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The genome of the mesopolyploid crop species Brassica rapa

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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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.

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DDBJ/GenBank/EMBL

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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.

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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.

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

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

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

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