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Genome sequence of the palaeopolyploid soybean

Author

Listed:
  • Jeremy Schmutz

    (HudsonAlpha Genome Sequencing Center, 601 Genome Way, Huntsville, Alabama 35806, USA
    Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, 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
    Purdue University, 915 W. State Street, West Lafayette, Indiana 47906, 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
    University of Maryland, College Park, Maryland 20742, 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
    Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, 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
    National Center for Soybean Biotechnology, 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)

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.

Suggested Citation

  • 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 , 2010. "Genome sequence of the palaeopolyploid soybean," Nature, Nature, vol. 463(7278), pages 178-183, January.
  • Handle: RePEc:nat:nature:v:463:y:2010:i:7278:d:10.1038_nature08670
    DOI: 10.1038/nature08670
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