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PMID: 24852848 Published · epublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes.

Nature communications ·Vol. 5 ·2014-05-23 ·Pages 3930

Liu S, Liu Y, Yang X, Tong C, Edwards D, Parkin IA, Zhao M, Ma J, Yu J, Huang S, Wang X, Wang J, Lu K, Fang Z, Bancroft I, Yang TJ, Hu Q, Wang X, Yue Z, Li H, Yang L, Wu J, Zhou Q, Wang W, King GJ, Pires JC, Lu C, Wu Z, Sampath P, Wang Z, Guo H, Pan S, Yang L, Min J, Zhang D, Jin D, Li W, Belcram H, Tu J, Guan M, Qi C, Du D, Li J, Jiang L, Batley J, Sharpe AG, Park BS, Ruperao P, Cheng F, Waminal NE, Huang Y, Dong C, Wang L, Li J, Hu Z, Zhuang M, Huang Y, Huang J, Shi J, Mei D, Liu J, Lee TH, Wang J, Jin H, Li Z, Li X, Zhang J, Xiao L, Zhou Y, Liu Z, Liu X, Qin R, Tang X, Liu W, Wang Y, Zhang Y, Lee J, Kim HH, Denoeud F, Xu X, Liang X, Hua W, Wang X, Wang J, Chalhoub B, Paterson AH

Abstract

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.

