The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes.
Polyploidization has provided much genetic variation for plant adaptive evolution, but the mechanisms by which the molecular evolution of polyploid genomes establishes genetic architecture underlying species differentiation are unclear. Brassica is an ideal model to increase knowledge of polyploid evolution. Here we describe a draft genome sequence of Brassica oleracea, comparing it with that of its sister species B. rapa to reveal numerous chromosome rearrangements and asymmetrical gene loss in duplicated genomic blocks, asymmetrical amplification of transposable elements, differential gene co-retention for specific pathways and variation in gene expression, including alternative splicing, among a large number of paralogous and orthologous genes. Genes related to the production of anticancer phytochemicals and morphological variations illustrate consequences of genome duplication and gene divergence, imparting biochemical and morphological variation to B. oleracea. This study provides insights into Brassica genome evolution and will underpin research into the many important crops in this genus.
1] The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China [2].
Shengyi
S
Liu
1] The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, The Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 10081, China [2].
Yumei
Y
Liu
1] Beijing Genome Institute-Shenzhen, Shenzhen 518083, China [2].
Xinhua
X
Yang
1] The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China [2].
Chaobo
C
Tong
1] Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, Brisbane, Queensland 4072, Australia [2].
David
D
Edwards
1] Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada S7N OX2 [2].
Isobel A P
IA
Parkin
1] The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China [2] Department of Agronomy, Purdue University, WSLR Building B018, West Lafayette, Indiana 47907, USA.
Meixia
M
Zhao
Department of Agronomy, Purdue University, WSLR Building B018, West Lafayette, Indiana 47907, USA.
Jianxin
J
Ma
The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China.
Jingyin
J
Yu
The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China.
Shunmou
S
Huang
1] Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605, USA [2] Center for Genomics and Computational Biology, School of Life Sciences, and School of Sciences, Hebei United University, Tangshan 063000, China.
Xiyin
X
Wang
Beijing Genome Institute-Shenzhen, Shenzhen 518083, China.
Junyi
J
Wang
College of Agronomy and Biotechnology, Southwest University, BeiBei District, Chongqing 400715, China.
Kun
K
Lu
The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, The Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 10081, China.
Zhiyuan
Z
Fang
Centre for Novel Agricultural Products (CNAP), Department of Biology, University of York, Wentworth Way, Heslington, York YO10 5DD, UK.
Ian
I
Bancroft
Department of Plant Sciences, Plant Genomics and Breeding Institute and Research Institute for Agriculture and Life Sciences, College of Agriculture & Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea.
Tae-Jin
TJ
Yang
The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China.
Qiong
Q
Hu
The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China.
Xinfa
X
Wang
Beijing Genome Institute-Shenzhen, Shenzhen 518083, China.
Zhen
Z
Yue
Sichuan Academy of Agricultural Sciences, Chengdu 610066, China.
Haojie
H
Li
Beijing Genome Institute-Shenzhen, Shenzhen 518083, China.
Linfeng
L
Yang
The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, The Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 10081, China.
Jian
J
Wu
Beijing Genome Institute-Shenzhen, Shenzhen 518083, China.
Qing
Q
Zhou
The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, The Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 10081, China.
Wanxin
W
Wang
Southern Cross Plant Science, Southern Cross University, Lismore, New South Wales 2480, Australia.
Graham J
GJ
King
Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211-7310, USA.
J Chris
JC
Pires
Beijing Genome Institute-Shenzhen, Shenzhen 518083, China.
Changxin
C
Lu
Beijing Genome Institute-Shenzhen, Shenzhen 518083, China.
Zhangyan
Z
Wu
Department of Plant Sciences, Plant Genomics and Breeding Institute and Research Institute for Agriculture and Life Sciences, College of Agriculture & Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea.
Perumal
P
Sampath
Beijing Genome Institute-Shenzhen, Shenzhen 518083, China.
Zhuo
Z
Wang
Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605, USA.
Hui
H
Guo
Beijing Genome Institute-Shenzhen, Shenzhen 518083, China.
Shengkai
S
Pan
The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, The Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 10081, China.
Limei
L
Yang
Beijing Genome Institute-Shenzhen, Shenzhen 518083, China.
Jiumeng
J
Min
Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605, USA.
Dong
D
Zhang
Center for Genomics and Computational Biology, School of Life Sciences, and School of Sciences, Hebei United University, Tangshan 063000, China.
Dianchuan
D
Jin
Beijing Genome Institute-Shenzhen, Shenzhen 518083, China.
Wanshun
W
Li
Organization and Evolution of Plant Genomes, Unité de Recherche en Génomique Végétale, Unité Mixte de Recherche 1165 (Institut National de Recherche Agronomique, Centre National de la Recherche Scientifique, Université Evry Val d'Essonne), Evry 91057, France.
Harry
H
Belcram
National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
Jinxing
J
Tu
College of Agronomy, Hunan Agricultural University, Changsha 410128, China.
Mei
M
Guan
Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.
Cunkou
C
Qi
Qinghai Academy of Agriculture and Forestry Sciences, National Key Laboratory Breeding Base for Innovation and Utilization of Plateau Crop Germplasm, Xining 810016, China.
Dezhi
D
Du
College of Agronomy and Biotechnology, Southwest University, BeiBei District, Chongqing 400715, China.
