Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

The genome of the mesopolyploid crop species Brassica rapa


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.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Figure 1: Chromosomal distribution of the main B. rapa genome features.
Figure 2
Figure 3: Segmental collinearity of the genomes of B. rapa and A. thaliana.
Figure 4: The density of orthologous genes in three subgenomes (LF, MF1 and MF2) of B. rapa compared to A. thaliana.
Figure 5: The over retention genes in B. rapa showing strong bias.

Accession codes




  1. 1

    Tang, H. et al. Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps. Genome Res. 18, 1944–1954 (2008).

    CAS  Article  PubMed Central  Google Scholar 

  2. 2

    Johnston, J.S. et al. Evolution of genome size in Brassicaceae. Ann. Bot. 95, 229–235 (2005).

    CAS  Article  PubMed Central  Google Scholar 

  3. 3

    Koch, M.A. & Kiefer, M. Genome evolution among cruciferous plants: a lecture from the comparison of the genetic maps of three diploid species—Capsella rubella, Arabidopsis lyrata subsp Petraea, and A. thaliana. Am. J. Bot. 92, 761–767 (2005).

    Article  Google Scholar 

  4. 4

    Yogeeswaran, K. et al. Comparative genome analyses of Arabidopsis spp.: inferring chromosomal rearrangement events in the evolutionary history of A. thaliana. Genome Res. 15, 505–515 (2005).

    CAS  Article  PubMed Central  Google Scholar 

  5. 5

    Bowers, J.E., Chapman, B.A., Rong, J. & Paterson, A.H. Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 422, 433–438 (2003).

    CAS  Article  Google Scholar 

  6. 6

    Yang, Y.W., Lai, K.N., Tai, P.Y. & Li, W.H. Rates of nucleotide substitution in angiosperm mitochondrial DNA sequences and dates of divergence between Brassica and other angiosperm lineages. J. Mol. Evol. 48, 597–604 (1999).

    CAS  Article  Google Scholar 

  7. 7

    Town, C.D. et al. Comparative genomics of Brassica oleracea and Arabidopsis thaliana reveal gene loss, fragmentation, and dispersal after polyploidy. Plant Cell 18, 1348–1359 (2006).

    CAS  Article  PubMed Central  Google Scholar 

  8. 8

    Lysak, M.A., Koch, M.A., Pecinka, A. & Schubert, I. Chromosome triplication found across the tribe Brassiceae. Genome Res. 15, 516–525 (2005).

    CAS  Article  PubMed Central  Google Scholar 

  9. 9

    Labana, K.S. & Gupta, M.L. Importance and origin. in Breeding Oilseed Brassicas (eds. Labana, K.S., Banga, S.S. & Banga, S.K.) 1–20 (Springer-Verlag, Berlin, Germany, 1993).

  10. 10

    Nagaharu, U. Genome analysis in Brassica with special reference to the experimental formation of B. napus and peculiar mode of fertilization. Jap. J. Bot. 7, 389–452 (1935).

    Google Scholar 

  11. 11

    O'Neill, C.M. & Bancroft, I. Comparative physical mapping of segments of the genome of Brassica oleracea var. alboglabra that are homoeologous to sequenced regions of chromosomes 4 and 5 of Arabidopsis thaliana. Plant J. 23, 233–243 (2000).

    CAS  Article  Google Scholar 

  12. 12

    Park, J.Y. et al. Physical mapping and microsynteny of Brassica rapa ssp. pekinensis genome corresponding to a 222 kbp gene-rich region of Arabidopsis chromosome 4 and partially duplicated on chromosome 5. Mol. Genet. Genomics 274, 579–588 (2005).

    CAS  Article  Google Scholar 

  13. 13

    Beilstein, M.A., Nagalingum, N.S., Clements, M.D., Manchester, S.R. & Mathews, S. Dated molecular phylogenies indicate a Miocene origin for Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA 107, 18724–18728 (2010).

    CAS  Article  Google Scholar 

  14. 14

    Mun, J.H. et al. Genome-wide comparative analysis of the Brassica rapa gene space reveals genome shrinkage and differential loss of duplicated genes after whole genome triplication. Genome Biol. 10, R111 (2009).

    Article  PubMed Central  Google Scholar 

  15. 15

    Mun, J.H. et al. Sequence and structure of Brassica rapa chromosome A3. Genome Biol. 11, R94 (2010).

    Article  PubMed Central  Google Scholar 

  16. 16

    Arabidopsis Genome Initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796–815 (2000).

  17. 17

    Ming, R. et al. The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature 452, 991–996 (2008).

    CAS  Article  PubMed Central  Google Scholar 

  18. 18

    Jaillon, O. et al. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449, 463–467 (2007).

    CAS  Article  Google Scholar 

  19. 19

    Sankoff, D., Zheng, C. & Zhu, Q. The collapse of gene complement following whole genome duplication. BMC Genomics 11, 313 (2010).

    Article  PubMed Central  Google Scholar 

  20. 20

    Messing, J. et al. Sequence composition and genome organization of maize. Proc. Natl. Acad. Sci. USA 101, 14349–14354 (2004).

    CAS  Article  Google Scholar 

  21. 21

    Schnable, J.C., Springer, N.M. & Freeling, M. Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss. Proc. Natl. Acad. Sci. USA 108, 4069–4074 (2011).

    CAS  Article  Google Scholar 

  22. 22

    Thomas, B.C., Pedersen, B. & Freeling, M. Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes. Genome Res. 16, 934–946 (2006).

    CAS  Article  PubMed Central  Google Scholar 

  23. 23

    Woodhouse, M.R. et al. Following tetraploidy in maize, a short deletion mechanism removed genes preferentially from one of the two homologs. PLoS Biol. 8, e1000409 (2010).

