Genome sequence of the palaeopolyploid soybean

Jeremy Schmutz, Steven B. Cannon, Jessica Schlueter, Jianxin Ma, Therese Mitros, William Nelson, David L. Hyten, Qijian Song, Jay J. Thelen, Jianlin Cheng, Dong Xu, Uffe Hellsten, Gregory D. May, Yeisoo Yu, Tetsuya Sakurai, Taishi Umezawa, Madan K. Bhattacharyya, Devinder Sandhu, Babu Valliyodan, Erika Lindquist, Myron Peto, David Grant, Shengqiang Shu, David Goodstein, Kerrie Barry, Montona Futrell-Griggs, Brian Abernathy, Jianchang Du, Zhixi Tian, Liucun Zhu, Navdeep Gill, Trupti Joshi, Marc Libault, Anand Sethuraman, Xue-Cheng Zhang, Kazuo Shinozaki, Henry T. Nguyen, Rod A. Wing, Perry Cregan, James Specht, Jane Grimwood, Dan Rokhsar, Gary Stacey, Randy C. Shoemaker and Scott A. Jackson ()
Additional contact information
Jeremy Schmutz: HudsonAlpha Genome Sequencing Center, 601 Genome Way, Huntsville, Alabama 35806, USA
Steven B. Cannon: USDA-ARS Corn Insects and Crop Genetics Research Unit, Ames, Iowa 50011, USA
Jessica Schlueter: 9201 University City Blvd, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, USA
Jianxin Ma: Purdue University, 915 W. State Street, West Lafayette, Indiana 47906, USA
Therese Mitros: Center for Integrative Genomics, University of California, Berkeley, California 94720, USA
William Nelson: Arizona Genomics Computational Laboratory, BIO5 Institute, 1657 E. Helen Street, The University of Arizona, Tucson, Arizona 85721, USA
David L. Hyten: USDA, ARS, Soybean Genomics and Improvement Laboratory, B006, BARC-West, Beltsville, Maryland 20705, USA
Qijian Song: USDA, ARS, Soybean Genomics and Improvement Laboratory, B006, BARC-West, Beltsville, Maryland 20705, USA
Jay J. Thelen: 109 Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211, USA
Jianlin Cheng: University of Missouri, Columbia, Missouri 65211, USA
Dong Xu: University of Missouri, Columbia, Missouri 65211, USA
Uffe Hellsten: Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA
Gregory D. May: The National Center for Genome Resources, 2935 Rodeo Park Drive East, Santa Fe, New Mexico 87505, USA
Yeisoo Yu: Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
Tetsuya Sakurai: RIKEN Plant Science Center
Taishi Umezawa: RIKEN Plant Science Center
Madan K. Bhattacharyya: Iowa State University, Ames, Iowa 50011, USA
Devinder Sandhu: University of Wisconsin-Stevens Point, Stevens Point, Wisconsin 54481, USA
Babu Valliyodan: National Center for Soybean Biotechnology, University of Missouri, Columbia, Missouri 65211, USA
Erika Lindquist: Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA
Myron Peto: USDA-ARS Corn Insects and Crop Genetics Research Unit, Ames, Iowa 50011, USA
David Grant: USDA-ARS Corn Insects and Crop Genetics Research Unit, Ames, Iowa 50011, USA
Shengqiang Shu: Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA
David Goodstein: Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA
Kerrie Barry: Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA
Montona Futrell-Griggs: Purdue University, 915 W. State Street, West Lafayette, Indiana 47906, USA
Brian Abernathy: Purdue University, 915 W. State Street, West Lafayette, Indiana 47906, USA
Jianchang Du: Purdue University, 915 W. State Street, West Lafayette, Indiana 47906, USA
Zhixi Tian: Purdue University, 915 W. State Street, West Lafayette, Indiana 47906, USA
Liucun Zhu: Purdue University, 915 W. State Street, West Lafayette, Indiana 47906, USA
Navdeep Gill: Purdue University, 915 W. State Street, West Lafayette, Indiana 47906, USA
Trupti Joshi: University of Missouri, Columbia, Missouri 65211, USA
Marc Libault: National Center for Soybean Biotechnology, University of Missouri, Columbia, Missouri 65211, USA
Anand Sethuraman: HudsonAlpha Genome Sequencing Center, 601 Genome Way, Huntsville, Alabama 35806, USA
Xue-Cheng Zhang: National Center for Soybean Biotechnology, University of Missouri, Columbia, Missouri 65211, USA
Kazuo Shinozaki: RIKEN Plant Science Center
Henry T. Nguyen: National Center for Soybean Biotechnology, University of Missouri, Columbia, Missouri 65211, USA
Rod A. Wing: Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
Perry Cregan: USDA, ARS, Soybean Genomics and Improvement Laboratory, B006, BARC-West, Beltsville, Maryland 20705, USA
James Specht: University of Nebraska, Lincoln, Nebraska 68583, USA
Jane Grimwood: HudsonAlpha Genome Sequencing Center, 601 Genome Way, Huntsville, Alabama 35806, USA
Dan Rokhsar: Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA
Gary Stacey: 109 Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211, USA
Randy C. Shoemaker: USDA-ARS Corn Insects and Crop Genetics Research Unit, Ames, Iowa 50011, USA
Scott A. Jackson: Purdue University, 915 W. State Street, West Lafayette, Indiana 47906, USA

Nature, 2010, vol. 463, issue 7278, 178-183

Abstract: Abstract Soybean (Glycine max) is one of the most important crop plants for seed protein and oil content, and for its capacity to fix atmospheric nitrogen through symbioses with soil-borne microorganisms. We sequenced the 1.1-gigabase genome by a whole-genome shotgun approach and integrated it with physical and high-density genetic maps to create a chromosome-scale draft sequence assembly. We predict 46,430 protein-coding genes, 70% more than Arabidopsis and similar to the poplar genome which, like soybean, is an ancient polyploid (palaeopolyploid). About 78% of the predicted genes occur in chromosome ends, which comprise less than one-half of the genome but account for nearly all of the genetic recombination. Genome duplications occurred at approximately 59 and 13 million years ago, resulting in a highly duplicated genome with nearly 75% of the genes present in multiple copies. The two duplication events were followed by gene diversification and loss, and numerous chromosome rearrangements. An accurate soybean genome sequence will facilitate the identification of the genetic basis of many soybean traits, and accelerate the creation of improved soybean varieties.

Date: 2010
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DOI: 10.1038/nature08670

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