Jiana
J
Li
Sichuan Academy of Agricultural Sciences, Chengdu 610066, China.
Liangcai
L
Jiang
Australian Research Council Centre of Excellence for Integrative Legume Research, University of Queensland, Brisbane, Queensland 4072, Australia.
Jacqueline
J
Batley
National Research Council Canada, Saskatoon, Saskatchewan, Canada S7N 0W9.
Andrew G
AG
Sharpe
The Agricultural Genome Center, National Academy of Agricultural Science, RDA, 126 Suin-Ro, Suwon 441-707, Republic of Korea.
Beom-Seok
BS
Park
Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, Brisbane, Queensland 4072, Australia.
Pradeep
P
Ruperao
The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, The Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 10081, China.
Feng
F
Cheng
1] Department of Plant Sciences, Plant Genomics and Breeding Institute and Research Institute for Agriculture and Life Sciences, College of Agriculture & Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea [2] Department of Life Science, Plant Biotechnology Institute, Sahmyook University, Seoul 139-742, Republic of Korea.
Nomar Espinosa
NE
Waminal
Beijing Genome Institute-Shenzhen, Shenzhen 518083, China.
Yin
Y
Huang
The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China.
Caihua
C
Dong
Center for Genomics and Computational Biology, School of Life Sciences, and School of Sciences, Hebei United University, Tangshan 063000, China.
Li
L
Wang
Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605, USA.
Jingping
J
Li
The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China.
Zhiyong
Z
Hu
The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, The Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 10081, China.
Mu
M
Zhuang
The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China.
Yi
Y
Huang
The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China.
Junyan
J
Huang
The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China.
Jiaqin
J
Shi
The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China.
Desheng
D
Mei
The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China.
Jing
J
Liu
Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605, USA.
Tae-Ho
TH
Lee
Center for Genomics and Computational Biology, School of Life Sciences, and School of Sciences, Hebei United University, Tangshan 063000, China.
Jinpeng
J
Wang
Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605, USA.
Huizhe
H
Jin
National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
Zaiyun
Z
Li
College of Agronomy, Hunan Agricultural University, Changsha 410128, China.
Xun
X
Li
Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.
Jiefu
J
Zhang
Qinghai Academy of Agriculture and Forestry Sciences, National Key Laboratory Breeding Base for Innovation and Utilization of Plateau Crop Germplasm, Xining 810016, China.
Lu
L
Xiao
National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
Yongming
Y
Zhou
College of Agronomy, Hunan Agricultural University, Changsha 410128, China.
Zhongsong
Z
Liu
School of Life Sciences, South-Central University for Nationality, Wuhan 430074, China.
Xuequn
X
Liu
School of Life Sciences, South-Central University for Nationality, Wuhan 430074, China.
Rui
R
Qin
Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605, USA.
Xu
X
Tang
Beijing Genome Institute-Shenzhen, Shenzhen 518083, China.
Wenbin
W
Liu
Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605, USA.
Yupeng
Y
Wang
The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, The Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 10081, China.
Yangyong
Y
Zhang
Department of Plant Sciences, Plant Genomics and Breeding Institute and Research Institute for Agriculture and Life Sciences, College of Agriculture & Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea.
Jonghoon
J
Lee
Department of Life Science, Plant Biotechnology Institute, Sahmyook University, Seoul 139-742, Republic of Korea.
Hyun Hee
HH
Kim
1] Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Génomique, BP5706 Evry 91057, France [2] Centre National de Recherche Scientifique (CNRS), Université d'Evry, UMR 8030, CP5706, Evry 91057, France.
France
F
Denoeud
Beijing Genome Institute-Shenzhen, Shenzhen 518083, China.
Xun
X
Xu
Beijing Genome Institute-Shenzhen, Shenzhen 518083, China.
Xinming
X
Liang
The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China.
Wei
W
Hua
The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, The Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 10081, China.
Xiaowu
X
Wang
1] Beijing Genome Institute-Shenzhen, Shenzhen 518083, China [2] Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark [3] King Abdulaziz University, Jeddah, 21589, Saudi Arabia [4] Department of Medicine and State Key Laboratory of Pharmaceutical Biotechnology, University of Hong Kong, 21 Sassoon Road, Hong Kong.
Jun
J
Wang
Organization and Evolution of Plant Genomes, Unité de Recherche en Génomique Végétale, Unité Mixte de Recherche 1165 (Institut National de Recherche Agronomique, Centre National de la Recherche Scientifique, Université Evry Val d'Essonne), Evry 91057, France.
Boulos
B
Chalhoub
Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605, USA.
Andrew H
AH
Paterson
D017360:Arabidopsis / Q000235:genetics; D001937:Brassica / Q000235:genetics*; D017124:Conserved Sequence; D004251:DNA Transposable Elements / Q000235:genetics; D019143:Evolution, Molecular; D005785:Gene Conversion; D018628:Gene Dosage; D020440:Gene Duplication; D015321:Gene Rearrangement / Q000235:genetics; D020131:Genes, Duplicate; D017343:Genes, Plant; D014644:Genetic Variation; D018745:Genome, Plant; D005961:Glucosinolates / Q000378:metabolism; D058977:Molecular Sequence Annotation; D011123:Polyploidy; D013045:Species Specificity; D026801:Synteny / Q000235:genetics
D004251:DNA Transposable Elements; D005961:Glucosinolates