The genome of the mesopolyploid crop species Brassica rapa

Xiaowu Wang; Hanzhong Wang; Jun Wang; Rifei Sun; Jian Wu; Shengyi Liu; Yinqi Bai; Jeong Hwan Mun; Ian Bancroft; Feng Cheng; Sanwen Huang; Xixiang Li; Wei Hua; Junyi Wang; Xiyin Wang; Michael Freeling; J. Chris Pires; Andrew H. Paterson; Boulos Chalhoub; Bo Wang; Alice Hayward; Andrew G. Sharpe; Beom Seok Park; Bernd Weisshaar; Binghang Liu; Bo Li; Bo Liu; Chaobo Tong; Chi Song; Christopher Duran; Chunfang Peng; Chunyu Geng; Chushin Koh; Chuyu Lin; David Edwards; Desheng Mu; Di Shen; Eleni Soumpourou; Fei Li; Fiona Fraser; Gavin Conant; Gilles Lassalle; Graham J. King; Guusje Bonnema; Haibao Tang; Haiping Wang; Harry Belcram; Heling Zhou; Hideki Hirakawa; Hiroshi Abe; Hui Guo; Hui Wang; Huizhe Jin; Isobel A.P. Parkin; Jacqueline Batley; Jeong Sun Kim; Jérémy Just; Jianwen Li; Jiaohui Xu; Jie Deng; Jin A. Kim; Jingping Li; Jingyin Yu; Jinling Meng; Jinpeng Wang; Jiumeng Min; Julie Poulain; Katsunori Hatakeyama; Kui Wu; Li Wang; Lu Fang; Martin Trick; Matthew G. Links; Meixia Zhao; Mina Jin; Nirala Ramchiary; Nizar Drou; Paul J. Berkman; Qingle Cai; Quanfei Huang; Ruiqiang Li; Satoshi Tabata; Shifeng Cheng; Shu Zhang; Shujiang Zhang; Shunmou Huang; Shusei Sato; Silong Sun; Soo Jin Kwon; Su Ryun Choi; Tae Ho Lee; Wei Fan; Xiang Zhao; Xu Tan; Xun Xu; Yan Wang; Yang Qiu; Ye Yin; Yingrui Li; Yongchen Du; Yongcui Liao; Yongpyo Lim; Yoshihiro Narusaka; Yupeng Wang; Zhenyi Wang; Zhenyu Li; Zhiwen Wang; Zhiyong Xiong; Zhonghua Zhang

doi:10.1038/ng.919

The genome of the mesopolyploid crop species Brassica rapa

Xiaowu Wang, Hanzhong Wang, Jun Wang, Rifei Sun, Jian Wu, Shengyi Liu, Yinqi Bai, Jeong Hwan Mun, Ian Bancroft, Feng Cheng, Sanwen Huang, Xixiang Li, Wei Hua, Junyi Wang, Xiyin Wang, Michael Freeling, J. Chris Pires, Andrew H. Paterson, Boulos Chalhoub, Bo WangAlice Hayward, Andrew G. Sharpe, Beom Seok Park, Bernd Weisshaar, Binghang Liu, Bo Li, Bo Liu, Chaobo Tong, Chi Song, Christopher Duran, Chunfang Peng, Chunyu Geng, Chushin Koh, Chuyu Lin, David Edwards, Desheng Mu, Di Shen, Eleni Soumpourou, Fei Li, Fiona Fraser, Gavin Conant, Gilles Lassalle, Graham J. King, Guusje Bonnema, Haibao Tang, Haiping Wang, Harry Belcram, Heling Zhou, Hideki Hirakawa, Hiroshi Abe, Hui Guo, Hui Wang, Huizhe Jin, Isobel A.P. Parkin, Jacqueline Batley, Jeong Sun Kim, Jérémy Just, Jianwen Li, Jiaohui Xu, Jie Deng, Jin A. Kim, Jingping Li, Jingyin Yu, Jinling Meng, Jinpeng Wang, Jiumeng Min, Julie Poulain, Katsunori Hatakeyama, Kui Wu, Li Wang, Lu Fang, Martin Trick, Matthew G. Links, Meixia Zhao, Mina Jin, Nirala Ramchiary, Nizar Drou, Paul J. Berkman, Qingle Cai, Quanfei Huang, Ruiqiang Li, Satoshi Tabata, Shifeng Cheng, Shu Zhang, Shujiang Zhang, Shunmou Huang, Shusei Sato, Silong Sun, Soo Jin Kwon, Su Ryun Choi, Tae Ho Lee, Wei Fan, Xiang Zhao, Xu Tan, Xun Xu, Yan Wang, Yang Qiu, Ye Yin, Yingrui Li, Yongchen Du, Yongcui Liao, Yongpyo Lim, Yoshihiro Narusaka, Yupeng Wang, Zhenyi Wang, Zhenyu Li, Zhiwen Wang, Zhiyong Xiong, Zhonghua Zhang

Center for Genomics and Systems Biology

Research output: Contribution to journal › Article › peer-review

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.

