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The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes

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Listed:
  • 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
    Purdue University)

  • 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
    Center for Genomics and Computational Biology, School of Life Sciences, and School of Sciences, Hebei United University)

  • 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
    Plant Biotechnology Institute, Sahmyook 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
    Centre National de Recherche Scientifique (CNRS), Université d'Evry, UMR 8030, CP5706)

  • 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
    University of Copenhagen, Ole Maaløes Vej 5, 2200
    King Abdulaziz University
    University of Hong Kong)

  • 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)

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.

Suggested Citation

  • 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 & Ia, 2014. "The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes," Nature Communications, Nature, vol. 5(1), pages 1-11, September.
    • Handle: RePEc:nat:natcom:v:5:y:2014:i:1:d:10.1038_ncomms4930
    DOI: 10.1038/ncomms4930
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    Cited by:

    1. Fei Shen & Shixiao Xu & Qi Shen & Changwei Bi & Martin A. Lysak, 2023. "The allotetraploid horseradish genome provides insights into subgenome diversification and formation of critical traits," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
    2. Weinan Sun & Linjie Xia & Jinwu Deng & Simin Sun & Dandan Yue & Jiaqi You & Maojun Wang & Shuangxia Jin & Longfu Zhu & Keith Lindsey & Xianlong Zhang & Xiyan Yang, 2024. "Evolution and subfunctionalization of CIPK6 homologous genes in regulating cotton drought resistance," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    3. Taikui Zhang & Weichen Huang & Lin Zhang & De-Zhu Li & Ji Qi & Hong Ma, 2024. "Phylogenomic profiles of whole-genome duplications in Poaceae and landscape of differential duplicate retention and losses among major Poaceae lineages," Nature Communications, Nature, vol. 15(1), pages 1-27, December.
    4. Mirjana Domazet-Lošo & Tin Široki & Korina Šimičević & Tomislav Domazet-Lošo, 2024. "Macroevolutionary dynamics of gene family gain and loss along multicellular eukaryotic lineages," Nature Communications, Nature, vol. 15(1), pages 1-22, December.
    5. Rahiel Hagos & Abdulwahab Saliu Shaibu & Lei Zhang & Xu Cai & Jianli Liang & Jian Wu & Runmao Lin & Xiaowu Wang, 2020. "Ethiopian Mustard ( Brassica carinata A. Braun) as an Alternative Energy Source and Sustainable Crop," Sustainability, MDPI, vol. 12(18), pages 1-12, September.
    6. Xiao Feng & Qipian Chen & Weihong Wu & Jiexin Wang & Guohong Li & Shaohua Xu & Shao Shao & Min Liu & Cairong Zhong & Chung-I Wu & Suhua Shi & Ziwen He, 2024. "Genomic evidence for rediploidization and adaptive evolution following the whole-genome triplication," Nature Communications, Nature, vol. 15(1), pages 1-15, December.

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