Genome sequence of the palaeopolyploid soybean

Authors

• Jeremy Schmutz, HudsonAlpha Genome Sequencing Center, Huntsville, AL
• Steven B. Cannon, USDA-ARS Corn Insects and Crop Genetics Research Unit, Ames, Iowa
• Jessica Schlueter, University of North Carolina at Charlotte
• Jianxin Ma, Purdue University
• Therese Mitros, University of California, Berkeley
• William Nelson, University of Arizona
• David L. Hyten, USDA-ARSFollow
• Qijian Song, USDA, ARS, Beltsville, MDFollow
• Jay J. Thelen, University of Missouri, Columbia
• Jianlin Cheng, University of Missouri, Columbia
• Dong Xu, University of Missouri, Columbia
• Uffe Hellsten, Joint Genome Institute, Walnut Creek, California
• Gregory D. May, National Center for Genome Resources, Santa Fe, NM
• Yeisoo Yu, University of Arizona
• Tetsuya Sakurai, RIKEN Plant Science Center, Yokohama, Japan
• Taishi Umezawa, RIKEN Plant Science Center, Yokohama, Japan
• Madan K. Bhattacharyya, Iowa State University
• Devinder Sandhu, University of Wisconsin-Stevens Point
• Babu Valliyodan, University of Missouri, Columbia
• Erika Lindquist, Joint Genome Institute, Walnut Creek, California
• Myron Peto, USDA-ARS Corn Insects and Crop Genetics Research Unit, Ames, Iowa
• David Grant, USDA-ARS Corn Insects and Crop Genetics Research Unit, Ames, Iowa
• Shengqiang Shu, Joint Genome Institute, Walnut Creek, California
• David Goodstein, Joint Genome Institute, Walnut Creek, California
• Kerrie Barry, Joint Genome Institute, Walnut Creek, California
• Montona Futrell-Griggs, Purdue University - Main Campus
• Brian Abernathy, Purdue University
• Jianchang Du, Purdue University
• Zhixi Tian, Purdue University
• Liucun Zhu, Purdue University
• Navdeep Gill, Purdue University
• Trupti Joshi, University of Missouri, Columbia
• Marc Libault, University of Missouri, ColumbiaFollow
• Ananad Sethuraman, HudsonAlpha Genome Sequencing Center, Huntsville, AL
• Xue-Cheng Zhang, University of Missouri, Columbia
• Kazuo Shinozaki, RIKEN Plant Science Center, Yokohama, Japan
• Henry T. Nguyen, University of Missouri, ColumbiaFollow
• Rod A. Wing, University of Arizona
• Perry Cregan, USDA, ARS, Beltsville, MD
• James E. Specht, University of Nebraska-LincolnFollow
• Jane Grimwood, HudsonAlpha Genome Sequencing Center, Huntsville, AL
• Dan Rokhsar, Joint Genome Institute, Walnut Creek, California
• Gary Stacey, University of Missouri, ColumbiaFollow
• Randy C. Shoemaker, USDA-ARS Corn Insects and Crop Genetics Research Unit, Ames, Iowa
• Scott A. Jackson, Purdue UniversityFollow

ORCID IDs

David L. Hyten

Document Type

Article

Date of this Version

1-2010

Comments

Published in Nature Vol 463, 14 January 2010, doi:10.1038/nature08670.

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.

All supplemental information is included in the downloadable PDF file, except for the data file for Supplementary Table S5, which is attached (below) as an "Additional file."