Letter | Published:

The genome of the mesopolyploid crop species Brassica rapa

Nature Genetics volume 43, pages 10351039 (2011) | Download Citation

Abstract

We report the annotation and analysis of the draft genome sequence of Brassica rapa accession Chiifu-401-42, a Chinese cabbage. We modeled 41,174 protein coding genes in the B. rapa genome, which has undergone genome triplication. We used Arabidopsis thaliana as an outgroup for investigating the consequences of genome triplication, such as structural and functional evolution. The extent of gene loss (fractionation) among triplicated genome segments varies, with one of the three copies consistently retaining a disproportionately large fraction of the genes expected to have been present in its ancestor. Variation in the number of members of gene families present in the genome may contribute to the remarkable morphological plasticity of Brassica species. The B. rapa genome sequence provides an important resource for studying the evolution of polyploid genomes and underpins the genetic improvement of Brassica oil and vegetable crops.

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Acknowledgements

This work was primarily funded by the Chinese Ministry of Science and Technology, Ministry of Agriculture, Ministry of Finance, the National Natural Science Foundation of China. Other funding sources included: Core Research Budget of the Non-profit Governmental Research Institution; the European Union 7th Framework Project; funds from Shenzhen Municipal Government of China; the Danish Natural Science Research Council; National Academy of Agricultural Science and the Next-Generation Biogreen21 Program, Rural Development Administration, Korea; the Technology Development Program for Agriculture and Forestry, Ministry for Food, Agriculture, Forestry and Fisheries, Korea; United Kingdom's Biotechnology and Biological Sciences Research Council; Institute National de la Recherche Agronomique, France; Japanese Kazusa DNA Research Institute Foundation; National Science Foundation, USA; Bielefeld University, Germany; the Australian Research Council; the Australian Grains Research and Development Corporation; Agriculture and Agri-Food Canada; and the National Research Council of Canada's Plant Biotechnology Institute. See the Supplementary Note for a full list of support and acknowledgments.

Author information

Affiliations

  1. Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences (IVF, CAAS), Beijing, China.

    • Xiaowu Wang
    • , Rifei Sun
    • , Jian Wu
    • , Feng Cheng
    • , Sanwen Huang
    • , Xixiang Li
    • , Bo Liu
    • , Di Shen
    • , Fei Li
    • , Haiping Wang
    • , Hui Wang
    • , Jie Deng
    • , Lu Fang
    • , Shujiang Zhang
    • , Silong Sun
    • , Yan Wang
    • , Yang Qiu
    • , Yongchen Du
    • , Yongcui Liao
    •  & Zhonghua Zhang
  2. Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China.

    • Hanzhong Wang
    • , Shengyi Liu
    • , Wei Hua
    • , Chaobo Tong
    • , Jingyin Yu
    • , Meixia Zhao
    •  & Shunmou Huang
  3. BGI-Shenzhen, Shenzhen, China.

    • Jun Wang
    • , Yinqi Bai
    • , Junyi Wang
    • , Bo Wang
    • , Binghang Liu
    • , Bo Li
    • , Chi Song
    • , Chunfang Peng
    • , Chunyu Geng
    • , Chuyu Lin
    • , Desheng Mu
    • , Heling Zhou
    • , Jianwen Li
    • , Jiaohui Xu
    • , Jiumeng Min
    • , Kui Wu
    • , Qingle Cai
    • , Quanfei Huang
    • , Ruiqiang Li
    • , Shifeng Cheng
    • , Shu Zhang
    • , Wei Fan
    • , Xiang Zhao
    • , Xun Xu
    • , Ye Yin
    • , Yingrui Li
    • , Zhenyu Li
    •  & Zhiwen Wang
  4. Department of Biology, University of Copenhagen, Copenhagen, Denmark.

    • Jun Wang
  5. Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, Suwon, Korea.

    • Jeong-Hwan Mun
    • , Beom-Seok Park
    • , Jeong-Sun Kim
    • , Jin A Kim
    • , Mina Jin
    •  & Soo-Jin Kwon
  6. John Innes Centre, Norwich Research Park, Colney, Norwich, UK.

    • Ian Bancroft
    • , Eleni Soumpourou
    • , Fiona Fraser
    • , Martin Trick
    •  & Nizar Drou
  7. Center for Genomics and Computational Biology, School of Life Sciences, Hebei United University, Tangshan, Hebei, China.

    • Xiyin Wang
    • , Jinpeng Wang
    • , Li Wang
    •  & Zhenyi Wang
  8. School of Sciences, Hebei United University, Tangshan, Hebei, China.

    • Xiyin Wang
    • , Jinpeng Wang
    • , Li Wang
    • , Yupeng Wang
    •  & Zhenyi Wang
  9. Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia, USA.

    • Xiyin Wang
    • , Andrew H Paterson
    • , Hui Guo
    • , Huizhe Jin
    • , Jingping Li
    • , Tae-Ho Lee
    •  & Xu Tan
  10. Department of Plant and Microbial Biology, University of California, Berkeley, California, USA.

    • Michael Freeling
    •  & Haibao Tang
  11. Division of Biological Sciences, Bond Life Sciences Center, University of Missouri, Columbia, Missouri, USA.

    • J Chris Pires
    •  & Zhiyong Xiong
  12. Organization and Evolution of Plant Genomes, Unité de Recherche en Génomique Végétale, Unité Mixte de Recherché 1165, (Inland Northwest Research Alliance-Centre National de la Recherche Scientifique, Université Evry Val d'Essonne), Evry, France.