MeSH Terms
Arabidopsis/genetics Brassica/genetics Conserved Sequence DNA Transposable Elements/genetics Evolution, Molecular Gene Conversion Gene Dosage Gene Duplication Gene Rearrangement/genetics Genes, Duplicate Genes, Plant Genetic Variation Genome, Plant Glucosinolates/metabolism Molecular Sequence Annotation Polyploidy Species Specificity Synteny/genetics
Chemicals
DNA Transposable Elements Glucosinolates
Authors & Affiliations
86 authors, click to expand affiliations / ORCID
Liu Shengyi
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].
Liu Yumei
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].
Yang Xinhua
1] Beijing Genome Institute-Shenzhen, Shenzhen 518083, China [2].
Tong Chaobo
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].
Edwards David
1] Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, Brisbane, Queensland 4072, Australia [2].
Parkin Isobel A P
1] Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada S7N OX2 [2].
Zhao Meixia
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.
Ma Jianxin
Department of Agronomy, Purdue University, WSLR Building B018, West Lafayette, Indiana 47907, USA.
Yu Jingyin
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.
Huang Shunmou
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.
Wang Xiyin
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.
Wang Junyi
Beijing Genome Institute-Shenzhen, Shenzhen 518083, China.
Lu Kun
College of Agronomy and Biotechnology, Southwest University, BeiBei District, Chongqing 400715, China.
Fang Zhiyuan
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.
Bancroft Ian
Centre for Novel Agricultural Products (CNAP), Department of Biology, University of York, Wentworth Way, Heslington, York YO10 5DD, UK.
Yang Tae-Jin
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.
Hu Qiong
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.
Wang Xinfa
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.
Yue Zhen
Beijing Genome Institute-Shenzhen, Shenzhen 518083, China.
Li Haojie
Sichuan Academy of Agricultural Sciences, Chengdu 610066, China.
Yang Linfeng
Beijing Genome Institute-Shenzhen, Shenzhen 518083, China.
Wu Jian
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.
Zhou Qing
Beijing Genome Institute-Shenzhen, Shenzhen 518083, China.
Wang Wanxin
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.
King Graham J
Southern Cross Plant Science, Southern Cross University, Lismore, New South Wales 2480, Australia.
Pires J Chris
Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211-7310, USA.
Lu Changxin
Beijing Genome Institute-Shenzhen, Shenzhen 518083, China.
Wu Zhangyan
Beijing Genome Institute-Shenzhen, Shenzhen 518083, China.
Sampath Perumal
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.
Wang Zhuo
Beijing Genome Institute-Shenzhen, Shenzhen 518083, China.
Guo Hui
Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605, USA.
Pan Shengkai
Beijing Genome Institute-Shenzhen, Shenzhen 518083, China.
Yang Limei
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.
Min Jiumeng
Beijing Genome Institute-Shenzhen, Shenzhen 518083, China.
Zhang Dong
Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605, USA.
Jin Dianchuan
Center for Genomics and Computational Biology, School of Life Sciences, and School of Sciences, Hebei United University, Tangshan 063000, China.
Li Wanshun
Beijing Genome Institute-Shenzhen, Shenzhen 518083, China.
Belcram Harry
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.
Tu Jinxing
National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
Guan Mei
College of Agronomy, Hunan Agricultural University, Changsha 410128, China.
Qi Cunkou
Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.
Du Dezhi
Qinghai Academy of Agriculture and Forestry Sciences, National Key Laboratory Breeding Base for Innovation and Utilization of Plateau Crop Germplasm, Xining 810016, China.
Li Jiana
College of Agronomy and Biotechnology, Southwest University, BeiBei District, Chongqing 400715, China.
Jiang Liangcai
Sichuan Academy of Agricultural Sciences, Chengdu 610066, China.
Batley Jacqueline
Australian Research Council Centre of Excellence for Integrative Legume Research, University of Queensland, Brisbane, Queensland 4072, Australia.
Sharpe Andrew G
National Research Council Canada, Saskatoon, Saskatchewan, Canada S7N 0W9.
Park Beom-Seok
The Agricultural Genome Center, National Academy of Agricultural Science, RDA, 126 Suin-Ro, Suwon 441-707, Republic of Korea.
Ruperao Pradeep
Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, Brisbane, Queensland 4072, Australia.
Cheng Feng
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.
Waminal Nomar Espinosa
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.
Huang Yin
Beijing Genome Institute-Shenzhen, Shenzhen 518083, China.
Dong Caihua
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.
Wang Li
Center for Genomics and Computational Biology, School of Life Sciences, and School of Sciences, Hebei United University, Tangshan 063000, China.
Li Jingping
Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605, USA.
Hu Zhiyong
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.
Zhuang Mu
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.
Huang Yi
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.
Huang Junyan
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.
Shi Jiaqin
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.
Mei Desheng
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.
Liu Jing
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.
Lee Tae-Ho
Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605, USA.
Wang Jinpeng
Center for Genomics and Computational Biology, School of Life Sciences, and School of Sciences, Hebei United University, Tangshan 063000, China.
Jin Huizhe
Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605, USA.
Li Zaiyun
National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
Li Xun
College of Agronomy, Hunan Agricultural University, Changsha 410128, China.
Zhang Jiefu
Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.
Xiao Lu
Qinghai Academy of Agriculture and Forestry Sciences, National Key Laboratory Breeding Base for Innovation and Utilization of Plateau Crop Germplasm, Xining 810016, China.
Zhou Yongming
National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
Liu Zhongsong
College of Agronomy, Hunan Agricultural University, Changsha 410128, China.
Liu Xuequn
School of Life Sciences, South-Central University for Nationality, Wuhan 430074, China.
Qin Rui
School of Life Sciences, South-Central University for Nationality, Wuhan 430074, China.
Tang Xu
Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605, USA.
Liu Wenbin
Beijing Genome Institute-Shenzhen, Shenzhen 518083, China.
Wang Yupeng
Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605, USA.
Zhang Yangyong
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.
Lee Jonghoon
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.
Kim Hyun Hee
Department of Life Science, Plant Biotechnology Institute, Sahmyook University, Seoul 139-742, Republic of Korea.
Denoeud France
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.
Xu Xun
Beijing Genome Institute-Shenzhen, Shenzhen 518083, China.
Liang Xinming
Beijing Genome Institute-Shenzhen, Shenzhen 518083, China.
Hua Wei
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.
Wang Xiaowu
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.
Wang Jun
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.
Chalhoub Boulos
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.
Paterson Andrew H
Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605, USA.
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Article Info
Journal
Nature communications
Abbr.
Nat Commun
ISSN
2041-1723
DOI
10.1038/ncomms4930
Published
2014-05-23
Epub
2014-00-23
Pages
3930
Language
English
Region
England
NLM ID
101528555
PMCID
PMC4279128
Subset
IM
Grants
Biotechnology and Biological Sciences Research Council · BB/E017363/1 · United Kingdom
Databases
GEO
GSE42891, GSE43245
External Links
PubMed source DOI: 10.1038/ncomms4930 PMC Full Text View journal details
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