Genome sequence of the palaeopolyploid soybean.
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.
Schmutz
Jeremy
J
HudsonAlpha Genome Sequencing Center, 601 Genome Way, Huntsville, Alabama 35806, USA.
Cannon
Steven B
SB
Schlueter
Jessica
J
Ma
Jianxin
J
Mitros
Therese
T
Nelson
William
W
Hyten
David L
DL
Song
Qijian
Q
Thelen
Jay J
JJ
Cheng
Jianlin
J
Xu
Dong
D
Hellsten
Uffe
U
May
Gregory D
GD
Yu
Yeisoo
Y
Sakurai
Tetsuya
T
Umezawa
Taishi
T
Bhattacharyya
Madan K
MK
Sandhu
Devinder
D
Valliyodan
Babu
B
Lindquist
Erika
E
Peto
Myron
M
Grant
David
D
Shu
Shengqiang
S
Goodstein
David
D
Barry
Kerrie
K
Futrell-Griggs
Montona
M
Abernathy
Brian
B
Du
Jianchang
J
Tian
Zhixi
Z
Zhu
Liucun
L
Gill
Navdeep
N
Joshi
Trupti
T
Libault
Marc
M
Sethuraman
Anand
A
Zhang
Xue-Cheng
XC
Shinozaki
Kazuo
K
Nguyen
Henry T
HT
Wing
Rod A
RA
Cregan
Perry
P
Specht
James
J
Grimwood
Jane
J
Rokhsar
Dan
D
Stacey
Gary
G
Shoemaker
Randy C
RC
Jackson
Scott A
SA
D017360:Arabidopsis / Q000235:genetics; D001947:Breeding; D032461:Chromosomes, Plant / Q000235:genetics; D019143:Evolution, Molecular; D020440:Gene Duplication; D020131:Genes, Duplicate / Q000235:genetics; D017343:Genes, Plant / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics*; D023281:Genomics; D008969:Molecular Sequence Data; D005810:Multigene Family / Q000235:genetics; D010802:Phylogeny; D055170:Plant Root Nodulation / Q000235:genetics; D011123:Polyploidy; D040641:Quantitative Trait Loci / Q000235:genetics; D011995:Recombination, Genetic; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics; D013024:Soybean Oil / Q000096:biosynthesis; D013025:Glycine max / Q000235:genetics*; D026801:Synteny / Q000235:genetics; D014157:Transcription Factors / Q000235:genetics
D014157:Transcription Factors; D013024:Soybean Oil