
- Elizabeth Ingenthron7,
- Matt Cordes7,
- Sara Kohlberg7,
- Jennifer Sgro7,
- Brandon Delgado7,
- Kelly Mead7,
- Asif Chinwalla7,
- Shawn Leonard7,
- Kevin Crouse7,
- Kristi Collura8,
- Dave Kudrna8,
- Jennifer Currie8,
- Ruifeng He8,
- Angelina Angelova8,
- Shanmugam Rajasekar8,
- Teri Mueller8,
- Rene Lomeli8,
- Gabriel Scara8,
- Ara Ko8,
- Krista Delaney8,
- Marina Wissotski8,
- Georgina Lopez8,
- David Campos8,
- Michele Braidotti8,
- Elizabeth Ashley8,
- Wolfgang Golser8,
- HyeRan Kim8,
- Seunghee Lee8,
- Jinke Lin8,
- Zeljko Dujmic8,
- Woojin Kim8,
- Jayson Talag8,
- Andrea Zuccolo8,
- Chuanzhu Fan8,
- Aswathy Sebastian8,
- Melissa Kramer6,
- Lori Spiegel6,
- Lidia Nascimento6,
- Theresa Zutavern6,
- Beth Miller6,
- Claude Ambroise6,
- Stephanie Muller6,
- Will Spooner6,
- Apurva Narechania6,
- Liya Ren6,
- Sharon Wei6,
- Sunita Kumari6,
- Ben Faga6,
- Michael J. Levy6,
- Linda McMahan6,
- Peter Van Buren6,
- Matthew W. Vaughn6,
- Kai Ying3,
- Cheng-Ting Yeh1,2,
- Scott J. Emrich9,10,
- Yi Jia3,
- Ananth Kalyanaraman9,11,
- An-Ping Hsia1,2,
- W. Brad Barbazuk12,
- Regina S. Baucom13,
- Thomas P. Brutnell14,
- Nicholas C. Carpita15,
- Cristian Chaparro16,
- Jer-Ming Chia6,
- Jean-Marc Deragon16,
- James C. Estill13,17,
- Yan Fu2,4,
- Jeffrey A. Jeddeloh18,
- Yujun Han13,17,
- Hyeran Lee19,
- Pinghua Li14,
- Damon R. Lisch20,
- Sanzhen Liu3,
- Zhijie Liu6,
- Dawn Holligan Nagel13,17,
- Maureen C. McCann21,
- Phillip SanMiguel22,
- Alan M. Myers23,
- Dan Nettleton24,
- John Nguyen25,
- Bryan W. Penning15,21,
- Lalit Ponnala26,
- Kevin L. Schneider27,
- David C. Schwartz28,
- Anupma Sharma27,
- Carol Soderlund29,
- Nathan M. Springer30,
- Qi Sun26,
- Hao Wang13,17,
- Michael Waterman25,
- Richard Westerman22,
- Thomas K. Wolfgruber27,
- Lixing Yang13,
- Yeisoo Yu29,
- Lifang Zhang6,
- Shiguo Zhou28,
- Qihui Zhu13,17,
- Jeffrey L. Bennetzen13,
- R. Kelly Dawe13,17,
- Jiming Jiang19,
- Ning Jiang31,
- Gernot G. Presting27,
- Susan R. Wessler13,17,
- Srinivas Aluru1,9,32,
- Robert A. Martienssen6,
- Sandra W. Clifton7,
- W. Richard McCombie6,
- Rod A. Wing8 and
- Richard K. Wilson7,33,‡
- 1Center for Plant Genomics, Iowa State University, Ames, IA 50011, USA.
- 2Department of Agronomy, Iowa State University, Ames, IA 50011, USA.
- 3Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA.
- 4Center for Carbon Capturing Crops, Iowa State University, Ames, IA 50011, USA.
- 5U.S. Department of Agriculture (USDA), North Atlantic Area, Robert Holley Center for Agriculture and Health, Ithaca, NY 14853, USA.
- 6Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
- 7The Genome Center at Washington University, St. Louis, MO 63108, USA.
- 8Arizona 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.
- 9Department of Electrical and Computer Engineering, Iowa State University, Ames, IA 50011, USA.
- 10Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556, USA.
- 11School of Electrical Engineering and Computer Science, Washington State University, Pullman, WA 99164, USA.
- 12Department of Botany, University of Florida, Gainesville, FL 32611, USA.
- 13Department of Genetics, University of Georgia, Athens, GA 30602, USA.
- 14Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA.
- 15Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA.
- 16Université de Perpignan Via Domitia, CNRS, Perpignan, France.
- 17Department of Plant Biology, University of Georgia, Athens, GA 30602, USA.
- 18NimbleGen, Madison, WI 53711, USA.
- 19Department of Horticulture, University of Wisconsin–Madison, Madison, WI 53706, USA.
- 20Department of Plant Biology, University of California, Berkeley, CA, 94720, USA.
- 21Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA.
- 22Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA.
- 23Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, 50011, USA.
- 24Department of Statistics, Iowa State University, Ames, IA 50011, USA.
- 25Departments of Mathematics, Biology, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA.
- 26Cornell University Computational Biology Service Unit, Cornell University, Ithaca, NY 14850, USA.
- 27Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, HI 96822, USA.
- 28Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, University of Wisconsin–Madison, Madison, WI 53706, USA.
- 29BIO5 Institute for Collaborative Research, University of Arizona, Tucson, AZ 85721, USA.
- 30Department of Plant Biology, University of Minnesota, St. Paul, MN 55108, USA.
- 31Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA.
- 32Indian Institute of Technology, Bombay, India.
- 33Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA.
- ‡To whom correspondence should be addressed. E-mail: rwilson{at}wustl.edu
Abstract
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.