Original language	English (US)
Pages (from-to)	1035-1040
Number of pages	6
Journal	Nature Genetics
Volume	43
Issue number	10
DOIs	https://doi.org/10.1038/ng.919
State	Published - Oct 2011

ASJC Scopus subject areas

Genetics

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10.1038/ng.919

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Wang, X, Wang, H, Wang, J, Sun, R, Wu, J, Liu, S, Bai, Y, Mun, JH, Bancroft, I, Cheng, F, Huang, S, Li, X, Hua, W, Wang, J, Wang, X, Freeling, M, Pires, JC, Paterson, AH, Chalhoub, B, Wang, B, Hayward, A, Sharpe, AG, Park, BS, Weisshaar, B, Liu, B, Li, B, Liu, B, Tong, C, Song, C, Duran, C, Peng, C, Geng, C, Koh, C, Lin, C, Edwards, D, Mu, D, Shen, D, Soumpourou, E, Li, F, Fraser, F, Conant, G, Lassalle, G, King, GJ, Bonnema, G, Tang, H, Wang, H, Belcram, H, Zhou, H, Hirakawa, H, Abe, H, Guo, H, Wang, H, Jin, H, Parkin, IAP, Batley, J, Kim, JS, Just, J, Li, J, Xu, J, Deng, J, Kim, JA, Li, J, Yu, J, Meng, J, Wang, J, Min, J, Poulain, J, Hatakeyama, K, Wu, K, Wang, L, Fang, L, Trick, M, Links, MG, Zhao, M, Jin, M, Ramchiary, N, Drou, N, Berkman, PJ, Cai, Q, Huang, Q, Li, R, Tabata, S, Cheng, S, Zhang, S, Zhang, S, Huang, S, Sato, S, Sun, S, Kwon, SJ, Choi, SR, Lee, TH, Fan, W, Zhao, X, Tan, X, Xu, X, Wang, Y, Qiu, Y, Yin, Y, Li, Y, Du, Y, Liao, Y, Lim, Y, Narusaka, Y, Wang, Y, Wang, Z, Li, Z, Wang, Z, Xiong, Z & Zhang, Z 2011, 'The genome of the mesopolyploid crop species Brassica rapa', Nature Genetics, vol. 43, no. 10, pp. 1035-1040. https://doi.org/10.1038/ng.919

@article{be8d9e9ed21c4cd19b845f417d262331,

title = "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.",

author = "Xiaowu Wang and Hanzhong Wang and Jun Wang and Rifei Sun and Jian Wu and Shengyi Liu and Yinqi Bai and Mun, {Jeong Hwan} and Ian Bancroft and Feng Cheng and Sanwen Huang and Xixiang Li and Wei Hua and Junyi Wang and Xiyin Wang and Michael Freeling and Pires, {J. Chris} and Paterson, {Andrew H.} and Boulos Chalhoub and Bo Wang and Alice Hayward and Sharpe, {Andrew G.} and Park, {Beom Seok} and Bernd Weisshaar and Binghang Liu and Bo Li and Bo Liu and Chaobo Tong and Chi Song and Christopher Duran and Chunfang Peng and Chunyu Geng and Chushin Koh and Chuyu Lin and David Edwards and Desheng Mu and Di Shen and Eleni Soumpourou and Fei Li and Fiona Fraser and Gavin Conant and Gilles Lassalle and King, {Graham J.} and Guusje Bonnema and Haibao Tang and Haiping Wang and Harry Belcram and Heling Zhou and Hideki Hirakawa and Hiroshi Abe and Hui Guo and Hui Wang and Huizhe Jin and Parkin, {Isobel A.P.} and Jacqueline Batley and Kim, {Jeong Sun} and J{\'e}r{\'e}my Just and Jianwen Li and Jiaohui Xu and Jie Deng and Kim, {Jin A.} and Jingping Li and Jingyin Yu and Jinling Meng and Jinpeng Wang and Jiumeng Min and Julie Poulain and Katsunori Hatakeyama and Kui Wu and Li Wang and Lu Fang and Martin Trick and Links, {Matthew G.} and Meixia Zhao and Mina Jin and Nirala Ramchiary and Nizar Drou and Berkman, {Paul J.} and Qingle Cai and Quanfei Huang and Ruiqiang Li and Satoshi Tabata and Shifeng Cheng and Shu Zhang and Shujiang Zhang and Shunmou Huang and Shusei Sato and Silong Sun and Kwon, {Soo Jin} and Choi, {Su Ryun} and Lee, {Tae Ho} and Wei Fan and Xiang Zhao and Xu Tan and Xun Xu and Yan Wang and Yang Qiu and Ye Yin and Yingrui Li and Yongchen Du and Yongcui Liao and Yongpyo Lim and Yoshihiro Narusaka and Yupeng Wang and Zhenyi Wang and Zhenyu Li and Zhiwen Wang and Zhiyong Xiong and Zhonghua Zhang",

