The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes

Shengyi Liu (), Yumei Liu, Xinhua Yang, Chaobo Tong, David Edwards, Isobel A. P. Parkin, Meixia Zhao, Jianxin Ma, Jingyin Yu, Shunmou Huang, Xiyin Wang, Junyi Wang, Kun Lu, Zhiyuan Fang, Ian Bancroft, Tae-Jin Yang, Qiong Hu, Xinfa Wang, Zhen Yue, Haojie Li, Linfeng Yang, Jian Wu, Qing Zhou, Wanxin Wang, Graham J King, J. Chris Pires, Changxin Lu, Zhangyan Wu, Perumal Sampath, Zhuo Wang, Hui Guo, Shengkai Pan, Limei Yang, Jiumeng Min, Dong Zhang, Dianchuan Jin, Wanshun Li, Harry Belcram, Jinxing Tu, Mei Guan, Cunkou Qi, Dezhi Du, Jiana Li, Liangcai Jiang, Jacqueline Batley, Andrew G Sharpe, Beom-Seok Park, Pradeep Ruperao, Feng Cheng, Nomar Espinosa Waminal, Yin Huang, Caihua Dong, Li Wang, Jingping Li, Zhiyong Hu, Mu Zhuang, Yi Huang, Junyan Huang, Jiaqin Shi, Desheng Mei, Jing Liu, Tae-Ho Lee, Jinpeng Wang, Huizhe Jin, Zaiyun Li, Xun Li, Jiefu Zhang, Lu Xiao, Yongming Zhou, Zhongsong Liu, Xuequn Liu, Rui Qin, Xu Tang, Wenbin Liu, Yupeng Wang, Yangyong Zhang, Jonghoon Lee, Hyun Hee Kim, France Denoeud, Xun Xu, Xinming Liang, Wei Hua, Xiaowu Wang, Jun Wang, Boulos Chalhoub and Andrew H Paterson
Additional contact information
Shengyi Liu: 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
Yumei Liu: 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
Xinhua Yang: Beijing Genome Institute-Shenzhen
Chaobo Tong: 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
David Edwards: Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland
Isobel A. P. Parkin: Agriculture and Agri-Food Canada
Meixia Zhao: 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
Jianxin Ma: Purdue University
Jingyin 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
Shunmou 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
Xiyin Wang: Plant Genome Mapping Laboratory, University of Georgia
Junyi Wang: Beijing Genome Institute-Shenzhen
Kun Lu: College of Agronomy and Biotechnology, Southwest University, BeiBei District
Zhiyuan Fang: 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
Ian Bancroft: Centre for Novel Agricultural Products (CNAP), University of York, Wentworth Way
Tae-Jin Yang: Plant Genomics and Breeding Institute and Research Institute for Agriculture and Life Sciences, College of Agriculture & Life Sciences, Seoul National University
Qiong 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
Xinfa Wang: 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
Zhen Yue: Beijing Genome Institute-Shenzhen
Haojie Li: Sichuan Academy of Agricultural Sciences
Linfeng Yang: Beijing Genome Institute-Shenzhen
Jian Wu: 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
Qing Zhou: Beijing Genome Institute-Shenzhen
Wanxin 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
Graham J King: Southern Cross Plant Science, Southern Cross University
J. Chris Pires: Bond Life Sciences Center, University of Missouri
Changxin Lu: Beijing Genome Institute-Shenzhen
Zhangyan Wu: Beijing Genome Institute-Shenzhen
Perumal Sampath: Plant Genomics and Breeding Institute and Research Institute for Agriculture and Life Sciences, College of Agriculture & Life Sciences, Seoul National University
Zhuo Wang: Beijing Genome Institute-Shenzhen
Hui Guo: Plant Genome Mapping Laboratory, University of Georgia
Shengkai Pan: Beijing Genome Institute-Shenzhen
Limei 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
Jiumeng Min: Beijing Genome Institute-Shenzhen
Dong Zhang: Plant Genome Mapping Laboratory, University of Georgia
Dianchuan Jin: Center for Genomics and Computational Biology, School of Life Sciences, and School of Sciences, Hebei United University
Wanshun Li: Beijing Genome Institute-Shenzhen
Harry Belcram: 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)
Jinxing Tu: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University
Mei Guan: College of Agronomy, Hunan Agricultural University
Cunkou Qi: Jiangsu Academy of Agricultural Sciences
Dezhi Du: Qinghai Academy of Agriculture and Forestry Sciences, National Key Laboratory Breeding Base for Innovation and Utilization of Plateau Crop Germplasm
Jiana Li: College of Agronomy and Biotechnology, Southwest University, BeiBei District
Liangcai Jiang: Sichuan Academy of Agricultural Sciences
Jacqueline Batley: Australian Research Council Centre of Excellence for Integrative Legume Research, University of Queensland
Andrew G Sharpe: National Research Council Canada
Beom-Seok Park: The Agricultural Genome Center, National Academy of Agricultural Science, RDA
Pradeep Ruperao: Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland
Feng Cheng: 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
Nomar Espinosa Waminal: Plant Genomics and Breeding Institute and Research Institute for Agriculture and Life Sciences, College of Agriculture & Life Sciences, Seoul National University
Yin Huang: Beijing Genome Institute-Shenzhen
Caihua Dong: 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
Li Wang: Center for Genomics and Computational Biology, School of Life Sciences, and School of Sciences, Hebei United University
Jingping Li: Plant Genome Mapping Laboratory, University of Georgia
Zhiyong 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
Mu Zhuang: 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
Yi 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
Junyan 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
Jiaqin 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
Desheng 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
Jing Liu: 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
Tae-Ho Lee: Plant Genome Mapping Laboratory, University of Georgia
Jinpeng Wang: Center for Genomics and Computational Biology, School of Life Sciences, and School of Sciences, Hebei United University
Huizhe Jin: Plant Genome Mapping Laboratory, University of Georgia
Zaiyun Li: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University
Xun Li: College of Agronomy, Hunan Agricultural University
Jiefu Zhang: Jiangsu Academy of Agricultural Sciences
Lu Xiao: Qinghai Academy of Agriculture and Forestry Sciences, National Key Laboratory Breeding Base for Innovation and Utilization of Plateau Crop Germplasm
Yongming Zhou: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University
Zhongsong Liu: College of Agronomy, Hunan Agricultural University
Xuequn Liu: School of Life Sciences, South-Central University for Nationality
Rui Qin: School of Life Sciences, South-Central University for Nationality
Xu Tang: Plant Genome Mapping Laboratory, University of Georgia
Wenbin Liu: Beijing Genome Institute-Shenzhen
Yupeng Wang: Plant Genome Mapping Laboratory, University of Georgia
Yangyong Zhang: 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
Jonghoon Lee: Plant Genomics and Breeding Institute and Research Institute for Agriculture and Life Sciences, College of Agriculture & Life Sciences, Seoul National University
Hyun Hee Kim: Plant Biotechnology Institute, Sahmyook University
France Denoeud: Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Génomique, BP5706
Xun Xu: Beijing Genome Institute-Shenzhen
Xinming Liang: Beijing Genome Institute-Shenzhen
Wei Hua: 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
Xiaowu 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
Jun Wang: Beijing Genome Institute-Shenzhen
Boulos Chalhoub: 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)
Andrew H Paterson: Plant Genome Mapping Laboratory, University of Georgia

Nature Communications, 2014, vol. 5, issue 1, 1-11

Abstract: 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.

Date: 2014
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DOI: 10.1038/ncomms4930

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