Whole-genome sequencing and intensive analysis of the undomesticated soybean (Glycine soja Sieb. and Zucc.) genome.
The genome of soybean (Glycine max), a commercially important crop, has recently been sequenced and is one of six crop species to have been sequenced. Here we report the genome sequence of G. soja, the undomesticated ancestor of G. max (in particular, G. soja var. IT182932). The 48.8-Gb Illumina Genome Analyzer (Illumina-GA) short DNA reads were aligned to the G. max reference genome and a consensus was determined for G. soja. This consensus sequence spanned 915.4 Mb, representing a coverage of 97.65% of the G. max published genome sequence and an average mapping depth of 43-fold. The nucleotide sequence of the G. soja genome, which contains 2.5 Mb of substituted bases and 406 kb of small insertions/deletions relative to G. max, is ∼0.31% different from that of G. max. In addition to the mapped 915.4-Mb consensus sequence, 32.4 Mb of large deletions and 8.3 Mb of novel sequence contigs in the G. soja genome were also detected. Nucleotide variants of G. soja versus G. max confirmed by Roche Genome Sequencer FLX sequencing showed a 99.99% concordance in single-nucleotide polymorphism and a 98.82% agreement in insertion/deletion calls on Illumina-GA reads. Data presented in this study suggest that the G. soja/G. max complex may be at least 0.27 million y old, appearing before the relatively recent event of domestication (6,000∼9,000 y ago). This suggests that soybean domestication is complicated and that more in-depth study of population genetics is needed. In any case, genome comparison of domesticated and undomesticated forms of soybean can facilitate its improvement.
Department of Plant Science and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea.
Moon Young
MY
Kim
Sunghoon
S
Lee
Kyujung
K
Van
Tae-Hyung
TH
Kim
Soon-Chun
SC
Jeong
Ik-Young
IY
Choi
Dae-Soo
DS
Kim
Yong-Seok
YS
Lee
Daeui
D
Park
Jianxin
J
Ma
Woo-Yeon
WY
Kim
Byoung-Chul
BC
Kim
Sungjin
S
Park
Kyung-A
KA
Lee
Dong Hyun
DH
Kim
Kil Hyun
KH
Kim
Jin Hee
JH
Shin
Young Eun
YE
Jang
Kyung Do
KD
Kim
Wei Xian
WX
Liu
Tanapon
T
Chaisan
Yang Jae
YJ
Kang
Yeong-Ho
YH
Lee
Kook-Hyung
KH
Kim
Jung-Kyung
JK
Moon
Jeremy
J
Schmutz
Scott A
SA
Jackson
Jong
J
Bhak
Suk-Ha
SH
Lee
D014644:Genetic Variation; D018745:Genome, Plant / Q000502:physiology*; D013025:Glycine max / Q000235:genetics*