The genome of the mesopolyploid crop species Brassica rapa

Journal name:
Nature Genetics
Volume:
43,
Pages:
1035–1039
Year published:
DOI:
doi:10.1038/ng.919
Received
Accepted
Published online

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.

At a glance

Figures

  1. Chromosomal distribution of the main B. rapa genome features.
    Figure 1: Chromosomal distribution of the main B. rapa genome features.

    Area charts quantify retrotransposons, genes (exons and introns) and DNA transposons. The x axis denotes the physical position along the B. rapa chromosomes in units of million (M) bases.

  2. Venn diagram showing unique and shared gene families between and among four sequenced dicotyledonous species (B. rapa, A. thaliana, C. papaya and V. vinifera).
    Figure 2: Venn diagram showing unique and shared gene families between and among four sequenced dicotyledonous species (B. rapa, A. thaliana, C. papaya and V. vinifera).
  3. Segmental collinearity of the genomes of B. rapa and A. thaliana.
    Figure 3: Segmental collinearity of the genomes of B. rapa and A. thaliana.

    Conserved collinear blocks of gene models are shown between the ten chromosomes of the B. rapa genome (horizontal axis) and the five chromosomes of the A. thaliana genome (vertical axis). These blocks are labeled A to X and are color coded by inferred ancestral chromosome following established convention.

  4. The density of orthologous genes in three subgenomes (LF, MF1 and MF2) of B. rapa compared to A. thaliana.
    Figure 4: The density of orthologous genes in three subgenomes (LF, MF1 and MF2) of B. rapa compared to A. thaliana.

    The x axis denotes the physical position of each A. thaliana gene locus. The y axis denotes the percentage of retained orthologous genes in B. rapa subgenomes around each A. thaliana gene, where 500 genes flanking each side of a certain gene locus were analyzed, giving a total window size of 1,001 genes.

  5. The over retention genes in B. rapa showing strong bias.
    Figure 5: The over retention genes in B. rapa showing strong bias.

    The x axis denotes the gene category. The y axis denotes the ratio of different copies in each category. The number of B. rapa orthologs of each class is indicated above each bar. RE, response to environment; RH, response to hormone; TF, transcription factor; CR, cytosolic ribosome; CW, cell wall. (a) The orange bar is the ratio of one- or two-copy orthologs, and the light green bar is the ratio of three copies. (b) The yellow bar is the ratio of one-copy orthologs, and the dark green bar is the ratio of two- or three-copy orthologs. The last category is the total sets of all orthologs listed as a control. The P value of each category is indicated under the bars. GO, Gene Ontology.

Accession codes

Referenced accessions

DDBJ/GenBank/EMBL

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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

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.

Xiaowu Wang1, Hanzhong Wang2, Jun Wang3,4, Rifei Sun1, Jian Wu1, Shengyi Liu2, Yinqi Bai3, Jeong-Hwan Mun5, Ian Bancroft6, Feng Cheng1, Sanwen Huang1, Xixiang Li1, Wei Hua2, Junyi Wang3, Xiyin Wang7,9, Michael Freeling10, J Chris Pires11, Andrew H Paterson9, Boulos Chalhoub12, Bo Wang3, Alice Hayward13,14, Andrew G Sharpe15, Beom-Seok Park5, Bernd Weisshaar16, Binghang Liu3, Bo Li3, Bo Liu1, Chaobo Tong2, Chi Song3, Christopher Duran13,17, Chunfang Peng3, Chunyu Geng3, Chushin Koh15, Chuyu Lin3, David Edwards13,17, Desheng Mu3, Di Shen1, Eleni Soumpourou6, Fei Li1, Fiona Fraser6, Gavin Conant18, Gilles Lassalle19, Graham J King20, Guusje Bonnema21, Haibao Tang10, Haiping Wang1, Harry Belcram12, Heling Zhou3, Hideki Hirakawa22, Hiroshi Abe23, Hui Guo9, Hui Wang1, Huizhe Jin9, Isobel A P Parkin24, Jacqueline Batley13,14, Jeong-Sun Kim5, Jérémy Just12, Jianwen Li3, Jiaohui Xu3, Jie Deng1, Jin A Kim5, Jingping Li9, Jingyin Yu2, Jinling Meng25, Jinpeng Wang7,8, Jiumeng Min3, Julie Poulain26, Jun Wang20, Katsunori Hatakeyama27, Kui Wu3, Li Wang7,8, Lu Fang1, Martin Trick6, Matthew G Links24, Meixia Zhao2, Mina Jin5, Nirala Ramchiary28, Nizar Drou6, Paul J Berkman13,17, Qingle Cai3, Quanfei Huang3, Ruiqiang Li3, Satoshi Tabata22, Shifeng Cheng3, Shu Zhang3, Shujiang Zhang1, Shunmou Huang2, Shusei Sato22, Silong Sun1, Soo-Jin Kwon5, Su-Ryun Choi28, Tae-Ho Lee9, Wei Fan3, Xiang Zhao3, Xu Tan9, Xun Xu3, Yan Wang1, Yang Qiu1, Ye Yin3, Yingrui Li3, Yongchen Du1, Yongcui Liao1, Yongpyo Lim28, Yoshihiro Narusaka29, Yupeng Wang8, Zhenyi Wang7,8, Zhenyu Li3, Zhiwen Wang3, Zhiyong Xiong11 & Zhonghua Zhang1

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