    • Boulos Chalhoub
    • , Harry Belcram
    •  & Jérémy Just
  13. University of Queensland, School of Agriculture and Food Sciences, Brisbane, Queensland, Australia.

    • Alice Hayward
    • , Christopher Duran
    • , David Edwards
    • , Jacqueline Batley
    •  & Paul J Berkman
  14. Australian Research Council Centre of Excellence for Integrative Legume Research, Brisbane, Queensland, Australia.

    • Alice Hayward
    •  & Jacqueline Batley
  15. National Research Council-Plant Biotechnology Institute, Saskatoon, Saskatchewan, Canada.

    • Andrew G Sharpe
    •  & Chushin Koh
  16. Center for Biotechnology, Bielefeld University, Bielefeld, Germany.

    • Bernd Weisshaar
  17. Australian Centre for Plant Functional Genomics, Brisbane, Queensland, Australia.

    • Christopher Duran
    • , David Edwards
    •  & Paul J Berkman
  18. Division of Animal Sciences, University of Missouri, Columbia, Missouri, USA.

    • Gavin Conant
  19. Inland Northwest Research Alliance-Agrocampus Rennes–University of Rennes 1, Unité Mixte de Recherché 118 Amélioration des Plantes et Biotechnologies Végétales, Le Rheu Cedex, France.

    • Gilles Lassalle
  20. Centre for Crop Genetic Improvement, Rothamsted Research, West Common, Harpenden, UK.

    • Graham J King
    •  & Jun Wang
  21. Droevendaalsesteeg 1, Wageningen University, Wageningen, The Netherlands.

    • Guusje Bonnema
  22. Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, Japan.

    • Hideki Hirakawa
    • , Satoshi Tabata
    •  & Shusei Sato
  23. Experimental Plant Division, RIKEN BioResource Center, Tsukuba, Japan.

    • Hiroshi Abe
  24. Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada.

    • Isobel A P Parkin
    •  & Matthew G Links
  25. National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.

    • Jinling Meng
  26. Genoscope, Institut de Génomique du Commissariat à l'Energie Atomique, 2 rue Gaston Crémieux, Evry, France.

    • Julie Poulain
  27. National Institute of Vegetable and Tea Science, Tsu, Japan.

    • Katsunori Hatakeyama
  28. Molecular Genetics and Genomics Lab, Department of Horticulture, Chungnam National University, Daejeon, Republic of Korea.

    • Nirala Ramchiary
    • , Su-Ryun Choi
    •  & Yongpyo Lim
  29. Research Institute for Biological Sciences, Okayama, Japan.

    • Yoshihiro Narusaka

Consortia

  1. The Brassica rapa Genome Sequencing Project Consortium

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Contributions

Principal investigators: Xiaowu Wang, J. Wu, S.L., Y.B., J.-H.M. and I.B. DNA and transcriptome sequencing: Bo Wang (group leader), Xiaowu Wang (group leader), B.C. (group leader), Jun Wang (BGI), K.W., J. Wu, S.L., W.H., B.-S.P., I.B., D.E., I.A.P.P., J.-H.M., H.A., Bernd Weisshaar, Shusei Sato, H.H., S.T., A.G.S., Y. Lim, G.B., J.B., C.L., C.G., J.P., S.-J.K., J.A.K., M.T., F.F., E.S., M.G.L., C.K., K.H., Y.N., P.J.B. and C.D. Sequence assembly: Junyi Wang (group leader), Jun Wang (BGI), D.M., Y. Li, X.X., Bo Liu, Silong Sun, Z.Z., Z.L., Binghang Liu, Q.C., Shu Zhang, Y.B., Zhiwen Wang, X.Z., C.S., J.Y. and J.J. Anchoring to linkage maps: J. Wu (group leader), W.H. (group leader), G.J.K., Y. Lim, B.-S.P., I.B., J.B., D.E., Yan Wang, Bo Liu, Silong Sun, Jun Wang (Rothamsted), I.A.P.P., J. Meng, Hui Wang, J.D., Y. Liao, Y.B., Haiping Wang, M.J., J.-S.K., S.-R.C., N.R. and A.H. Annotation: Y.B. (group leader), S.L. (group leader), R.L., W.F., Q.H., F.C., Bo Liu, D.E., J. Min, Jianwen Li, C.P., H.Z., Shunmou Huang, B.C., J.J., H.B., G.L., N.D. and M.T. Stabilizing the genome of a polyploidy dicotyledonous species: F.C. (group leader), Sanwen Huang (group leader), Y.B., Xiaowu Wang, B. Li, S.C., Y.Y., J.X. and C.T. Comparative genomics: Xiaowu Wang (group leader), J.C.P. (group leader), Xiyin Wang (group leader), I.B., F.C., H.T., G.C., H.G., T.-H.L., Jinpeng Wang and Zhenyi Wang. Retention of genes duplicated by polyploidy: M.F. (group leader), A.H.P. (group leader), F.C., H.T., Bo Liu, Silong Sun, L.F., Z.X., M.Z., Jingping Li, H.J. and X.T. Characteristics of a crop genome: J. Wu (group leader), X.L. (group leader), R.S., Hanzhong Wang, Y.D., Xiaowu Wang, Hui Wang, J.D., D.S., Y.Q., Shujiang Zhang, F.L., L.W. and Yupeng Wang.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Xiaowu Wang or Hanzhong Wang or Rifei Sun or Jun Wang.

Supplementary information

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    Supplementary Text and Figures

    Supplementary Note, Supplementary Tables 1–21 and Supplementary Figures 1–25.

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DOI

https://doi.org/10.1038/ng.919

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