note = "Funding Information: 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{\textquoteright}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{\textquoteright}s Plant Biotechnology Institute. See the Supplementary Note for a full list of support and acknowledgments.",

year = "2011",

month = oct,

doi = "10.1038/ng.919",

language = "English (US)",

volume = "43",

pages = "1035--1040",

journal = "Nature Genetics",

issn = "1061-4036",

publisher = "Nature Research",

number = "10",

}

TY - JOUR

T1 - The genome of the mesopolyploid crop species Brassica rapa

AU - Wang, Xiaowu

AU - Wang, Hanzhong

AU - Wang, Jun

AU - Sun, Rifei

AU - Wu, Jian

AU - Liu, Shengyi

AU - Bai, Yinqi

AU - Mun, Jeong Hwan

AU - Bancroft, Ian

AU - Cheng, Feng

AU - Huang, Sanwen

AU - Li, Xixiang

AU - Hua, Wei

AU - Wang, Junyi

AU - Wang, Xiyin

AU - Freeling, Michael

AU - Pires, J. Chris

AU - Paterson, Andrew H.

AU - Chalhoub, Boulos

AU - Wang, Bo

AU - Hayward, Alice

AU - Sharpe, Andrew G.

AU - Park, Beom Seok

AU - Weisshaar, Bernd

AU - Liu, Binghang

AU - Li, Bo

AU - Liu, Bo

AU - Tong, Chaobo

AU - Song, Chi

AU - Duran, Christopher

AU - Peng, Chunfang

AU - Geng, Chunyu

AU - Koh, Chushin

AU - Lin, Chuyu

AU - Edwards, David

AU - Mu, Desheng

AU - Shen, Di

AU - Soumpourou, Eleni

AU - Li, Fei

AU - Fraser, Fiona

AU - Conant, Gavin

AU - Lassalle, Gilles

AU - King, Graham J.

AU - Bonnema, Guusje

AU - Tang, Haibao

AU - Wang, Haiping

AU - Belcram, Harry

AU - Zhou, Heling

AU - Hirakawa, Hideki

AU - Abe, Hiroshi

AU - Guo, Hui

AU - Wang, Hui

AU - Jin, Huizhe

AU - Parkin, Isobel A.P.

AU - Batley, Jacqueline

AU - Kim, Jeong Sun

AU - Just, Jérémy

AU - Li, Jianwen

AU - Xu, Jiaohui

AU - Deng, Jie

AU - Kim, Jin A.

AU - Li, Jingping

AU - Yu, Jingyin

AU - Meng, Jinling

AU - Wang, Jinpeng

AU - Min, Jiumeng

AU - Poulain, Julie

AU - Hatakeyama, Katsunori

AU - Wu, Kui

AU - Wang, Li

AU - Fang, Lu

AU - Trick, Martin

AU - Links, Matthew G.

AU - Zhao, Meixia

AU - Jin, Mina

AU - Ramchiary, Nirala

AU - Drou, Nizar

AU - Berkman, Paul J.

AU - Cai, Qingle

AU - Huang, Quanfei

AU - Li, Ruiqiang

AU - Tabata, Satoshi

AU - Cheng, Shifeng

AU - Zhang, Shu

AU - Zhang, Shujiang

AU - Huang, Shunmou

AU - Sato, Shusei

AU - Sun, Silong

AU - Kwon, Soo Jin

AU - Choi, Su Ryun

AU - Lee, Tae Ho

AU - Fan, Wei

AU - Zhao, Xiang

AU - Tan, Xu

AU - Xu, Xun

AU - Wang, Yan

AU - Qiu, Yang

AU - Yin, Ye

AU - Li, Yingrui

AU - Du, Yongchen

AU - Liao, Yongcui

AU - Lim, Yongpyo

AU - Narusaka, Yoshihiro

AU - Wang, Yupeng

AU - Wang, Zhenyi

AU - Li, Zhenyu

AU - Wang, Zhiwen

AU - Xiong, Zhiyong

AU - Zhang, Zhonghua

N1 - Funding Information: 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.

PY - 2011/10

Y1 - 2011/10

N2 - 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.

AB - 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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SP - 1035

EP - 1040

JO - Nature Genetics

JF - Nature Genetics

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ER -

The genome of the mesopolyploid crop species Brassica rapa

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