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 Paterson; Boulos Chalhoub; Bo Wang; Alice Hayward; Andrew 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 King; Guusje Bonnema; Haibao Tang; Haiping Wang; Harry Belcram; Heling Zhou; Hideki Hirakawa; Hiroshi Abe; Hui Guo; Hui Wang; Huizhe Jin; Isobel Parkin; Jacqueline Batley; Jeong-Sun Kim; Jérémy Just; Jianwen Li; Jiaohui Xu; Jie Deng; Jin Hyun Kim; Jingping Li; Jingyin Yu; Jinling Meng; Jinpeng Wang; Jiumeng Min; Julie Poulain; Katsunori Hatakeyama; Kui Wu; Li Wang; Lu Fang; Martin Trick; Matthew Links; Meixia Zhao; Mina Jin; Nirala Ramchiary; Nizar Drou; Paul 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

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 Paterson, Boulos Chalhoub, Bo WangAlice Hayward, Andrew 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 King, Guusje Bonnema, Haibao Tang, Haiping Wang, Harry Belcram, Heling Zhou, Hideki Hirakawa, Hiroshi Abe, Hui Guo, Hui Wang, Huizhe Jin, Isobel Parkin, Jacqueline Batley, Jeong-Sun Kim, Jérémy Just, Jianwen Li, Jiaohui Xu, Jie Deng, Jin Hyun Kim, Jingping Li, Jingyin Yu, Jinling Meng, Jinpeng Wang, Jiumeng Min, Julie Poulain, Katsunori Hatakeyama, Kui Wu, Li Wang, Lu Fang, Martin Trick, Matthew Links, Meixia Zhao, Mina Jin, Nirala Ramchiary, Nizar Drou, Paul 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

Genome Research and Molecular Bio Medicine

1304 Citations (Scopus)

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
Journal	Nature Genetics
Volume	43
Issue number	10
Pages (from-to)	1035-1039
Number of pages	5
ISSN	1061-4036
DOIs	https://doi.org/10.1038/ng.919
Publication status	Published - Oct 2011

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10.1038/ng.919

http://dx.doi.org/10.1038/ng.919

Cite this

Wang, X, Wang, H, Wang, J, Sun, R, Wu, J, Liu, S, Bai, Y, Mun, J-H, Bancroft, I, Cheng, F, Huang, S, Li, X, Hua, W, Wang, J, Wang, X, Freeling, M, Pires, JC, Paterson, A, Chalhoub, B, Wang, B, Hayward, A, Sharpe, A, Park, B-S, 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, G, Bonnema, G, Tang, H, Wang, H, Belcram, H, Zhou, H, Hirakawa, H, Abe, H, Guo, H, Wang, H, Jin, H, Parkin, I, Batley, J, Kim, J-S, Just, J, Li, J, Xu, J, Deng, J, Kim, JH, Li, J, Yu, J, Meng, J, Wang, J, Min, J, Poulain, J, Hatakeyama, K, Wu, K, Wang, L, Fang, L, Trick, M, Links, M, Zhao, M, Jin, M, Ramchiary, N, Drou, N, Berkman, P, Cai, Q, Huang, Q, Li, R, Tabata, S, Cheng, S, Zhang, S, Zhang, S, Huang, S, Sato, S, Sun, S, Kwon, S-J, Choi, S-R, Lee, T-H, Fan, W, Zhao, X, Tan, X, Xu, X, Wang, Y, Qiu, Y, Yin, Y & Li, Y 2011, 'The genome of the mesopolyploid crop species Brassica rapa', Nature Genetics, vol. 43, no. 10, pp. 1035-1039. https://doi.org/10.1038/ng.919

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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 Jeong-Hwan Mun 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 Andrew Paterson and Boulos Chalhoub and Bo Wang and Alice Hayward and Andrew Sharpe and Beom-Seok Park 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 Graham King 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 Isobel Parkin and Jacqueline Batley and Jeong-Sun Kim and J{\'e}r{\'e}my Just and Jianwen Li and Jiaohui Xu and Jie Deng and Kim, {Jin Hyun} 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 Matthew Links and Meixia Zhao and Mina Jin and Nirala Ramchiary and Nizar Drou and Paul Berkman 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 Soo-Jin Kwon and Su-Ryun Choi and Tae-Ho Lee and Wei Fan and Xiang Zhao and Xu Tan and Xun Xu and Yan Wang and Yang Qiu and Ye Yin and Yingrui Li",

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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

AU - Chalhoub, Boulos

AU - Wang, Bo

AU - Hayward, Alice

AU - Sharpe, Andrew

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

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AU - Conant, Gavin

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AU - Just, Jérémy

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AU - Xu, Jiaohui

AU - Deng, Jie

AU - Kim, Jin Hyun

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AU - Yu, Jingyin

AU - Meng, Jinling

AU - Wang, Jinpeng

AU - Min, Jiumeng

AU - Poulain, Julie

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AU - Wu, Kui

AU - Wang, Li

AU - Fang, Lu

AU - Trick, Martin

AU - Links, Matthew

AU - Zhao, Meixia

AU - Jin, Mina

AU - Ramchiary, Nirala

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AU - Berkman, Paul

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

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