    Article  PubMed Central  Google Scholar 

  24. 24

    Wang, X., Tang, H., Bowers, J.E. & Paterson, A.H. Comparative inference of illegitimate recombination between rice and sorghum duplicated genes produced by polyploidization. Genome Res. 19, 1026–1032 (2009).

    CAS  Article  PubMed Central  Google Scholar 

  25. 25

    Wang, X.Y., Tang, H.B. & Paterson, A.H. Seventy million years of concerted evolution of a homoeologous chromosome pair, in parallel, in major poaceae lineages. Plant Cell 23, 27–37 (2011).

    Article  PubMed Central  Google Scholar 

  26. 26

    Birchler, J.A. & Veitia, R.A. The gene balance hypothesis: from classical genetics to modern genomics. Plant Cell 19, 395–402 (2007).

    CAS  Article  PubMed Central  Google Scholar 

  27. 27

    Ha, M., Kim, E.D. & Chen, Z.J. Duplicate genes increase expression diversity in closely related species and allopolyploids. Proc. Natl. Acad. Sci. USA 106, 2295–2300 (2009).

    CAS  Article  Google Scholar 

  28. 28

    Paterson, A.H., Lan, T.H., Amasino, R., Osborn, T.C. & Quiros, C. Brassica genomics: a complement to, and early beneficiary of, the Arabidopsis sequence. Genome Biol. 2, R1011 (2001).

    Article  Google Scholar 

  29. 29

    Teale, W.D., Paponov, I.A. & Palme, K. Auxin in action: signalling, transport and the control of plant growth and development. Nat. Rev. Mol. Cell Biol. 7, 847–859 (2006).

    CAS  Article  Google Scholar 

  30. 30

    Theologis, A. et al. Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana. Nature 408, 816–820 (2000).

    Article  Google Scholar 

  31. 31

    Vanneste, S. & Friml, J. Auxin: a trigger for change in plant development. Cell 136, 1005–1016 (2009).

    CAS  Article  Google Scholar 

  32. 32

    Reeves, P.A. & Olmstead, R.G. Evolution of the TCP gene family in Asteridae: cladistic and network approaches to understanding regulatory gene family diversification and its impact on morphological evolution. Mol. Biol. Evol. 20, 1997–2009 (2003).

    CAS  Article  Google Scholar 

  33. 33

    Michaels, S.D. & Amasino, R.M. FLOWERING LOCUS C encodes a novel MADS domain protein that acts as a repressor of flowering. Plant Cell 11, 949–956 (1999).

    CAS  Article  PubMed Central  Google Scholar 

  34. 34

    Levy, Y.Y., Mesnage, S., Mylne, J.S., Gendall, A.R. & Dean, C. Multiple roles of Arabidopsis VRN1 in vernalization and flowering time control. Science 297, 243–246 (2002).

    CAS  Article  Google Scholar 

  35. 35

    Günl, M., Liew, E.F., David, K. & Putterill, J. Analysis of a post-translational steroid induction system for GIGANTEA in Arabidopsis. BMC Plant Biol. 9, 141 (2009).

    Article  PubMed Central  Google Scholar 

  36. 36

    Li, D. et al. A repressor complex governs the integration of flowering signals in Arabidopsis. Dev. Cell 15, 110–120 (2008).

    CAS  Article  Google Scholar 

  37. 37

    Ledger, S., Strayer, C., Ashton, F., Kay, S.A. & Putterill, J. Analysis of the function of two circadian-regulated CONSTANS-LIKE genes. Plant J. 26, 15–22 (2001).

    CAS  Article  Google Scholar 

  38. 38

    Paterson, A.H. et al. The Sorghum bicolor genome and the diversification of grasses. Nature 457, 551–556 (2009).

    CAS  Article  Google Scholar 

  39. 39

    Li, R. et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 20, 265–272 (2010).

    CAS  Article  PubMed Central  Google Scholar 

  40. 40

    Li, R. et al. The sequence and de novo assembly of the giant panda genome. Nature 463, 311–317 (2010).

    CAS  Article  Google Scholar 

  41. 41

    Delcher, A.L., Phillippy, A., Carlton, J. & Salzberg, S.L. Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Res. 30, 2478–2483 (2002).

    Article  PubMed Central  Google Scholar 

  42. 42

    Parkin, I.A. et al. Segmental structure of the Brassica napus genome based on comparative analysis with Arabidopsis thaliana. Genetics 171, 765–781 (2005).

    CAS  Article  PubMed Central  Google Scholar 

  43. 43

    Birney, E., Clamp, M. & Durbin, R. GeneWise and Genomewise. Genome Res. 14, 988–995 (2004).

    CAS  Article  PubMed Central  Google Scholar 

  44. 44

    Haas, B.J. et al. Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res. 31, 5654–5666 (2003).

    CAS  Article  PubMed Central  Google Scholar 

  45. 45

    Elsik, C.G. et al. Creating a honey bee consensus gene set. Genome Biol. 8, R13 (2007).

    Article  PubMed Central  Google Scholar 

  46. 46

    Li, L., Stoeckert, C.J. & Roos, D.S. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 13, 2178–2189 (2003).

    CAS  Article  PubMed Central  Google Scholar 

  47. 47

    Tamura, K., Dudley, J., Nei, M. & Kumar, S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24, 1596–1599 (2007).

    CAS  Article  Google Scholar 

Download references


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





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.

Corresponding authors

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

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Note, Supplementary Tables 1–21 and Supplementary Figures 1–25. (PDF 3166 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

The Brassica rapa Genome Sequencing Project Consortium., Wang, X., Wang, H. et al. The genome of the mesopolyploid crop species Brassica rapa. Nat Genet 43, 1035–1039 (2011).

Download citation

Further reading


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing