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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">The <italic>Brassica oleracea</italic> genome reveals the asymmetrical evolution of polyploid
genomes</title><author><name sortKey="Liu, Shengyi" sort="Liu, Shengyi" uniqKey="Liu S" first="Shengyi" last="Liu">Shengyi Liu</name><affiliation><nlm:aff id="a1"><institution>The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences</institution>, Wuhan 430062,<country>China</country></nlm:aff></affiliation><affiliation><nlm:aff id="a30">These are joint first authors</nlm:aff></affiliation></author><author><name sortKey="Liu, Yumei" sort="Liu, Yumei" uniqKey="Liu Y" first="Yumei" last="Liu">Yumei Liu</name><affiliation><nlm:aff id="a2"><institution>The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, The Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences</institution>, Beijing 10081,<country>China</country></nlm:aff></affiliation><affiliation><nlm:aff id="a30">These are joint first authors</nlm:aff></affiliation></author><author><name sortKey="Yang, Xinhua" sort="Yang, Xinhua" uniqKey="Yang X" first="Xinhua" last="Yang">Xinhua Yang</name><affiliation><nlm:aff id="a3"><institution>Beijing Genome Institute-Shenzhen</institution>, Shenzhen 518083,<country>China</country></nlm:aff></affiliation><affiliation><nlm:aff id="a30">These are joint first authors</nlm:aff></affiliation></author><author><name sortKey="Tong, Chaobo" sort="Tong, Chaobo" uniqKey="Tong C" first="Chaobo" last="Tong">Chaobo Tong</name><affiliation><nlm:aff id="a1"><institution>The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences</institution>, Wuhan 430062,<country>China</country></nlm:aff></affiliation><affiliation><nlm:aff id="a30">These are joint first authors</nlm:aff></affiliation></author><author><name sortKey="Edwards, David" sort="Edwards, David" uniqKey="Edwards D" first="David" last="Edwards">David Edwards</name><affiliation><nlm:aff id="a4"><institution>Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland</institution>, Brisbane, Queensland 4072,<country>Australia</country></nlm:aff></affiliation><affiliation><nlm:aff id="a30">These are joint first authors</nlm:aff></affiliation></author><author><name sortKey="Parkin, Isobel A P" sort="Parkin, Isobel A P" uniqKey="Parkin I" first="Isobel A. P." last="Parkin">Isobel A. P. Parkin</name><affiliation><nlm:aff id="a5"><institution>Agriculture and Agri-Food Canada</institution>, Saskatoon, Saskatchewan,<country>Canada</country> S7N OX2</nlm:aff></affiliation><affiliation><nlm:aff id="a30">These are joint first authors</nlm:aff></affiliation></author><author><name sortKey="Zhao, Meixia" sort="Zhao, Meixia" uniqKey="Zhao M" first="Meixia" last="Zhao">Meixia Zhao</name><affiliation><nlm:aff id="a1"><institution>The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences</institution>, Wuhan 430062,<country>China</country></nlm:aff></affiliation><affiliation><nlm:aff id="a6"><institution>Department of Agronomy, Purdue University</institution>, WSLR Building B018, West Lafayette, Indiana 47907,<country>USA</country></nlm:aff></affiliation></author><author><name sortKey="Ma, Jianxin" sort="Ma, Jianxin" uniqKey="Ma J" first="Jianxin" last="Ma">Jianxin Ma</name><affiliation><nlm:aff id="a6"><institution>Department of Agronomy, Purdue University</institution>, WSLR Building B018, West Lafayette, Indiana 47907,<country>USA</country></nlm:aff></affiliation></author><author><name sortKey="Yu, Jingyin" sort="Yu, Jingyin" uniqKey="Yu J" first="Jingyin" last="Yu">Jingyin Yu</name><affiliation><nlm:aff id="a1"><institution>The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences</institution>, Wuhan 430062,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Huang, Shunmou" sort="Huang, Shunmou" uniqKey="Huang S" first="Shunmou" last="Huang">Shunmou Huang</name><affiliation><nlm:aff id="a1"><institution>The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences</institution>, Wuhan 430062,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Wang, Xiyin" sort="Wang, Xiyin" uniqKey="Wang X" first="Xiyin" last="Wang">Xiyin Wang</name><affiliation><nlm:aff id="a7"><institution>Plant Genome Mapping Laboratory, University of Georgia</institution>, Athens, Georgia 30605,<country>USA</country></nlm:aff></affiliation><affiliation><nlm:aff id="a8"><institution>Center for Genomics and Computational Biology, School of Life Sciences, and School of Sciences, Hebei United University</institution>, Tangshan 063000,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Wang, Junyi" sort="Wang, Junyi" uniqKey="Wang J" first="Junyi" last="Wang">Junyi Wang</name><affiliation><nlm:aff id="a3"><institution>Beijing Genome Institute-Shenzhen</institution>, Shenzhen 518083,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Lu, Kun" sort="Lu, Kun" uniqKey="Lu K" first="Kun" last="Lu">Kun Lu</name><affiliation><nlm:aff id="a9"><institution>College of Agronomy and Biotechnology, Southwest University, BeiBei District</institution>, Chongqing 400715,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Fang, Zhiyuan" sort="Fang, Zhiyuan" uniqKey="Fang Z" first="Zhiyuan" last="Fang">Zhiyuan Fang</name><affiliation><nlm:aff id="a2"><institution>The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, The Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences</institution>, Beijing 10081,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Bancroft, Ian" sort="Bancroft, Ian" uniqKey="Bancroft I" first="Ian" last="Bancroft">Ian Bancroft</name><affiliation><nlm:aff id="a10"><institution>Centre for Novel Agricultural Products (CNAP), Department of Biology, University of York, Wentworth Way</institution>, Heslington, York YO10 5DD,<country>UK</country></nlm:aff></affiliation></author><author><name sortKey="Yang, Tae Jin" sort="Yang, Tae Jin" uniqKey="Yang T" first="Tae-Jin" last="Yang">Tae-Jin Yang</name><affiliation><nlm:aff id="a11"><institution>Department of Plant Sciences, Plant Genomics and Breeding Institute and Research Institute for Agriculture and Life Sciences, College of Agriculture & Life Sciences, Seoul National University</institution>, Seoul 151-921,<country>Republic of Korea</country></nlm:aff></affiliation></author><author><name sortKey="Hu, Qiong" sort="Hu, Qiong" uniqKey="Hu Q" first="Qiong" last="Hu">Qiong Hu</name><affiliation><nlm:aff id="a1"><institution>The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences</institution>, Wuhan 430062,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Wang, Xinfa" sort="Wang, Xinfa" uniqKey="Wang X" first="Xinfa" last="Wang">Xinfa Wang</name><affiliation><nlm:aff id="a1"><institution>The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences</institution>, Wuhan 430062,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Yue, Zhen" sort="Yue, Zhen" uniqKey="Yue Z" first="Zhen" last="Yue">Zhen Yue</name><affiliation><nlm:aff id="a3"><institution>Beijing Genome Institute-Shenzhen</institution>, Shenzhen 518083,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Li, Haojie" sort="Li, Haojie" uniqKey="Li H" first="Haojie" last="Li">Haojie Li</name><affiliation><nlm:aff id="a12"><institution>Sichuan Academy of Agricultural Sciences</institution>, Chengdu 610066,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Yang, Linfeng" sort="Yang, Linfeng" uniqKey="Yang L" first="Linfeng" last="Yang">Linfeng Yang</name><affiliation><nlm:aff id="a3"><institution>Beijing Genome Institute-Shenzhen</institution>, Shenzhen 518083,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Wu, Jian" sort="Wu, Jian" uniqKey="Wu J" first="Jian" last="Wu">Jian Wu</name><affiliation><nlm:aff id="a2"><institution>The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, The Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences</institution>, Beijing 10081,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Zhou, Qing" sort="Zhou, Qing" uniqKey="Zhou Q" first="Qing" last="Zhou">Qing Zhou</name><affiliation><nlm:aff id="a3"><institution>Beijing Genome Institute-Shenzhen</institution>, Shenzhen 518083,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Wang, Wanxin" sort="Wang, Wanxin" uniqKey="Wang W" first="Wanxin" last="Wang">Wanxin Wang</name><affiliation><nlm:aff id="a2"><institution>The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, The Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences</institution>, Beijing 10081,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="King, Graham J" sort="King, Graham J" uniqKey="King G" first="Graham J" last="King">Graham J. King</name><affiliation><nlm:aff id="a13"><institution>Southern Cross Plant Science, Southern Cross University</institution>, Lismore, New South Wales 2480,<country>Australia</country></nlm:aff></affiliation></author><author><name sortKey="Pires, J Chris" sort="Pires, J Chris" uniqKey="Pires J" first="J. Chris" last="Pires">J. Chris Pires</name><affiliation><nlm:aff id="a14"><institution>Bond Life Sciences Center, University of Missouri</institution>, Columbia, Missouri 65211-7310,<country>USA</country></nlm:aff></affiliation></author><author><name sortKey="Lu, Changxin" sort="Lu, Changxin" uniqKey="Lu C" first="Changxin" last="Lu">Changxin Lu</name><affiliation><nlm:aff id="a3"><institution>Beijing Genome Institute-Shenzhen</institution>, Shenzhen 518083,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Wu, Zhangyan" sort="Wu, Zhangyan" uniqKey="Wu Z" first="Zhangyan" last="Wu">Zhangyan Wu</name><affiliation><nlm:aff id="a3"><institution>Beijing Genome Institute-Shenzhen</institution>, Shenzhen 518083,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Sampath, Perumal" sort="Sampath, Perumal" uniqKey="Sampath P" first="Perumal" last="Sampath">Perumal Sampath</name><affiliation><nlm:aff id="a11"><institution>Department of Plant Sciences, Plant Genomics and Breeding Institute and Research Institute for Agriculture and Life Sciences, College of Agriculture & Life Sciences, Seoul National University</institution>, Seoul 151-921,<country>Republic of Korea</country></nlm:aff></affiliation></author><author><name sortKey="Wang, Zhuo" sort="Wang, Zhuo" uniqKey="Wang Z" first="Zhuo" last="Wang">Zhuo Wang</name><affiliation><nlm:aff id="a3"><institution>Beijing Genome Institute-Shenzhen</institution>, Shenzhen 518083,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Guo, Hui" sort="Guo, Hui" uniqKey="Guo H" first="Hui" last="Guo">Hui Guo</name><affiliation><nlm:aff id="a7"><institution>Plant Genome Mapping Laboratory, University of Georgia</institution>, Athens, Georgia 30605,<country>USA</country></nlm:aff></affiliation></author><author><name sortKey="Pan, Shengkai" sort="Pan, Shengkai" uniqKey="Pan S" first="Shengkai" last="Pan">Shengkai Pan</name><affiliation><nlm:aff id="a3"><institution>Beijing Genome Institute-Shenzhen</institution>, Shenzhen 518083,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Yang, Limei" sort="Yang, Limei" uniqKey="Yang L" first="Limei" last="Yang">Limei Yang</name><affiliation><nlm:aff id="a2"><institution>The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, The Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences</institution>, Beijing 10081,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Min, Jiumeng" sort="Min, Jiumeng" uniqKey="Min J" first="Jiumeng" last="Min">Jiumeng Min</name><affiliation><nlm:aff id="a3"><institution>Beijing Genome Institute-Shenzhen</institution>, Shenzhen 518083,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Zhang, Dong" sort="Zhang, Dong" uniqKey="Zhang D" first="Dong" last="Zhang">Dong Zhang</name><affiliation><nlm:aff id="a7"><institution>Plant Genome Mapping Laboratory, University of Georgia</institution>, Athens, Georgia 30605,<country>USA</country></nlm:aff></affiliation></author><author><name sortKey="Jin, Dianchuan" sort="Jin, Dianchuan" uniqKey="Jin D" first="Dianchuan" last="Jin">Dianchuan Jin</name><affiliation><nlm:aff id="a8"><institution>Center for Genomics and Computational Biology, School of Life Sciences, and School of Sciences, Hebei United University</institution>, Tangshan 063000,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Li, Wanshun" sort="Li, Wanshun" uniqKey="Li W" first="Wanshun" last="Li">Wanshun Li</name><affiliation><nlm:aff id="a3"><institution>Beijing Genome Institute-Shenzhen</institution>, Shenzhen 518083,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Belcram, Harry" sort="Belcram, Harry" uniqKey="Belcram H" first="Harry" last="Belcram">Harry Belcram</name><affiliation><nlm:aff id="a15"><institution>Organization and Evolution of Plant Genomes, Unité de Recherche en Génomique Végétale, Unité Mixte de Recherche 1165 (Institut National de Recherche Agronomique, Centre National de la Recherche Scientifique, Université Evry Val d’Essonne)</institution>, Evry 91057,<country>France</country></nlm:aff></affiliation></author><author><name sortKey="Tu, Jinxing" sort="Tu, Jinxing" uniqKey="Tu J" first="Jinxing" last="Tu">Jinxing Tu</name><affiliation><nlm:aff id="a16"><institution>National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University</institution>, Wuhan 430070,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Guan, Mei" sort="Guan, Mei" uniqKey="Guan M" first="Mei" last="Guan">Mei Guan</name><affiliation><nlm:aff id="a17"><institution>College of Agronomy, Hunan Agricultural University</institution>, Changsha 410128,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Qi, Cunkou" sort="Qi, Cunkou" uniqKey="Qi C" first="Cunkou" last="Qi">Cunkou Qi</name><affiliation><nlm:aff id="a18"><institution>Jiangsu Academy of Agricultural Sciences</institution>, Nanjing 210014,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Du, Dezhi" sort="Du, Dezhi" uniqKey="Du D" first="Dezhi" last="Du">Dezhi Du</name><affiliation><nlm:aff id="a19"><institution>Qinghai Academy of Agriculture and Forestry Sciences, National Key Laboratory Breeding Base for Innovation and Utilization of Plateau Crop Germplasm</institution>, Xining 810016,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Li, Jiana" sort="Li, Jiana" uniqKey="Li J" first="Jiana" last="Li">Jiana Li</name><affiliation><nlm:aff id="a9"><institution>College of Agronomy and Biotechnology, Southwest University, BeiBei District</institution>, Chongqing 400715,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Jiang, Liangcai" sort="Jiang, Liangcai" uniqKey="Jiang L" first="Liangcai" last="Jiang">Liangcai Jiang</name><affiliation><nlm:aff id="a12"><institution>Sichuan Academy of Agricultural Sciences</institution>, Chengdu 610066,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Batley, Jacqueline" sort="Batley, Jacqueline" uniqKey="Batley J" first="Jacqueline" last="Batley">Jacqueline Batley</name><affiliation><nlm:aff id="a20"><institution>Australian Research Council Centre of Excellence for Integrative Legume Research, University of Queensland</institution>, Brisbane, Queensland 4072,<country>Australia</country></nlm:aff></affiliation></author><author><name sortKey="Sharpe, Andrew G" sort="Sharpe, Andrew G" uniqKey="Sharpe A" first="Andrew G" last="Sharpe">Andrew G. Sharpe</name><affiliation><nlm:aff id="a21"><institution>National Research Council Canada</institution>, Saskatoon, Saskatchewan,<country>Canada</country> S7N 0W9</nlm:aff></affiliation></author><author><name sortKey="Park, Beom Seok" sort="Park, Beom Seok" uniqKey="Park B" first="Beom-Seok" last="Park">Beom-Seok Park</name><affiliation><nlm:aff id="a22"><institution>The Agricultural Genome Center, National Academy of Agricultural Science, RDA</institution>, 126 Suin-Ro, Suwon 441-707,<country>Republic of Korea</country></nlm:aff></affiliation></author><author><name sortKey="Ruperao, Pradeep" sort="Ruperao, Pradeep" uniqKey="Ruperao P" first="Pradeep" last="Ruperao">Pradeep Ruperao</name><affiliation><nlm:aff id="a4"><institution>Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland</institution>, Brisbane, Queensland 4072,<country>Australia</country></nlm:aff></affiliation></author><author><name sortKey="Cheng, Feng" sort="Cheng, Feng" uniqKey="Cheng F" first="Feng" last="Cheng">Feng Cheng</name><affiliation><nlm:aff id="a2"><institution>The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, The Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences</institution>, Beijing 10081,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Waminal, Nomar Espinosa" sort="Waminal, Nomar Espinosa" uniqKey="Waminal N" first="Nomar Espinosa" last="Waminal">Nomar Espinosa Waminal</name><affiliation><nlm:aff id="a11"><institution>Department of Plant Sciences, Plant Genomics and Breeding Institute and Research Institute for Agriculture and Life Sciences, College of Agriculture & Life Sciences, Seoul National University</institution>, Seoul 151-921,<country>Republic of Korea</country></nlm:aff></affiliation><affiliation><nlm:aff id="a23"><institution>Department of Life Science, Plant Biotechnology Institute, Sahmyook University</institution>, Seoul 139-742,<country>Republic of Korea</country></nlm:aff></affiliation></author><author><name sortKey="Huang, Yin" sort="Huang, Yin" uniqKey="Huang Y" first="Yin" last="Huang">Yin Huang</name><affiliation><nlm:aff id="a3"><institution>Beijing Genome Institute-Shenzhen</institution>, Shenzhen 518083,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Dong, Caihua" sort="Dong, Caihua" uniqKey="Dong C" first="Caihua" last="Dong">Caihua Dong</name><affiliation><nlm:aff id="a1"><institution>The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences</institution>, Wuhan 430062,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Wang, Li" sort="Wang, Li" uniqKey="Wang L" first="Li" last="Wang">Li Wang</name><affiliation><nlm:aff id="a8"><institution>Center for Genomics and Computational Biology, School of Life Sciences, and School of Sciences, Hebei United University</institution>, Tangshan 063000,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Li, Jingping" sort="Li, Jingping" uniqKey="Li J" first="Jingping" last="Li">Jingping Li</name><affiliation><nlm:aff id="a7"><institution>Plant Genome Mapping Laboratory, University of Georgia</institution>, Athens, Georgia 30605,<country>USA</country></nlm:aff></affiliation></author><author><name sortKey="Hu, Zhiyong" sort="Hu, Zhiyong" uniqKey="Hu Z" first="Zhiyong" last="Hu">Zhiyong Hu</name><affiliation><nlm:aff id="a1"><institution>The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences</institution>, Wuhan 430062,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Zhuang, Mu" sort="Zhuang, Mu" uniqKey="Zhuang M" first="Mu" last="Zhuang">Mu Zhuang</name><affiliation><nlm:aff id="a2"><institution>The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, The Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences</institution>, Beijing 10081,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Huang, Yi" sort="Huang, Yi" uniqKey="Huang Y" first="Yi" last="Huang">Yi Huang</name><affiliation><nlm:aff id="a1"><institution>The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences</institution>, Wuhan 430062,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Huang, Junyan" sort="Huang, Junyan" uniqKey="Huang J" first="Junyan" last="Huang">Junyan Huang</name><affiliation><nlm:aff id="a1"><institution>The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences</institution>, Wuhan 430062,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Shi, Jiaqin" sort="Shi, Jiaqin" uniqKey="Shi J" first="Jiaqin" last="Shi">Jiaqin Shi</name><affiliation><nlm:aff id="a1"><institution>The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences</institution>, Wuhan 430062,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Mei, Desheng" sort="Mei, Desheng" uniqKey="Mei D" first="Desheng" last="Mei">Desheng Mei</name><affiliation><nlm:aff id="a1"><institution>The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences</institution>, Wuhan 430062,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Liu, Jing" sort="Liu, Jing" uniqKey="Liu J" first="Jing" last="Liu">Jing Liu</name><affiliation><nlm:aff id="a1"><institution>The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences</institution>, Wuhan 430062,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Lee, Tae Ho" sort="Lee, Tae Ho" uniqKey="Lee T" first="Tae-Ho" last="Lee">Tae-Ho Lee</name><affiliation><nlm:aff id="a7"><institution>Plant Genome Mapping Laboratory, University of Georgia</institution>, Athens, Georgia 30605,<country>USA</country></nlm:aff></affiliation></author><author><name sortKey="Wang, Jinpeng" sort="Wang, Jinpeng" uniqKey="Wang J" first="Jinpeng" last="Wang">Jinpeng Wang</name><affiliation><nlm:aff id="a8"><institution>Center for Genomics and Computational Biology, School of Life Sciences, and School of Sciences, Hebei United University</institution>, Tangshan 063000,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Jin, Huizhe" sort="Jin, Huizhe" uniqKey="Jin H" first="Huizhe" last="Jin">Huizhe Jin</name><affiliation><nlm:aff id="a7"><institution>Plant Genome Mapping Laboratory, University of Georgia</institution>, Athens, Georgia 30605,<country>USA</country></nlm:aff></affiliation></author><author><name sortKey="Li, Zaiyun" sort="Li, Zaiyun" uniqKey="Li Z" first="Zaiyun" last="Li">Zaiyun Li</name><affiliation><nlm:aff id="a16"><institution>National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University</institution>, Wuhan 430070,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Li, Xun" sort="Li, Xun" uniqKey="Li X" first="Xun" last="Li">Xun Li</name><affiliation><nlm:aff id="a17"><institution>College of Agronomy, Hunan Agricultural University</institution>, Changsha 410128,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Zhang, Jiefu" sort="Zhang, Jiefu" uniqKey="Zhang J" first="Jiefu" last="Zhang">Jiefu Zhang</name><affiliation><nlm:aff id="a18"><institution>Jiangsu Academy of Agricultural Sciences</institution>, Nanjing 210014,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Xiao, Lu" sort="Xiao, Lu" uniqKey="Xiao L" first="Lu" last="Xiao">Lu Xiao</name><affiliation><nlm:aff id="a19"><institution>Qinghai Academy of Agriculture and Forestry Sciences, National Key Laboratory Breeding Base for Innovation and Utilization of Plateau Crop Germplasm</institution>, Xining 810016,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Zhou, Yongming" sort="Zhou, Yongming" uniqKey="Zhou Y" first="Yongming" last="Zhou">Yongming Zhou</name><affiliation><nlm:aff id="a16"><institution>National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University</institution>, Wuhan 430070,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Liu, Zhongsong" sort="Liu, Zhongsong" uniqKey="Liu Z" first="Zhongsong" last="Liu">Zhongsong Liu</name><affiliation><nlm:aff id="a17"><institution>College of Agronomy, Hunan Agricultural University</institution>, Changsha 410128,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Liu, Xuequn" sort="Liu, Xuequn" uniqKey="Liu X" first="Xuequn" last="Liu">Xuequn Liu</name><affiliation><nlm:aff id="a24"><institution>School of Life Sciences, South-Central University for Nationality</institution>, Wuhan 430074,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Qin, Rui" sort="Qin, Rui" uniqKey="Qin R" first="Rui" last="Qin">Rui Qin</name><affiliation><nlm:aff id="a24"><institution>School of Life Sciences, South-Central University for Nationality</institution>, Wuhan 430074,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Tang, Xu" sort="Tang, Xu" uniqKey="Tang X" first="Xu" last="Tang">Xu Tang</name><affiliation><nlm:aff id="a7"><institution>Plant Genome Mapping Laboratory, University of Georgia</institution>, Athens, Georgia 30605,<country>USA</country></nlm:aff></affiliation></author><author><name sortKey="Liu, Wenbin" sort="Liu, Wenbin" uniqKey="Liu W" first="Wenbin" last="Liu">Wenbin Liu</name><affiliation><nlm:aff id="a3"><institution>Beijing Genome Institute-Shenzhen</institution>, Shenzhen 518083,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Wang, Yupeng" sort="Wang, Yupeng" uniqKey="Wang Y" first="Yupeng" last="Wang">Yupeng Wang</name><affiliation><nlm:aff id="a7"><institution>Plant Genome Mapping Laboratory, University of Georgia</institution>, Athens, Georgia 30605,<country>USA</country></nlm:aff></affiliation></author><author><name sortKey="Zhang, Yangyong" sort="Zhang, Yangyong" uniqKey="Zhang Y" first="Yangyong" last="Zhang">Yangyong Zhang</name><affiliation><nlm:aff id="a2"><institution>The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, The Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences</institution>, Beijing 10081,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Lee, Jonghoon" sort="Lee, Jonghoon" uniqKey="Lee J" first="Jonghoon" last="Lee">Jonghoon Lee</name><affiliation><nlm:aff id="a11"><institution>Department of Plant Sciences, Plant Genomics and Breeding Institute and Research Institute for Agriculture and Life Sciences, College of Agriculture & Life Sciences, Seoul National University</institution>, Seoul 151-921,<country>Republic of Korea</country></nlm:aff></affiliation></author><author><name sortKey="Kim, Hyun Hee" sort="Kim, Hyun Hee" uniqKey="Kim H" first="Hyun Hee" last="Kim">Hyun Hee Kim</name><affiliation><nlm:aff id="a23"><institution>Department of Life Science, Plant Biotechnology Institute, Sahmyook University</institution>, Seoul 139-742,<country>Republic of Korea</country></nlm:aff></affiliation></author><author><name sortKey="Denoeud, France" sort="Denoeud, France" uniqKey="Denoeud F" first="France" last="Denoeud">France Denoeud</name><affiliation><nlm:aff id="a25"><institution>Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Génomique, BP5706</institution> Evry 91057,<country>France</country></nlm:aff></affiliation><affiliation><nlm:aff id="a26"><institution>Centre National de Recherche Scientifique (CNRS), Université d'Evry, UMR 8030, CP5706</institution>, Evry 91057,<country>France</country></nlm:aff></affiliation></author><author><name sortKey="Xu, Xun" sort="Xu, Xun" uniqKey="Xu X" first="Xun" last="Xu">Xun Xu</name><affiliation><nlm:aff id="a3"><institution>Beijing Genome Institute-Shenzhen</institution>, Shenzhen 518083,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Liang, Xinming" sort="Liang, Xinming" uniqKey="Liang X" first="Xinming" last="Liang">Xinming Liang</name><affiliation><nlm:aff id="a3"><institution>Beijing Genome Institute-Shenzhen</institution>, Shenzhen 518083,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Hua, Wei" sort="Hua, Wei" uniqKey="Hua W" first="Wei" last="Hua">Wei Hua</name><affiliation><nlm:aff id="a1"><institution>The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences</institution>, Wuhan 430062,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Wang, Xiaowu" sort="Wang, Xiaowu" uniqKey="Wang X" first="Xiaowu" last="Wang">Xiaowu Wang</name><affiliation><nlm:aff id="a2"><institution>The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, The Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences</institution>, Beijing 10081,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Wang, Jun" sort="Wang, Jun" uniqKey="Wang J" first="Jun" last="Wang">Jun Wang</name><affiliation><nlm:aff id="a3"><institution>Beijing Genome Institute-Shenzhen</institution>, Shenzhen 518083,<country>China</country></nlm:aff></affiliation><affiliation><nlm:aff id="a27"><institution>Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200</institution>, Copenhagen,<country>Denmark</country></nlm:aff></affiliation><affiliation><nlm:aff id="a28"><institution>King Abdulaziz University</institution>, Jeddah, 21589,<country>Saudi Arabia</country></nlm:aff></affiliation><affiliation><nlm:aff id="a29"><institution>Department of Medicine and State Key Laboratory of Pharmaceutical Biotechnology, University of Hong Kong</institution>, 21 Sassoon Road,<country>Hong Kong</country></nlm:aff></affiliation></author><author><name sortKey="Chalhoub, Boulos" sort="Chalhoub, Boulos" uniqKey="Chalhoub B" first="Boulos" last="Chalhoub">Boulos Chalhoub</name><affiliation><nlm:aff id="a15"><institution>Organization and Evolution of Plant Genomes, Unité de Recherche en Génomique Végétale, Unité Mixte de Recherche 1165 (Institut National de Recherche Agronomique, Centre National de la Recherche Scientifique, Université Evry Val d’Essonne)</institution>, Evry 91057,<country>France</country></nlm:aff></affiliation></author><author><name sortKey="Paterson, Andrew H" sort="Paterson, Andrew H" uniqKey="Paterson A" first="Andrew H" last="Paterson">Andrew H. Paterson</name><affiliation><nlm:aff id="a7"><institution>Plant Genome Mapping Laboratory, University of Georgia</institution>, Athens, Georgia 30605,<country>USA</country></nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">24852848</idno><idno type="pmc">4279128</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4279128</idno><idno type="RBID">PMC:4279128</idno><idno type="doi">10.1038/ncomms4930</idno><date when="2014">2014</date><idno type="wicri:Area/Pmc/Corpus">000109</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000109</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">The <italic>Brassica oleracea</italic> genome reveals the asymmetrical evolution of polyploid
genomes</title><author><name sortKey="Liu, Shengyi" sort="Liu, Shengyi" uniqKey="Liu S" first="Shengyi" last="Liu">Shengyi Liu</name><affiliation><nlm:aff id="a1"><institution>The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences</institution>, Wuhan 430062,<country>China</country></nlm:aff></affiliation><affiliation><nlm:aff id="a30">These are joint first authors</nlm:aff></affiliation></author><author><name sortKey="Liu, Yumei" sort="Liu, Yumei" uniqKey="Liu Y" first="Yumei" last="Liu">Yumei Liu</name><affiliation><nlm:aff id="a2"><institution>The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, The Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences</institution>, Beijing 10081,<country>China</country></nlm:aff></affiliation><affiliation><nlm:aff id="a30">These are joint first authors</nlm:aff></affiliation></author><author><name sortKey="Yang, Xinhua" sort="Yang, Xinhua" uniqKey="Yang X" first="Xinhua" last="Yang">Xinhua Yang</name><affiliation><nlm:aff id="a3"><institution>Beijing Genome Institute-Shenzhen</institution>, Shenzhen 518083,<country>China</country></nlm:aff></affiliation><affiliation><nlm:aff id="a30">These are joint first authors</nlm:aff></affiliation></author><author><name sortKey="Tong, Chaobo" sort="Tong, Chaobo" uniqKey="Tong C" first="Chaobo" last="Tong">Chaobo Tong</name><affiliation><nlm:aff id="a1"><institution>The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences</institution>, Wuhan 430062,<country>China</country></nlm:aff></affiliation><affiliation><nlm:aff id="a30">These are joint first authors</nlm:aff></affiliation></author><author><name sortKey="Edwards, David" sort="Edwards, David" uniqKey="Edwards D" first="David" last="Edwards">David Edwards</name><affiliation><nlm:aff id="a4"><institution>Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland</institution>, Brisbane, Queensland 4072,<country>Australia</country></nlm:aff></affiliation><affiliation><nlm:aff id="a30">These are joint first authors</nlm:aff></affiliation></author><author><name sortKey="Parkin, Isobel A P" sort="Parkin, Isobel A P" uniqKey="Parkin I" first="Isobel A. P." last="Parkin">Isobel A. P. Parkin</name><affiliation><nlm:aff id="a5"><institution>Agriculture and Agri-Food Canada</institution>, Saskatoon, Saskatchewan,<country>Canada</country> S7N OX2</nlm:aff></affiliation><affiliation><nlm:aff id="a30">These are joint first authors</nlm:aff></affiliation></author><author><name sortKey="Zhao, Meixia" sort="Zhao, Meixia" uniqKey="Zhao M" first="Meixia" last="Zhao">Meixia Zhao</name><affiliation><nlm:aff id="a1"><institution>The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences</institution>, Wuhan 430062,<country>China</country></nlm:aff></affiliation><affiliation><nlm:aff id="a6"><institution>Department of Agronomy, Purdue University</institution>, WSLR Building B018, West Lafayette, Indiana 47907,<country>USA</country></nlm:aff></affiliation></author><author><name sortKey="Ma, Jianxin" sort="Ma, Jianxin" uniqKey="Ma J" first="Jianxin" last="Ma">Jianxin Ma</name><affiliation><nlm:aff id="a6"><institution>Department of Agronomy, Purdue University</institution>, WSLR Building B018, West Lafayette, Indiana 47907,<country>USA</country></nlm:aff></affiliation></author><author><name sortKey="Yu, Jingyin" sort="Yu, Jingyin" uniqKey="Yu J" first="Jingyin" last="Yu">Jingyin Yu</name><affiliation><nlm:aff id="a1"><institution>The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences</institution>, Wuhan 430062,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Huang, Shunmou" sort="Huang, Shunmou" uniqKey="Huang S" first="Shunmou" last="Huang">Shunmou Huang</name><affiliation><nlm:aff id="a1"><institution>The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences</institution>, Wuhan 430062,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Wang, Xiyin" sort="Wang, Xiyin" uniqKey="Wang X" first="Xiyin" last="Wang">Xiyin Wang</name><affiliation><nlm:aff id="a7"><institution>Plant Genome Mapping Laboratory, University of Georgia</institution>, Athens, Georgia 30605,<country>USA</country></nlm:aff></affiliation><affiliation><nlm:aff id="a8"><institution>Center for Genomics and Computational Biology, School of Life Sciences, and School of Sciences, Hebei United University</institution>, Tangshan 063000,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Wang, Junyi" sort="Wang, Junyi" uniqKey="Wang J" first="Junyi" last="Wang">Junyi Wang</name><affiliation><nlm:aff id="a3"><institution>Beijing Genome Institute-Shenzhen</institution>, Shenzhen 518083,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Lu, Kun" sort="Lu, Kun" uniqKey="Lu K" first="Kun" last="Lu">Kun Lu</name><affiliation><nlm:aff id="a9"><institution>College of Agronomy and Biotechnology, Southwest University, BeiBei District</institution>, Chongqing 400715,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Fang, Zhiyuan" sort="Fang, Zhiyuan" uniqKey="Fang Z" first="Zhiyuan" last="Fang">Zhiyuan Fang</name><affiliation><nlm:aff id="a2"><institution>The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, The Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences</institution>, Beijing 10081,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Bancroft, Ian" sort="Bancroft, Ian" uniqKey="Bancroft I" first="Ian" last="Bancroft">Ian Bancroft</name><affiliation><nlm:aff id="a10"><institution>Centre for Novel Agricultural Products (CNAP), Department of Biology, University of York, Wentworth Way</institution>, Heslington, York YO10 5DD,<country>UK</country></nlm:aff></affiliation></author><author><name sortKey="Yang, Tae Jin" sort="Yang, Tae Jin" uniqKey="Yang T" first="Tae-Jin" last="Yang">Tae-Jin Yang</name><affiliation><nlm:aff id="a11"><institution>Department of Plant Sciences, Plant Genomics and Breeding Institute and Research Institute for Agriculture and Life Sciences, College of Agriculture & Life Sciences, Seoul National University</institution>, Seoul 151-921,<country>Republic of Korea</country></nlm:aff></affiliation></author><author><name sortKey="Hu, Qiong" sort="Hu, Qiong" uniqKey="Hu Q" first="Qiong" last="Hu">Qiong Hu</name><affiliation><nlm:aff id="a1"><institution>The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences</institution>, Wuhan 430062,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Wang, Xinfa" sort="Wang, Xinfa" uniqKey="Wang X" first="Xinfa" last="Wang">Xinfa Wang</name><affiliation><nlm:aff id="a1"><institution>The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences</institution>, Wuhan 430062,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Yue, Zhen" sort="Yue, Zhen" uniqKey="Yue Z" first="Zhen" last="Yue">Zhen Yue</name><affiliation><nlm:aff id="a3"><institution>Beijing Genome Institute-Shenzhen</institution>, Shenzhen 518083,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Li, Haojie" sort="Li, Haojie" uniqKey="Li H" first="Haojie" last="Li">Haojie Li</name><affiliation><nlm:aff id="a12"><institution>Sichuan Academy of Agricultural Sciences</institution>, Chengdu 610066,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Yang, Linfeng" sort="Yang, Linfeng" uniqKey="Yang L" first="Linfeng" last="Yang">Linfeng Yang</name><affiliation><nlm:aff id="a3"><institution>Beijing Genome Institute-Shenzhen</institution>, Shenzhen 518083,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Wu, Jian" sort="Wu, Jian" uniqKey="Wu J" first="Jian" last="Wu">Jian Wu</name><affiliation><nlm:aff id="a2"><institution>The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, The Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences</institution>, Beijing 10081,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Zhou, Qing" sort="Zhou, Qing" uniqKey="Zhou Q" first="Qing" last="Zhou">Qing Zhou</name><affiliation><nlm:aff id="a3"><institution>Beijing Genome Institute-Shenzhen</institution>, Shenzhen 518083,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Wang, Wanxin" sort="Wang, Wanxin" uniqKey="Wang W" first="Wanxin" last="Wang">Wanxin Wang</name><affiliation><nlm:aff id="a2"><institution>The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, The Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences</institution>, Beijing 10081,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="King, Graham J" sort="King, Graham J" uniqKey="King G" first="Graham J" last="King">Graham J. King</name><affiliation><nlm:aff id="a13"><institution>Southern Cross Plant Science, Southern Cross University</institution>, Lismore, New South Wales 2480,<country>Australia</country></nlm:aff></affiliation></author><author><name sortKey="Pires, J Chris" sort="Pires, J Chris" uniqKey="Pires J" first="J. Chris" last="Pires">J. Chris Pires</name><affiliation><nlm:aff id="a14"><institution>Bond Life Sciences Center, University of Missouri</institution>, Columbia, Missouri 65211-7310,<country>USA</country></nlm:aff></affiliation></author><author><name sortKey="Lu, Changxin" sort="Lu, Changxin" uniqKey="Lu C" first="Changxin" last="Lu">Changxin Lu</name><affiliation><nlm:aff id="a3"><institution>Beijing Genome Institute-Shenzhen</institution>, Shenzhen 518083,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Wu, Zhangyan" sort="Wu, Zhangyan" uniqKey="Wu Z" first="Zhangyan" last="Wu">Zhangyan Wu</name><affiliation><nlm:aff id="a3"><institution>Beijing Genome Institute-Shenzhen</institution>, Shenzhen 518083,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Sampath, Perumal" sort="Sampath, Perumal" uniqKey="Sampath P" first="Perumal" last="Sampath">Perumal Sampath</name><affiliation><nlm:aff id="a11"><institution>Department of Plant Sciences, Plant Genomics and Breeding Institute and Research Institute for Agriculture and Life Sciences, College of Agriculture & Life Sciences, Seoul National University</institution>, Seoul 151-921,<country>Republic of Korea</country></nlm:aff></affiliation></author><author><name sortKey="Wang, Zhuo" sort="Wang, Zhuo" uniqKey="Wang Z" first="Zhuo" last="Wang">Zhuo Wang</name><affiliation><nlm:aff id="a3"><institution>Beijing Genome Institute-Shenzhen</institution>, Shenzhen 518083,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Guo, Hui" sort="Guo, Hui" uniqKey="Guo H" first="Hui" last="Guo">Hui Guo</name><affiliation><nlm:aff id="a7"><institution>Plant Genome Mapping Laboratory, University of Georgia</institution>, Athens, Georgia 30605,<country>USA</country></nlm:aff></affiliation></author><author><name sortKey="Pan, Shengkai" sort="Pan, Shengkai" uniqKey="Pan S" first="Shengkai" last="Pan">Shengkai Pan</name><affiliation><nlm:aff id="a3"><institution>Beijing Genome Institute-Shenzhen</institution>, Shenzhen 518083,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Yang, Limei" sort="Yang, Limei" uniqKey="Yang L" first="Limei" last="Yang">Limei Yang</name><affiliation><nlm:aff id="a2"><institution>The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, The Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences</institution>, Beijing 10081,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Min, Jiumeng" sort="Min, Jiumeng" uniqKey="Min J" first="Jiumeng" last="Min">Jiumeng Min</name><affiliation><nlm:aff id="a3"><institution>Beijing Genome Institute-Shenzhen</institution>, Shenzhen 518083,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Zhang, Dong" sort="Zhang, Dong" uniqKey="Zhang D" first="Dong" last="Zhang">Dong Zhang</name><affiliation><nlm:aff id="a7"><institution>Plant Genome Mapping Laboratory, University of Georgia</institution>, Athens, Georgia 30605,<country>USA</country></nlm:aff></affiliation></author><author><name sortKey="Jin, Dianchuan" sort="Jin, Dianchuan" uniqKey="Jin D" first="Dianchuan" last="Jin">Dianchuan Jin</name><affiliation><nlm:aff id="a8"><institution>Center for Genomics and Computational Biology, School of Life Sciences, and School of Sciences, Hebei United University</institution>, Tangshan 063000,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Li, Wanshun" sort="Li, Wanshun" uniqKey="Li W" first="Wanshun" last="Li">Wanshun Li</name><affiliation><nlm:aff id="a3"><institution>Beijing Genome Institute-Shenzhen</institution>, Shenzhen 518083,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Belcram, Harry" sort="Belcram, Harry" uniqKey="Belcram H" first="Harry" last="Belcram">Harry Belcram</name><affiliation><nlm:aff id="a15"><institution>Organization and Evolution of Plant Genomes, Unité de Recherche en Génomique Végétale, Unité Mixte de Recherche 1165 (Institut National de Recherche Agronomique, Centre National de la Recherche Scientifique, Université Evry Val d’Essonne)</institution>, Evry 91057,<country>France</country></nlm:aff></affiliation></author><author><name sortKey="Tu, Jinxing" sort="Tu, Jinxing" uniqKey="Tu J" first="Jinxing" last="Tu">Jinxing Tu</name><affiliation><nlm:aff id="a16"><institution>National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University</institution>, Wuhan 430070,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Guan, Mei" sort="Guan, Mei" uniqKey="Guan M" first="Mei" last="Guan">Mei Guan</name><affiliation><nlm:aff id="a17"><institution>College of Agronomy, Hunan Agricultural University</institution>, Changsha 410128,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Qi, Cunkou" sort="Qi, Cunkou" uniqKey="Qi C" first="Cunkou" last="Qi">Cunkou Qi</name><affiliation><nlm:aff id="a18"><institution>Jiangsu Academy of Agricultural Sciences</institution>, Nanjing 210014,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Du, Dezhi" sort="Du, Dezhi" uniqKey="Du D" first="Dezhi" last="Du">Dezhi Du</name><affiliation><nlm:aff id="a19"><institution>Qinghai Academy of Agriculture and Forestry Sciences, National Key Laboratory Breeding Base for Innovation and Utilization of Plateau Crop Germplasm</institution>, Xining 810016,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Li, Jiana" sort="Li, Jiana" uniqKey="Li J" first="Jiana" last="Li">Jiana Li</name><affiliation><nlm:aff id="a9"><institution>College of Agronomy and Biotechnology, Southwest University, BeiBei District</institution>, Chongqing 400715,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Jiang, Liangcai" sort="Jiang, Liangcai" uniqKey="Jiang L" first="Liangcai" last="Jiang">Liangcai Jiang</name><affiliation><nlm:aff id="a12"><institution>Sichuan Academy of Agricultural Sciences</institution>, Chengdu 610066,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Batley, Jacqueline" sort="Batley, Jacqueline" uniqKey="Batley J" first="Jacqueline" last="Batley">Jacqueline Batley</name><affiliation><nlm:aff id="a20"><institution>Australian Research Council Centre of Excellence for Integrative Legume Research, University of Queensland</institution>, Brisbane, Queensland 4072,<country>Australia</country></nlm:aff></affiliation></author><author><name sortKey="Sharpe, Andrew G" sort="Sharpe, Andrew G" uniqKey="Sharpe A" first="Andrew G" last="Sharpe">Andrew G. Sharpe</name><affiliation><nlm:aff id="a21"><institution>National Research Council Canada</institution>, Saskatoon, Saskatchewan,<country>Canada</country> S7N 0W9</nlm:aff></affiliation></author><author><name sortKey="Park, Beom Seok" sort="Park, Beom Seok" uniqKey="Park B" first="Beom-Seok" last="Park">Beom-Seok Park</name><affiliation><nlm:aff id="a22"><institution>The Agricultural Genome Center, National Academy of Agricultural Science, RDA</institution>, 126 Suin-Ro, Suwon 441-707,<country>Republic of Korea</country></nlm:aff></affiliation></author><author><name sortKey="Ruperao, Pradeep" sort="Ruperao, Pradeep" uniqKey="Ruperao P" first="Pradeep" last="Ruperao">Pradeep Ruperao</name><affiliation><nlm:aff id="a4"><institution>Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland</institution>, Brisbane, Queensland 4072,<country>Australia</country></nlm:aff></affiliation></author><author><name sortKey="Cheng, Feng" sort="Cheng, Feng" uniqKey="Cheng F" first="Feng" last="Cheng">Feng Cheng</name><affiliation><nlm:aff id="a2"><institution>The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, The Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences</institution>, Beijing 10081,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Waminal, Nomar Espinosa" sort="Waminal, Nomar Espinosa" uniqKey="Waminal N" first="Nomar Espinosa" last="Waminal">Nomar Espinosa Waminal</name><affiliation><nlm:aff id="a11"><institution>Department of Plant Sciences, Plant Genomics and Breeding Institute and Research Institute for Agriculture and Life Sciences, College of Agriculture & Life Sciences, Seoul National University</institution>, Seoul 151-921,<country>Republic of Korea</country></nlm:aff></affiliation><affiliation><nlm:aff id="a23"><institution>Department of Life Science, Plant Biotechnology Institute, Sahmyook University</institution>, Seoul 139-742,<country>Republic of Korea</country></nlm:aff></affiliation></author><author><name sortKey="Huang, Yin" sort="Huang, Yin" uniqKey="Huang Y" first="Yin" last="Huang">Yin Huang</name><affiliation><nlm:aff id="a3"><institution>Beijing Genome Institute-Shenzhen</institution>, Shenzhen 518083,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Dong, Caihua" sort="Dong, Caihua" uniqKey="Dong C" first="Caihua" last="Dong">Caihua Dong</name><affiliation><nlm:aff id="a1"><institution>The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences</institution>, Wuhan 430062,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Wang, Li" sort="Wang, Li" uniqKey="Wang L" first="Li" last="Wang">Li Wang</name><affiliation><nlm:aff id="a8"><institution>Center for Genomics and Computational Biology, School of Life Sciences, and School of Sciences, Hebei United University</institution>, Tangshan 063000,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Li, Jingping" sort="Li, Jingping" uniqKey="Li J" first="Jingping" last="Li">Jingping Li</name><affiliation><nlm:aff id="a7"><institution>Plant Genome Mapping Laboratory, University of Georgia</institution>, Athens, Georgia 30605,<country>USA</country></nlm:aff></affiliation></author><author><name sortKey="Hu, Zhiyong" sort="Hu, Zhiyong" uniqKey="Hu Z" first="Zhiyong" last="Hu">Zhiyong Hu</name><affiliation><nlm:aff id="a1"><institution>The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences</institution>, Wuhan 430062,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Zhuang, Mu" sort="Zhuang, Mu" uniqKey="Zhuang M" first="Mu" last="Zhuang">Mu Zhuang</name><affiliation><nlm:aff id="a2"><institution>The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, The Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences</institution>, Beijing 10081,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Huang, Yi" sort="Huang, Yi" uniqKey="Huang Y" first="Yi" last="Huang">Yi Huang</name><affiliation><nlm:aff id="a1"><institution>The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences</institution>, Wuhan 430062,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Huang, Junyan" sort="Huang, Junyan" uniqKey="Huang J" first="Junyan" last="Huang">Junyan Huang</name><affiliation><nlm:aff id="a1"><institution>The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences</institution>, Wuhan 430062,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Shi, Jiaqin" sort="Shi, Jiaqin" uniqKey="Shi J" first="Jiaqin" last="Shi">Jiaqin Shi</name><affiliation><nlm:aff id="a1"><institution>The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences</institution>, Wuhan 430062,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Mei, Desheng" sort="Mei, Desheng" uniqKey="Mei D" first="Desheng" last="Mei">Desheng Mei</name><affiliation><nlm:aff id="a1"><institution>The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences</institution>, Wuhan 430062,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Liu, Jing" sort="Liu, Jing" uniqKey="Liu J" first="Jing" last="Liu">Jing Liu</name><affiliation><nlm:aff id="a1"><institution>The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences</institution>, Wuhan 430062,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Lee, Tae Ho" sort="Lee, Tae Ho" uniqKey="Lee T" first="Tae-Ho" last="Lee">Tae-Ho Lee</name><affiliation><nlm:aff id="a7"><institution>Plant Genome Mapping Laboratory, University of Georgia</institution>, Athens, Georgia 30605,<country>USA</country></nlm:aff></affiliation></author><author><name sortKey="Wang, Jinpeng" sort="Wang, Jinpeng" uniqKey="Wang J" first="Jinpeng" last="Wang">Jinpeng Wang</name><affiliation><nlm:aff id="a8"><institution>Center for Genomics and Computational Biology, School of Life Sciences, and School of Sciences, Hebei United University</institution>, Tangshan 063000,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Jin, Huizhe" sort="Jin, Huizhe" uniqKey="Jin H" first="Huizhe" last="Jin">Huizhe Jin</name><affiliation><nlm:aff id="a7"><institution>Plant Genome Mapping Laboratory, University of Georgia</institution>, Athens, Georgia 30605,<country>USA</country></nlm:aff></affiliation></author><author><name sortKey="Li, Zaiyun" sort="Li, Zaiyun" uniqKey="Li Z" first="Zaiyun" last="Li">Zaiyun Li</name><affiliation><nlm:aff id="a16"><institution>National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University</institution>, Wuhan 430070,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Li, Xun" sort="Li, Xun" uniqKey="Li X" first="Xun" last="Li">Xun Li</name><affiliation><nlm:aff id="a17"><institution>College of Agronomy, Hunan Agricultural University</institution>, Changsha 410128,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Zhang, Jiefu" sort="Zhang, Jiefu" uniqKey="Zhang J" first="Jiefu" last="Zhang">Jiefu Zhang</name><affiliation><nlm:aff id="a18"><institution>Jiangsu Academy of Agricultural Sciences</institution>, Nanjing 210014,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Xiao, Lu" sort="Xiao, Lu" uniqKey="Xiao L" first="Lu" last="Xiao">Lu Xiao</name><affiliation><nlm:aff id="a19"><institution>Qinghai Academy of Agriculture and Forestry Sciences, National Key Laboratory Breeding Base for Innovation and Utilization of Plateau Crop Germplasm</institution>, Xining 810016,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Zhou, Yongming" sort="Zhou, Yongming" uniqKey="Zhou Y" first="Yongming" last="Zhou">Yongming Zhou</name><affiliation><nlm:aff id="a16"><institution>National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University</institution>, Wuhan 430070,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Liu, Zhongsong" sort="Liu, Zhongsong" uniqKey="Liu Z" first="Zhongsong" last="Liu">Zhongsong Liu</name><affiliation><nlm:aff id="a17"><institution>College of Agronomy, Hunan Agricultural University</institution>, Changsha 410128,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Liu, Xuequn" sort="Liu, Xuequn" uniqKey="Liu X" first="Xuequn" last="Liu">Xuequn Liu</name><affiliation><nlm:aff id="a24"><institution>School of Life Sciences, South-Central University for Nationality</institution>, Wuhan 430074,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Qin, Rui" sort="Qin, Rui" uniqKey="Qin R" first="Rui" last="Qin">Rui Qin</name><affiliation><nlm:aff id="a24"><institution>School of Life Sciences, South-Central University for Nationality</institution>, Wuhan 430074,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Tang, Xu" sort="Tang, Xu" uniqKey="Tang X" first="Xu" last="Tang">Xu Tang</name><affiliation><nlm:aff id="a7"><institution>Plant Genome Mapping Laboratory, University of Georgia</institution>, Athens, Georgia 30605,<country>USA</country></nlm:aff></affiliation></author><author><name sortKey="Liu, Wenbin" sort="Liu, Wenbin" uniqKey="Liu W" first="Wenbin" last="Liu">Wenbin Liu</name><affiliation><nlm:aff id="a3"><institution>Beijing Genome Institute-Shenzhen</institution>, Shenzhen 518083,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Wang, Yupeng" sort="Wang, Yupeng" uniqKey="Wang Y" first="Yupeng" last="Wang">Yupeng Wang</name><affiliation><nlm:aff id="a7"><institution>Plant Genome Mapping Laboratory, University of Georgia</institution>, Athens, Georgia 30605,<country>USA</country></nlm:aff></affiliation></author><author><name sortKey="Zhang, Yangyong" sort="Zhang, Yangyong" uniqKey="Zhang Y" first="Yangyong" last="Zhang">Yangyong Zhang</name><affiliation><nlm:aff id="a2"><institution>The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, The Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences</institution>, Beijing 10081,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Lee, Jonghoon" sort="Lee, Jonghoon" uniqKey="Lee J" first="Jonghoon" last="Lee">Jonghoon Lee</name><affiliation><nlm:aff id="a11"><institution>Department of Plant Sciences, Plant Genomics and Breeding Institute and Research Institute for Agriculture and Life Sciences, College of Agriculture & Life Sciences, Seoul National University</institution>, Seoul 151-921,<country>Republic of Korea</country></nlm:aff></affiliation></author><author><name sortKey="Kim, Hyun Hee" sort="Kim, Hyun Hee" uniqKey="Kim H" first="Hyun Hee" last="Kim">Hyun Hee Kim</name><affiliation><nlm:aff id="a23"><institution>Department of Life Science, Plant Biotechnology Institute, Sahmyook University</institution>, Seoul 139-742,<country>Republic of Korea</country></nlm:aff></affiliation></author><author><name sortKey="Denoeud, France" sort="Denoeud, France" uniqKey="Denoeud F" first="France" last="Denoeud">France Denoeud</name><affiliation><nlm:aff id="a25"><institution>Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Génomique, BP5706</institution> Evry 91057,<country>France</country></nlm:aff></affiliation><affiliation><nlm:aff id="a26"><institution>Centre National de Recherche Scientifique (CNRS), Université d'Evry, UMR 8030, CP5706</institution>, Evry 91057,<country>France</country></nlm:aff></affiliation></author><author><name sortKey="Xu, Xun" sort="Xu, Xun" uniqKey="Xu X" first="Xun" last="Xu">Xun Xu</name><affiliation><nlm:aff id="a3"><institution>Beijing Genome Institute-Shenzhen</institution>, Shenzhen 518083,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Liang, Xinming" sort="Liang, Xinming" uniqKey="Liang X" first="Xinming" last="Liang">Xinming Liang</name><affiliation><nlm:aff id="a3"><institution>Beijing Genome Institute-Shenzhen</institution>, Shenzhen 518083,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Hua, Wei" sort="Hua, Wei" uniqKey="Hua W" first="Wei" last="Hua">Wei Hua</name><affiliation><nlm:aff id="a1"><institution>The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences</institution>, Wuhan 430062,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Wang, Xiaowu" sort="Wang, Xiaowu" uniqKey="Wang X" first="Xiaowu" last="Wang">Xiaowu Wang</name><affiliation><nlm:aff id="a2"><institution>The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, The Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences</institution>, Beijing 10081,<country>China</country></nlm:aff></affiliation></author><author><name sortKey="Wang, Jun" sort="Wang, Jun" uniqKey="Wang J" first="Jun" last="Wang">Jun Wang</name><affiliation><nlm:aff id="a3"><institution>Beijing Genome Institute-Shenzhen</institution>, Shenzhen 518083,<country>China</country></nlm:aff></affiliation><affiliation><nlm:aff id="a27"><institution>Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200</institution>, Copenhagen,<country>Denmark</country></nlm:aff></affiliation><affiliation><nlm:aff id="a28"><institution>King Abdulaziz University</institution>, Jeddah, 21589,<country>Saudi Arabia</country></nlm:aff></affiliation><affiliation><nlm:aff id="a29"><institution>Department of Medicine and State Key Laboratory of Pharmaceutical Biotechnology, University of Hong Kong</institution>, 21 Sassoon Road,<country>Hong Kong</country></nlm:aff></affiliation></author><author><name sortKey="Chalhoub, Boulos" sort="Chalhoub, Boulos" uniqKey="Chalhoub B" first="Boulos" last="Chalhoub">Boulos Chalhoub</name><affiliation><nlm:aff id="a15"><institution>Organization and Evolution of Plant Genomes, Unité de Recherche en Génomique Végétale, Unité Mixte de Recherche 1165 (Institut National de Recherche Agronomique, Centre National de la Recherche Scientifique, Université Evry Val d’Essonne)</institution>, Evry 91057,<country>France</country></nlm:aff></affiliation></author><author><name sortKey="Paterson, Andrew H" sort="Paterson, Andrew H" uniqKey="Paterson A" first="Andrew H" last="Paterson">Andrew H. Paterson</name><affiliation><nlm:aff id="a7"><institution>Plant Genome Mapping Laboratory, University of Georgia</institution>, Athens, Georgia 30605,<country>USA</country></nlm:aff></affiliation></author></analytic><series><title level="j">Nature Communications</title><idno type="eISSN">2041-1723</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Polyploidization has provided much genetic variation for plant adaptive evolution,
but the mechanisms by which the molecular evolution of polyploid genomes establishes
genetic architecture underlying species differentiation are unclear. <italic>Brassica</italic>is an ideal model to increase knowledge of polyploid evolution. Here we describe a
draft genome sequence of <italic>Brassica oleracea</italic>, comparing it with that of its
sister species <italic>B. rapa</italic> to reveal numerous chromosome rearrangements and
asymmetrical gene loss in duplicated genomic blocks, asymmetrical amplification of
transposable elements, differential gene co-retention for specific pathways and
variation in gene expression, including alternative splicing, among a large number
of paralogous and orthologous genes. Genes related to the production of anticancer
phytochemicals and morphological variations illustrate consequences of genome
duplication and gene divergence, imparting biochemical and morphological variation
to <italic>B. oleracea</italic>. This study provides insights into <italic>Brassica</italic> genome
evolution and will underpin research into the many important crops in this
genus.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Kopsell, D A" uniqKey="Kopsell D">D. A. Kopsell</name></author><author><name sortKey="Kopsell, D E" uniqKey="Kopsell D">D. E. Kopsell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Halkier, B A" uniqKey="Halkier B">B. A. Halkier</name></author><author><name sortKey="Gershenzon, J" uniqKey="Gershenzon J">J. Gershenzon</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Khwaja, F S" uniqKey="Khwaja F">F. S. Khwaja</name></author><author><name sortKey="Wynne, S" uniqKey="Wynne S">S. Wynne</name></author><author><name sortKey="Posey, I" uniqKey="Posey I">I. Posey</name></author><author><name sortKey="Djakiew, D" uniqKey="Djakiew D">D. Djakiew</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Li, Y" uniqKey="Li Y">Y. Li</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Higdon, J V" uniqKey="Higdon J">J. V. Higdon</name></author><author><name sortKey="Delage, B" uniqKey="Delage B">B. Delage</name></author><author><name sortKey="Williams, D E" uniqKey="Williams D">D. E. Williams</name></author><author><name sortKey="Dashwood, R X0a H" uniqKey="Dashwood R">R.
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contrib-type="author"><name><surname>Kim</surname><given-names>Hyun Hee</given-names></name><xref ref-type="aff" rid="a23">23</xref></contrib><contrib contrib-type="author"><name><surname>Denoeud</surname><given-names>France</given-names></name><xref ref-type="aff" rid="a25">25</xref><xref ref-type="aff" rid="a26">26</xref></contrib><contrib contrib-type="author"><name><surname>Xu</surname><given-names>Xun</given-names></name><xref ref-type="aff" rid="a3">3</xref></contrib><contrib contrib-type="author"><name><surname>Liang</surname><given-names>Xinming</given-names></name><xref ref-type="aff" rid="a3">3</xref></contrib><contrib contrib-type="author"><name><surname>Hua</surname><given-names>Wei</given-names></name><xref ref-type="aff" rid="a1">1</xref></contrib><contrib contrib-type="author"><name><surname>Wang</surname><given-names>Xiaowu</given-names></name><xref ref-type="aff" rid="a2">2</xref></contrib><contrib contrib-type="author"><name><surname>Wang</surname><given-names>Jun</given-names></name><xref ref-type="aff" rid="a3">3</xref><xref ref-type="aff" rid="a27">27</xref><xref ref-type="aff" rid="a28">28</xref><xref ref-type="aff" rid="a29">29</xref></contrib><contrib contrib-type="author"><name><surname>Chalhoub</surname><given-names>Boulos</given-names></name><xref ref-type="aff" rid="a15">15</xref></contrib><contrib contrib-type="author"><name><surname>Paterson</surname><given-names>Andrew H</given-names></name><xref ref-type="aff" rid="a7">7</xref></contrib><aff id="a1"><label>1</label><institution>The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture of PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences</institution>, Wuhan 430062,<country>China</country></aff><aff id="a2"><label>2</label><institution>The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, The Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences</institution>, Beijing 10081,<country>China</country></aff><aff id="a3"><label>3</label><institution>Beijing Genome Institute-Shenzhen</institution>, Shenzhen 518083,<country>China</country></aff><aff id="a4"><label>4</label><institution>Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland</institution>, Brisbane, Queensland 4072,<country>Australia</country></aff><aff id="a5"><label>5</label><institution>Agriculture and Agri-Food Canada</institution>, Saskatoon, Saskatchewan,<country>Canada</country> S7N OX2</aff><aff id="a6"><label>6</label><institution>Department of Agronomy, Purdue University</institution>, WSLR Building B018, West Lafayette, Indiana 47907,<country>USA</country></aff><aff id="a7"><label>7</label><institution>Plant Genome Mapping Laboratory, University of Georgia</institution>, Athens, Georgia 30605,<country>USA</country></aff><aff id="a8"><label>8</label><institution>Center for Genomics and Computational Biology, School of Life Sciences, and School of Sciences, Hebei United University</institution>, Tangshan 063000,<country>China</country></aff><aff id="a9"><label>9</label><institution>College of Agronomy and Biotechnology, Southwest University, BeiBei District</institution>, Chongqing 400715,<country>China</country></aff><aff id="a10"><label>10</label><institution>Centre for Novel Agricultural Products (CNAP), Department of Biology, University of York, Wentworth Way</institution>, Heslington, York YO10 5DD,<country>UK</country></aff><aff id="a11"><label>11</label><institution>Department of Plant Sciences, Plant Genomics and Breeding Institute and Research Institute for Agriculture and Life Sciences, College of Agriculture & Life Sciences, Seoul National University</institution>, Seoul 151-921,<country>Republic of Korea</country></aff><aff id="a12"><label>12</label><institution>Sichuan Academy of Agricultural Sciences</institution>, Chengdu 610066,<country>China</country></aff><aff id="a13"><label>13</label><institution>Southern Cross Plant Science, Southern Cross University</institution>, Lismore, New South Wales 2480,<country>Australia</country></aff><aff id="a14"><label>14</label><institution>Bond Life Sciences Center, University of Missouri</institution>, Columbia, Missouri 65211-7310,<country>USA</country></aff><aff id="a15"><label>15</label><institution>Organization and Evolution of Plant Genomes, Unité de Recherche en Génomique Végétale, Unité Mixte de Recherche 1165 (Institut National de Recherche Agronomique, Centre National de la Recherche Scientifique, Université Evry Val d’Essonne)</institution>, Evry 91057,<country>France</country></aff><aff id="a16"><label>16</label><institution>National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University</institution>, Wuhan 430070,<country>China</country></aff><aff id="a17"><label>17</label><institution>College of Agronomy, Hunan Agricultural University</institution>, Changsha 410128,<country>China</country></aff><aff id="a18"><label>18</label><institution>Jiangsu Academy of Agricultural Sciences</institution>, Nanjing 210014,<country>China</country></aff><aff id="a19"><label>19</label><institution>Qinghai Academy of Agriculture and Forestry Sciences, National Key Laboratory Breeding Base for Innovation and Utilization of Plateau Crop Germplasm</institution>, Xining 810016,<country>China</country></aff><aff id="a20"><label>20</label><institution>Australian Research Council Centre of Excellence for Integrative Legume Research, University of Queensland</institution>, Brisbane, Queensland 4072,<country>Australia</country></aff><aff id="a21"><label>21</label><institution>National Research Council Canada</institution>, Saskatoon, Saskatchewan,<country>Canada</country> S7N 0W9</aff><aff id="a22"><label>22</label><institution>The Agricultural Genome Center, National Academy of Agricultural Science, RDA</institution>, 126 Suin-Ro, Suwon 441-707,<country>Republic of Korea</country></aff><aff id="a23"><label>23</label><institution>Department of Life Science, Plant Biotechnology Institute, Sahmyook University</institution>, Seoul 139-742,<country>Republic of Korea</country></aff><aff id="a24"><label>24</label><institution>School of Life Sciences, South-Central University for Nationality</institution>, Wuhan 430074,<country>China</country></aff><aff id="a25"><label>25</label><institution>Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Génomique, BP5706</institution> Evry 91057,<country>France</country></aff><aff id="a26"><label>26</label><institution>Centre National de Recherche Scientifique (CNRS), Université d'Evry, UMR 8030, CP5706</institution>, Evry 91057,<country>France</country></aff><aff id="a27"><label>27</label><institution>Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200</institution>, Copenhagen,<country>Denmark</country></aff><aff id="a28"><label>28</label><institution>King Abdulaziz University</institution>, Jeddah, 21589,<country>Saudi Arabia</country></aff><aff id="a29"><label>29</label><institution>Department of Medicine and State Key Laboratory of Pharmaceutical Biotechnology, University of Hong Kong</institution>, 21 Sassoon Road,<country>Hong Kong</country></aff><aff id="a30"><label>30</label>These are joint first authors</aff></contrib-group><author-notes><corresp id="c1"><label>a</label><email>liusy@oilcrops.cn</email></corresp></author-notes><pub-date pub-type="epub"><day>23</day><month>05</month><year>2014</year></pub-date><volume>5</volume><elocation-id>3930</elocation-id><history><date date-type="received"><day>23</day><month>10</month><year>2013</year></date><date date-type="accepted"><day>22</day><month>04</month><year>2014</year></date></history><permissions><copyright-statement>Copyright © 2014, Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights
Reserved.</copyright-statement><copyright-year>2014</copyright-year><copyright-holder>Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights
Reserved.</copyright-holder><license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by-nc-sa/3.0/"><pmc-comment>author-paid</pmc-comment>
<license-p>This work is licensed under a Creative Commons
Attribution-NonCommercial-ShareAlike 3.0 Unported License. The images or other third
party material in this article are included in the article’s Creative
Commons license, unless indicated otherwise in the credit line; if the material is
not included under the Creative Commons license, users will need to obtain
permission from the license holder to reproduce the material. To view a copy of this
license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/</license-p></license></permissions><abstract><p>Polyploidization has provided much genetic variation for plant adaptive evolution,
but the mechanisms by which the molecular evolution of polyploid genomes establishes
genetic architecture underlying species differentiation are unclear. <italic>Brassica</italic>is an ideal model to increase knowledge of polyploid evolution. Here we describe a
draft genome sequence of <italic>Brassica oleracea</italic>, comparing it with that of its
sister species <italic>B. rapa</italic> to reveal numerous chromosome rearrangements and
asymmetrical gene loss in duplicated genomic blocks, asymmetrical amplification of
transposable elements, differential gene co-retention for specific pathways and
variation in gene expression, including alternative splicing, among a large number
of paralogous and orthologous genes. Genes related to the production of anticancer
phytochemicals and morphological variations illustrate consequences of genome
duplication and gene divergence, imparting biochemical and morphological variation
to <italic>B. oleracea</italic>. This study provides insights into <italic>Brassica</italic> genome
evolution and will underpin research into the many important crops in this
genus.</p></abstract><abstract abstract-type="web-summary"><p><inline-graphic id="i1" xlink:href="ncomms4930-i1.jpg"></inline-graphic><italic>Brassica oleracea</italic> is plant species comprising economically important vegetable
crops. Here, the authors report the draft genome sequence of <italic>B. oleracea</italic> and,
through a comparative analysis with the closely related <italic>B. rapa</italic>, reveal insights
into <italic>Brassica</italic> evolution and divergence of interspecific genomes and intraspecific
subgenomes.</p></abstract></article-meta></front><body><p>B<italic>rassica oleracea</italic> comprises many important vegetable crops including cauliflower,
broccoli, cabbages, Brussels sprouts, kohlrabi and kales. The species demonstrates
extreme morphological diversity and crop forms, with various members grown for their
leaves, flowers and stems. About 76 million tons of <italic>Brassica</italic> vegetables were
produced in 2010, with a value of 14.85 billion dollars ( <ext-link ext-link-type="uri" xlink:href="http://faostat.fao.org/">http://faostat.fao.org/</ext-link>). Most <italic>B.
oleracea</italic> crops are high in protein<xref ref-type="bibr" rid="b1">1</xref> and carotenoids<xref ref-type="bibr" rid="b2">2</xref>, and contain diverse glucosinolates (GSLs) that function as unique phytochemicals for
plant defence against fungal and bacterial pathogens<xref ref-type="bibr" rid="b3">3</xref> and on consumption
have been shown to have potent anticancer properties<xref ref-type="bibr" rid="b4">4</xref><xref ref-type="bibr" rid="b5">5</xref><xref ref-type="bibr" rid="b6">6</xref>.</p><p><italic>B. oleracea</italic> is a member of the family <italic>Brassicaceae</italic> (~\n338
genera and 3,709 species)<xref ref-type="bibr" rid="b7">7</xref> and one of three diploid <italic>Brassica</italic>species in the classical triangle of U<xref ref-type="bibr" rid="b8">8</xref> that also includes diploids <italic>B.
rapa</italic> (AA) and <italic>B. nigra</italic> (BB) and allotetraploids <italic>B. juncea</italic> (AABB),
<italic>B. napus</italic> (AACC) and <italic>B. carinata</italic> (BBCC). These allotetraploid species
are important oilseed crops, accounting for 12% of world edible oil production (
<ext-link ext-link-type="uri" xlink:href="http://faostat.fao.org/">http://faostat.fao.org/</ext-link>). As the
origin and relationship between these species is clear, the timing and nature of the
evolutionary events associated with <italic>Brassica</italic> divergence and speciation can be
revealed by interspecific genome comparison. Each of the <italic>Brassica</italic> genomes retains
evidence of recursive whole-genome duplication (WGD) events<xref ref-type="bibr" rid="b9">9</xref><xref ref-type="bibr" rid="b10">10</xref> (<xref ref-type="supplementary-material" rid="S1">Supplementary Fig. 1</xref>) and have undergone a
<italic>Brassiceae</italic>-lineage-specific whole-genome triplication (WGT)<xref ref-type="bibr" rid="b11">11</xref><xref ref-type="bibr" rid="b12">12</xref> since their divergence from the <italic>Arabidopsis</italic> lineage. These
events were followed by diploidization that involved substantial genome reshuffling and
gene losses<xref ref-type="bibr" rid="b11">11</xref><xref ref-type="bibr" rid="b12">12</xref><xref ref-type="bibr" rid="b13">13</xref><xref ref-type="bibr" rid="b14">14</xref><xref ref-type="bibr" rid="b15">15</xref>. Because of this, <italic>Brassica</italic> species
are a model for the study of polyploid genome evolution (<xref ref-type="supplementary-material" rid="S1">Supplementary Fig. 2</xref>), mechanisms of duplicated gene
loss, neo- and sub-functionalization, and associated impact on morphological diversity
and species differentiation.</p><p>We report a draft genome sequence of <italic>B. oleracea</italic> and its comprehensive genomic
comparison with the genome of sister species <italic>B. rapa</italic>, which diverged from a
common ancestor ~\n4 MYA. These data provide insights into the dynamics of
<italic>Brassica</italic> genome evolution and divergence, and serve as important resources
for <italic>Brassica</italic> vegetable and oilseed crop breeding. Furthermore, this genome will
support studies of the large range of morphological variation found within <italic>B.
oleracea</italic>, which includes sexually compatible crops such as cabbages, cauliflower
and broccoli that are important for their economic, nutritional and potent anticancer
value.</p><sec disp-level="1" sec-type="results"><title>Results</title><sec disp-level="2"><title><italic>B. oleracea</italic> genome assembly and annotation</title><p>Complementing the sequencing of the smaller <italic>B. rapa</italic> genome<xref ref-type="bibr" rid="b11">11</xref>, a draft genome assembly of <italic>B. oleracea</italic> var. <italic>capitata</italic> line
02–12 was produced by interleaving Illumina, Roche 454 and Sanger
sequence data. This assembly represents 85% of the estimated 630 Mb
genome, and includes >98% of the gene space (<xref ref-type="supplementary-material" rid="S1">Supplementary Methods</xref>, <xref ref-type="supplementary-material" rid="S1">Supplementary Tables 1–3, 7 and 8</xref>and <xref ref-type="supplementary-material" rid="S1">Supplementary Fig. 3</xref>). The
assembly was anchored to a new genetic map<xref ref-type="bibr" rid="b16">16</xref> to produce nine
pseudo-chromosomes that account for 72% of the assembly, and validated by
comparison with a <italic>B. oleracea</italic> physical map<xref ref-type="bibr" rid="b17">17</xref>, a
high-density <italic>B. napus</italic> genetic map<xref ref-type="bibr" rid="b18">18</xref> and complete BAC
sequences (<xref ref-type="supplementary-material" rid="S1">Supplementary Figs
4–9</xref> and <xref ref-type="supplementary-material" rid="S1">Supplementary Tables 4 and 5</xref>). For comparative analyses, identical
genome annotation pipelines were used for annotation of protein-coding genes and
transposable elements (TEs) for <italic>B. oleracea</italic> and <italic>B. rapa</italic>.</p><p>A total of 45,758 protein-coding genes were predicted, with a mean transcript
length of 1,761 bp, a mean coding length of 1,037 bp, and
a mean of 4.55 exons per gene (<xref ref-type="table" rid="t1">Table 1</xref>, <xref ref-type="supplementary-material" rid="S1">Supplementary Methods</xref>, <xref ref-type="supplementary-material" rid="S1">Supplementary Table 6</xref> and <xref ref-type="supplementary-material" rid="S1">Supplementary Fig. 10</xref>), similar to <italic>A.
thaliana</italic><xref ref-type="bibr" rid="b19">19</xref> and <italic>B. rapa</italic><xref ref-type="bibr" rid="b11">11</xref>. Publicly
available ESTs, together with RNA sequencing (RNA-seq) data generated in this
study, support 94% of predicted gene models (<xref ref-type="supplementary-material" rid="S1">Supplementary Tables 7 and 8</xref>), and 91.6% of
predicted genes have a match in at least one public protein database (<xref ref-type="supplementary-material" rid="S1">Supplementary Tables 9 and 10</xref>, and
<xref ref-type="supplementary-material" rid="S1">Supplementary Fig. 11</xref>). Of the
45,758 predicted genes, 13,032 produce alternative splicing (AS) variants with
intron retention and exon skipping (<xref ref-type="supplementary-material" rid="S1">Supplementary Table 11</xref>). Genome annotation also predicted 3,756
non-coding RNAs (miRNA, tRNA, rRNA and snRNA) (<xref ref-type="supplementary-material" rid="S1">Supplementary Table 12</xref>).</p><p>A combination of structure-based analyses and homology-based comparisons resulted
in the identification of 13,382 TEs with clearly identified terminal boundaries,
including 5,107 retrotransposons and 8,275 DNA transposons (<xref ref-type="supplementary-material" rid="S1">Supplementary Methods</xref>, <xref ref-type="supplementary-material" rid="S1">Supplementary Fig. 12</xref> and <xref ref-type="supplementary-material" rid="S1">Supplementary Table 13</xref>). These elements
together with numerous truncated elements or TE remnants make up 38.80% of the
assembled portion of the <italic>B. oleracea</italic> genome, whereas TEs account for only
21.47% of the <italic>B. rapa</italic> genome assembly. Copia (11.64%) and gypsy (7.84%)
retroelements are the major constituents of the repetitive fraction, and are
unevenly distributed across each chromosome, with retrotransposons predominantly
found in pericentromeric or heterochromatic regions (<xref ref-type="supplementary-material" rid="S1">Supplementary Fig. 13</xref>) in <italic>B. oleracea</italic>.
Tentative physical positions of some of the centromeres were determined based on
homologue and phylogenetic analysis of the centromere-specific 76 bp
tandem repeats CentBo-1 and CentBo-2 and copia-type retrotransposon (CentCRBo)
(<xref ref-type="supplementary-material" rid="S1">Supplementary Table 14</xref> and
<xref ref-type="supplementary-material" rid="S1">Supplementary Figs
14–17</xref>). The distribution of 45S and 5S rDNA sequences were
also visualized by fluorescent <italic>in situ</italic> hybridization (<xref ref-type="supplementary-material" rid="S1">Supplementary Figs 18 and 19</xref>), leading to a
predicted karyotype ideogram for <italic>B. oleracea</italic> (<xref ref-type="supplementary-material" rid="S1">Supplementary Fig. 20</xref>). An extra-centromeric
locus with colocalized centromeric satellite repeat CentBo-1 and the centromeric
retrotransposon CRBo-1 was observed on the long arm of chromosome 6 (<xref ref-type="supplementary-material" rid="S1">Supplementary Figs
18–20</xref>). A comprehensive database for the genome information is
accessible at <ext-link ext-link-type="uri" xlink:href="http://www.ocri-genomics.org/bolbase/index.html">http://www.ocri-genomics.org/bolbase/index.html</ext-link>.</p></sec><sec disp-level="2"><title>Conserved syntenic blocks and genome rearrangement after WGT</title><p>The relatively complete triplicated regions in <italic>B. oleracea</italic> and <italic>B.
rapa</italic> were constructed and they relate to the 24 ancestral crucifer
blocks (A–X) in <italic>A. thaliana</italic><xref ref-type="bibr" rid="b20">20</xref>. Further the
triplicated blocks resulting from WGT in the two <italic>Brassica</italic> species were
partitioned into three subgenomes: LF (Least-fractionated), MF1
(Medium-fractionated) and MF2 (Most-fractionated)<xref ref-type="bibr" rid="b11">11</xref> (<xref ref-type="fig" rid="f1">Fig. 1a</xref>, <xref ref-type="supplementary-material" rid="S1">Supplementary Methods</xref>, <xref ref-type="supplementary-material" rid="S1">Supplementary Tables 15 and 16</xref>, and <xref ref-type="supplementary-material" rid="S1">Supplementary Figs 21–26</xref>). These
syntenic blocks occupy the majority of the genome assemblies of <italic>A.
thaliana</italic> (19,628 genes, 72.24% of 27,169 genes), <italic>B. oleracea</italic>(26,485 genes, 57.88%) and <italic>B. rapa</italic> (26,698 genes, 64.84%), and provide a
foundation for comparative analyses of chromosomal rearrangement, gene loss and
divergence of retained paralogues after WGT. Massive gene loss occurred in an
asymmetrical and reciprocal fashion in the three subgenomes of each species and
was largely completed before the <italic>B. oleracea–B. rapa</italic>divergence (<xref ref-type="fig" rid="f1">Fig. 1c</xref>, <xref ref-type="supplementary-material" rid="S1">Supplementary Tables 17–19</xref> and
<xref ref-type="supplementary-material" rid="S1">Supplementary Figs
25–27</xref>). The timing of this evolutionary process was
supported by the estimated timing of WGT ~\n15.9 million years ago
(MYA), and species divergence ~\n4.6 MYA, based on synonymous
substitution (Ks) rates of genes located in the blocks (<xref ref-type="fig" rid="f1">Fig.
1b</xref> and <xref ref-type="supplementary-material" rid="S1">Supplementary Table
20</xref>). Gene loss occurred mainly through small deletions that may be
caused by illegitimate recombination<xref ref-type="bibr" rid="b21">21</xref><xref ref-type="bibr" rid="b22">22</xref> (<xref ref-type="supplementary-material" rid="S1">Supplementary Fig. 27</xref>), consistent with
observations in other plant genomes.</p><p>Abundant genome rearrangement following WGT and subsequent <italic>Brassica</italic>species divergence resulted in complex mosaics of triplicated ancestral genomic
blocks in the A and C genomes (<xref ref-type="fig" rid="f1">Fig. 1a</xref> and <xref ref-type="supplementary-material" rid="S1">Supplementary Fig. 28</xref>). At least 19 major,
and numerous fine-scale, chromosome rearrangements occurred, which differentiate
the two <italic>Brassica</italic> species (<xref ref-type="supplementary-material" rid="S1">Supplementary Fig. 29</xref>). This is in agreement with previous
comparative studies based on chromosome painting<xref ref-type="bibr" rid="b12">12</xref><xref ref-type="bibr" rid="b23">23</xref> and
genetic mapping<xref ref-type="bibr" rid="b24">24</xref><xref ref-type="bibr" rid="b25">25</xref>. The extensive chromosome reshuffling in
<italic>Brassica</italic> is in contrast to that observed in other taxa, such as the
highly syntenic tomato–potato and pear–apple genomes, each
with longer divergence times and less genome rearrangement<xref ref-type="bibr" rid="b26">26</xref><xref ref-type="bibr" rid="b27">27</xref>.
This difference may be a consequence of mesopolyploidy in <italic>Brassica</italic>.</p></sec><sec disp-level="2"><title>Greater TEs accumulation in <italic>B. oleracea</italic> than <italic>B.
rapa</italic></title><p>Both retro- (22.13%) and DNA (16.67%) TEs appear to be greater amplified in <italic>B.
oleracea</italic> relative to <italic>B. rapa</italic> (9.43 and 12.04%) (<xref ref-type="fig" rid="f2">Fig. 2a</xref> and <xref ref-type="supplementary-material" rid="S1">Supplementary
Table 13</xref>). We constructed 1,362 gap-free contig-contig syntenic
regions by clustering orthologous <italic>B. rapa</italic>—<italic>B. oleracea</italic>genes using MCscan (<xref ref-type="supplementary-material" rid="S1">Supplementary Figs 29
and 30</xref>). The <italic>B. oleracea</italic> TE length (34.03% of the 259.6M) is
3.4 times greater than that of the syntenic <italic>B. rapa</italic> regions (16.73% of
the 155.0M) (<xref ref-type="fig" rid="f2">Fig. 2c</xref>, <xref ref-type="supplementary-material" rid="S1">Supplementary Tables 21 and 22</xref>, and <xref ref-type="supplementary-material" rid="S1">Supplementary Fig. 31</xref>). Phylogenetic
analysis revealed that <italic>B. oleracea</italic> has both more LTR retrotransposon
(LTR-RT) families, and more members in most families than <italic>B. rapa</italic> (<xref ref-type="fig" rid="f2">Fig. 2d</xref> and <xref ref-type="supplementary-material" rid="S1">Supplementary Figs 12, 32 and 33</xref>). Furthermore, two new lineages of
LTR-RTs, <italic>Brassica Copia</italic> Retrotransposon and <italic>Brassica Gypsy</italic>Retrotransposon, were defined in both <italic>Brassica</italic> species (<xref ref-type="supplementary-material" rid="S1">Supplementary Fig. 33</xref>). Analysis of LTR
insertion time revealed that ~\n98% of <italic>B. oleracea</italic> intact
LTR-RTs amplified continuously over the ~\n4 million years (MY) since
the <italic>B. oleracea</italic>–<italic>B. rapa</italic> split, whereas
~\n68% of <italic>B. rapa</italic> intact LTR-RTs amplified rapidly within the
last 1 MY, predominantly in the recent 0.2 MY (<xref ref-type="fig" rid="f2">Fig. 2b</xref> and
<xref ref-type="supplementary-material" rid="S1">Supplementary Fig. 34</xref>). Hence,
LTR-RTs expanded more in the intergenic space of euchromatic regions in <italic>B.
oleracea</italic> than <italic>B. rapa</italic>. This agrees with previous observations
based on comparison of BAC sequences between the A and C genomes<xref ref-type="bibr" rid="b28">28</xref>. As a consequence of continuous TE amplification over the last 4 MY, the
genome size of <italic>B. oleracea</italic> is ~\n30% larger than that of <italic>B.
rapa</italic> although the two genomes share the same ploidy and are largely
collinear.</p></sec><sec disp-level="2"><title>Species-specific genes and tandemly duplicated genes</title><p>While the genomes of <italic>B. oleracea</italic> and <italic>B. rapa</italic> are highly similar in
terms of total gene clusters/sequences and the gene number in each cluster,
there are also a large number of species-specific genes in the two species. A
total of 66.5% (34,237 genes) of <italic>B. oleracea</italic> genes and 74.9% (34,324) of
<italic>B. rapa</italic> genes were clustered into OrthoMCL groups (<xref ref-type="supplementary-material" rid="S1">Supplementary Table 23</xref> and <xref ref-type="supplementary-material" rid="S1">Supplementary Fig. 35</xref>). We identified 9,832
<italic>B. oleracea</italic>-specific and 5,735 <italic>B. rapa</italic>-specific genes, of
which 77% were supported by gene expression and/or a clear <italic>Arabidopsis</italic>homologue (<xref ref-type="supplementary-material" rid="S1">Supplementary Table 24</xref>).
Of them, >90% of these specific genes were validated for their absence in
the counterpart genomes by reciprocal mapping of raw clean reads (<xref ref-type="supplementary-material" rid="S1">Supplementary Tables 25 and 26</xref>). Most
<italic>Brassica</italic>-specific genes are randomly distributed along the
chromosomes (<xref ref-type="supplementary-material" rid="S1">Supplementary Figs 36 and
37</xref>). More than 80% of the species-specific genes were surrounded by
non-specific genes (<xref ref-type="supplementary-material" rid="S1">Supplementary Fig.
38</xref>), suggesting that deletion of individual genes may be the major
mechanism underlying gene loss and the difference in gene numbers between <italic>B.
oleracea</italic> and <italic>B. rapa</italic>.</p><p>Tandem duplication produces clusters of duplicated genes and contributes to the
expansion of gene families<xref ref-type="bibr" rid="b29">29</xref>. We identified 1,825, 2,111 and
1,554 gene clusters containing 4,365, 5,181 and 4,170 tandemly duplicated genes
in <italic>B. oleracea</italic>, <italic>B. rapa</italic> and <italic>A. thaliana</italic>, respectively
(<xref ref-type="fig" rid="f3">Fig. 3a</xref>, <xref ref-type="supplementary-material" rid="S1">Supplementary Tables 27 and 28</xref> and <xref ref-type="supplementary-material" rid="S1">Supplementary Fig. 39</xref>). The wide range of
sequence divergence of tandem gene pairs in each species suggests that tandem
gene duplication occurred continuously throughout the evolutionary history of
these species, rather than in discrete bursts (<xref ref-type="supplementary-material" rid="S1">Supplementary Figs 40 and 41</xref>). Their
continuous and asymmetrical occurrence after species divergence resulted in 522,
697 and 815 species-specific tandem clusters in the three genomes. The frequency
of tandem duplication is independent of the total gene content, suggesting that
genome triplication has not inhibited its occurrence. Tandemly duplicated genes
are preferentially enriched for gene ontology (GO) categories related to defence
response and pathways related to secondary metabolism such as indole alkaloid
biosynthesis and tropane, piperidine and pyridine alkaloid biosynthesis (<xref ref-type="fig" rid="f3">Fig. 3b</xref>, <xref ref-type="supplementary-material" rid="S1">Supplementary Tables 29–32</xref> and <xref ref-type="supplementary-material" rid="S1">Supplementary Fig. 42</xref>). Over 44.0 and 51.9%
of the NBS-encoding resistance genes are tandemly duplicated in <italic>B.
oleracea</italic> and <italic>B. rapa</italic>, respectively (<xref ref-type="supplementary-material" rid="S1">Supplementary Table 33</xref>).</p></sec><sec disp-level="2"><title>Biased loss and retention of genes after WGT/WGD</title><p>Following polyploidization, reversion of gene numbers towards diploid levels
through gene loss has been widely observed in plants<xref ref-type="bibr" rid="b30">30</xref>. However,
in <italic>Brassica</italic> this only appears to be true for collinear genes in the
conserved syntenic regions, with a loss of ~\n60% of the predicted
post-triplication gene set, nearly restoring the pre-triplication gene number.
This is reflected in an overall retention rate of 1.2-fold of <italic>A. thaliana</italic>orthologous genes in corresponding syntenic regions (<xref ref-type="fig" rid="f1">Fig.
1c</xref> and <xref ref-type="supplementary-material" rid="S1">Supplementary Table
18</xref>). In contrast, in terms of genes that have no collinear gene in
<italic>A. thaliana</italic> and either <italic>Brassica</italic> species (hereafter called
non-collinear genes), gene retention rates is 2.5-fold the <italic>A. thaliana</italic>gene number in <italic>B. oleracea</italic> and 1.9-fold in <italic>B. rapa</italic>, both
significantly higher than the expected rates (<italic>P</italic> value
<2.2e–16;<xref ref-type="supplementary-material" rid="S1">Supplementary Table 34</xref>). For these retained genes, the numbers of the
genes that are common in the two <italic>Brassica</italic> species are 11,746 in <italic>B.
oleracea</italic> and 10,411 in <italic>B. rapa</italic>. Most of these genes are supported
by expression and/or the presence of an <italic>Arabidopsis</italic> homologue (<xref ref-type="supplementary-material" rid="S1">Supplementary Table 35</xref>). More than
61% of these genes have homologues present as collinear genes and 16% also are
homologous to other non-collinear genes, indicating gene movement from
triplicated syntenic regions and being similar to observations in <italic>A.
thaliana</italic>, where half of the genes are nonsyntenic within rosids<xref ref-type="bibr" rid="b31">31</xref>. This suggests that the breakdown of the triplicated syntenic
relationship has not only prevented gene loss and a move towards
pre-triplication gene numbers but has also maintained a higher gene density, and
thus maintained WGT-derived genes for species evolution.</p><p>The presence of a large number of the retained paralogous genes in the syntenic
regions led us to examine whether genes in some functional categories have
preferentially been over-retained, as observed in other plants<xref ref-type="bibr" rid="b29">29</xref>.
The results indicate that WGT-produced paralogous genes are over-retained in GO
categories associated with regulation of metabolic and biosynthetic processes,
RNA metabolism and transcription factors (<xref ref-type="supplementary-material" rid="S1">Supplementary Table 36</xref> and <xref ref-type="supplementary-material" rid="S1">Supplementary Figs 43–45</xref>), and the two <italic>Brassica</italic>species exhibit similar patterns of gene category retention. From a study of
KEGG pathways, we also found that WGT-produced <italic>Brassica</italic> paralogous genes
contribute 40–60% of total genes for 90% of KEGG pathways (<xref ref-type="fig" rid="f3">Fig. 3c</xref> and <xref ref-type="supplementary-material" rid="S1">Supplementary Fig. 43</xref>), and are functionally enriched in primary or
core metabolic processes such as oxidative phosphorylation, carbon fixation,
photosynthesis, circadian rhythm<xref ref-type="bibr" rid="b32">32</xref> and lipid metabolism (<xref ref-type="supplementary-material" rid="S1">Supplementary Tables 36 and 37</xref> and
<xref ref-type="supplementary-material" rid="S1">Supplementary Figs
43–45</xref>). Notably, the pathways associated with energy
metabolism have been enhanced in both <italic>Brassica</italic> species. For instance, in
the oxidative phosphorylation pathway, there are 161 genes in <italic>A.
thaliana</italic>, but 241 in <italic>B. oleracea</italic> and 208 in <italic>B. rapa</italic>. The
majority (143/241 and 142/208) of these <italic>Brassica</italic> genes are multiple
paralogues residing in the triplicated syntenic regions, and more than half of
these paralogues have been retained as three copies, significantly higher than
observed for other genes in the triplication regions (<xref ref-type="fig" rid="f3">Fig.
3d</xref> and <xref ref-type="supplementary-material" rid="S1">Supplementary Fig.
43</xref>).</p><p>Phylogenetic analyses show that WGT led to an expansion of genes involved in
auxin functioning (AUX, IAA, GH3, PIN, SAUR, TAA, TIR, TPL and YUCCA),
morphology specification (TCP), and flowering time control (FLC, CO, VRN1,
LFY, AP1 and GI) (<xref ref-type="supplementary-material" rid="S1">Supplementary
Table 38</xref> and <xref ref-type="supplementary-material" rid="S1">Supplementary Figs
46–61</xref>), and that most <italic>Arabidopsis</italic> genes in these
families have two or three orthologs in <italic>Brassica</italic> species. These
WGT-produced duplicated genes may provide important sources of evolutionary
innovation<xref ref-type="bibr" rid="b33">33</xref> and contribute to the extreme morphological
diversity in <italic>Brassica</italic> species.</p></sec><sec disp-level="2"><title>Divergence of duplicated genes in the <italic>Brassica</italic> genomes</title><p>The largest genetic foundation for plant genome evolution and new species
formation is the differentiation of retained paralogous and orthologous genes.
Around 38% (4,302/11,493) of all paralogous gene pairs in <italic>B. oleracea</italic> and
~\n36% (4,089/11,448) in <italic>B. rapa</italic> have different predicted exon
numbers (<xref ref-type="supplementary-material" rid="S1">Supplementary Data 1</xref>, <xref ref-type="supplementary-material" rid="S1">Supplementary Tables 39 and 40</xref> and
<xref ref-type="supplementary-material" rid="S1">Supplementary Fig. 62</xref>). There
are 6,571 orthologous gene pairs with different exon numbers, accounting for
27.6% of total gene pairs (23,823). Some paralogous or orthologous pairs have
high Ks values and low sequence similarity (<xref ref-type="supplementary-material" rid="S1">Supplementary Fig. 63</xref>), indicating sequence
differentiation. Of these paralogous genes, some offer appreciable opportunity
for non-reciprocal DNA exchanges (gene conversion). About 8% of the 4,296
homologous quartets in <italic>B. rapa</italic> and <italic>B. oleracea</italic> have been affected
by gene conversion (<xref ref-type="fig" rid="f4">Fig. 4a</xref>, <xref ref-type="supplementary-material" rid="S1">Supplementary Table 41</xref> and <xref ref-type="supplementary-material" rid="S1">Supplementary Fig. 64</xref>) and about one-sixth
(53) of converted genes were inferred to have experienced independent conversion
events in both <italic>Brassica</italic> species, a parallelism sometimes observed in
other plants<xref ref-type="bibr" rid="b11">11</xref><xref ref-type="bibr" rid="b34">34</xref>. Around 40–44% of conversion events
involved paralogues in the less-fractionated subgenomes LF in both species,
substantially higher than the other two subgenomes (<xref ref-type="supplementary-material" rid="S1">Supplementary Table 41</xref>). This finding
suggests that gene conversion is related to homologous gene density, which
determines the likelihood of illegitimate recombination.</p><p>Analysis of RNA-seq data generated from callus, root, leaf, stem, flower and
silique of <italic>B. oleracea</italic> and <italic>B. rapa</italic> suggests that >40% of
WGT paralogous gene pairs are differentially expressed in these species (<xref ref-type="fig" rid="f4">Fig. 4b</xref> and <xref ref-type="supplementary-material" rid="S1">Supplementary Fig. 65</xref>), suggesting potential subfunctionalization of
these genes. In both species, a general trend of expression differentiation was
alpha-WGD paralogous genes (~\n46%) > WGT paralogous genes
(~\n42%) > tandemly duplicated genes (~\n35%)
(<xref ref-type="fig" rid="f4">Fig. 4b</xref>, <xref ref-type="supplementary-material" rid="S1">Supplementary Fig. 66</xref> and <xref ref-type="supplementary-material" rid="S1">Supplementary Tables 42 and 43</xref>). Different tissues harbour
approximately the same number of differentially expressed duplicates, but this
number was slightly higher in flower tissue. The expression level of genes in
the LF subgenome was significantly higher than corresponding syntenic genes in
the more fractionated subgenomes (MF1 and MF2) while no expression dominance
relationship was observed between the subgenomes MF1 and MF2 (<xref ref-type="fig" rid="f4">Fig. 4c</xref>, <xref ref-type="supplementary-material" rid="S1">Supplementary Table
44</xref> and <xref ref-type="supplementary-material" rid="S1">Supplementary Fig.
67</xref>). Duplicated transcription factor gene pairs showed less
differentiated expression (~\n38%) than the expected ratio at the
genome-wide level (<xref ref-type="fig" rid="f4">Fig. 4d</xref> and <xref ref-type="supplementary-material" rid="S1">Supplementary Table 45</xref>), while paralogues
with GO categories related to membrane, catalytic activity and defence response
exhibited a higher ratio of differentiated expression (<xref ref-type="fig" rid="f4">Fig.
4e</xref> and <xref ref-type="supplementary-material" rid="S1">Supplementary Table
46</xref>). Of <italic>B. oleracea–B. rapa</italic> orthologous gene pairs
(23,823 in total), ~\n42% were differentially expressed across all
tissues (<xref ref-type="supplementary-material" rid="S1">Supplementary Tables 42 and
43</xref>).</p><p>Furthermore, many paralogues generate different transcripts, resulting in
expression differentiation. Analysis of AS variants of paralogous gene pairs
that have identical numbers of exons demonstrated that these variants (either
different variants or differential expression of the same variants) cause
>20% and >44% of such paralogous genes to be differentially
expressed in <italic>B. oleracea</italic> and <italic>B. rapa</italic>, respectively (<xref ref-type="fig" rid="f4">Fig. 4f</xref> and <xref ref-type="supplementary-material" rid="S1">Supplementary
Table 47</xref>). For orthologous gene pairs of <italic>B. oleracea</italic> and <italic>B.
rapa</italic>, 35.5% (8,467) of gene pairs showed differential expression due to
AS variation. When only counting intron retention and exon skipping, 9.3%
(2,215) of gene pairs differ. Divergence in AS variants of gene pairs presents
an important layer of gene regulation, as reported<xref ref-type="bibr" rid="b35">35</xref><xref ref-type="bibr" rid="b36">36</xref><xref ref-type="bibr" rid="b37">37</xref><xref ref-type="bibr" rid="b38">38</xref>,
and thus provides a genetic basis for species evolution and new species
formation.</p></sec><sec disp-level="2"><title>Unique GSLs metabolism pathways</title><p>GSLs and hydrolysis products have been of long-standing interest due to their
role in plant defence and anticancer properties. Compared with <italic>B. rapa</italic>and <italic>B. napus</italic>, <italic>B. oleracea</italic> has the greatest GSL profile diversity,
with wide qualitative and quantitative variation<xref ref-type="bibr" rid="b39">39</xref><xref ref-type="bibr" rid="b40">40</xref>. We
identified 101 and 105 GSL biosynthesis genes in <italic>B. rapa</italic> and <italic>B.
oleracea</italic>, respectively, and 22 GSL catabolism genes in each species
(<xref ref-type="fig" rid="f5">Fig. 5a</xref>, <xref ref-type="supplementary-material" rid="S1">Supplementary Table 48</xref> and <xref ref-type="supplementary-material" rid="S1">Supplementary Data 2</xref>). In the GSL biosynthesis and catabolism
pathways, tandem genes (41.4%, 40.7% and 33.9% in <italic>A. thaliana</italic>, <italic>B.
oleracea</italic> and <italic>B. rapa</italic>, respectively) were present in a much higher
proportion than the genome-wide average (<xref ref-type="supplementary-material" rid="S1">Supplementary Table 32</xref>). The observed variation of GSL profiles is
mainly attributed to the duplication of two genes, <italic>methylthioalkylmalate</italic>(<italic>MAM</italic>) <italic>synthase</italic> and <italic>2-oxoglutarate-dependent dioxygenase</italic>(<italic>AOP</italic>).</p><p>In <italic>Arabidopsis</italic>, the <italic>MAM</italic> family contains three tandemly duplicated
and functionally diverse members (<italic>MAM1</italic>, <italic>MAM2</italic> and <italic>MAM3</italic>), and functional analysis demonstrated that
MAM2 (absent in ecotype
Columbia) and MAM1 catalyses
the condensation reaction of the first and the first two elongation cycles for
the synthesis of dominant 3 and 4 carbon (C) side-chain aliphatic GSLs,
respectively<xref ref-type="bibr" rid="b40">40</xref><xref ref-type="bibr" rid="b41">41</xref>, while MAM3 is assumed to contribute to the production of all GSL
chain lengths<xref ref-type="bibr" rid="b42">42</xref>. In <italic>B. rapa</italic> and <italic>B. oleracea</italic>,
<italic>MAM1</italic>/<italic>MAM2</italic> genes experienced independent tandem duplication to
produce 6 and 5 orthologs respectively (<xref ref-type="fig" rid="f5">Fig. 5b,c</xref>). The
main GSLs in <italic>B. oleracea</italic> are 4C and 3C GSLs (progoitrin, gluconapin, glucoraphanin and sinigrin)<xref ref-type="bibr" rid="b43">43</xref>, while those
in <italic>B. rapa</italic> are 4C and 5C GSLs (gluconapin and glucobrassicanapin)<xref ref-type="bibr" rid="b39">39</xref> (<xref ref-type="fig" rid="f5">Fig.
5a</xref>). Based on the results of expression and phylogenetic analyses, we
found a pair of genes Bol017070 and Bra013007, which are the only orthologous genes showing high
expression in <italic>B. oleracea</italic> but silenced in <italic>B. rapa</italic> (<xref ref-type="fig" rid="f5">Fig. 5a</xref>). This expression difference most likely leads to greater
accumulation of the 3C GSL anticancer precursor sinigrin in <italic>B. oleracea</italic>.
Meanwhile, the expression level of MAM3 in <italic>B. rapa</italic> is much higher than in
<italic>B. oleracea</italic>, explaining the accumulation of 5C GSL glucobrassicanapin in <italic>B. rapa</italic>.
Other genes affecting specific anticancer GLS products are <italic>AOPs.</italic>Previously, research has reported four gene loci involved in the side-chain
modifications of aliphatic GSLs in <italic>Arabidopsis</italic>. Two tandemly duplicated
genes <italic>AOP2</italic> and
<italic>AOP3</italic> catalyse
the formation of alkenyl and hydroxyalkyl GSLs, respectively. When both
<italic>AOPs</italic> are non-functional, the plant accumulates the precursor
methylsulfinyl alkyl GSL. We identified three <italic>AOP2</italic> genes in <italic>B.
oleracea</italic> (<xref ref-type="fig" rid="f5">Fig. 5d</xref>), but two are non-functional due
to the presence of premature stop codons. In contrast, all three
<italic>AOP2</italic> copies are
functional in <italic>B. rapa</italic><xref ref-type="bibr" rid="b44">44</xref>. No <italic>AOP3</italic> homologue has been
identified in <italic>Brassica</italic>. This analysis supports GSL content surveys and
explains why glucoraphanin is
abundant in <italic>B. oleracea</italic>, but not in <italic>B. rapa</italic>.</p></sec></sec><sec disp-level="1" sec-type="discussion"><title>Discussion</title><p>The <italic>Brassica</italic> genomes experienced WGT<xref ref-type="bibr" rid="b11">11</xref><xref ref-type="bibr" rid="b12">12</xref><xref ref-type="bibr" rid="b25">25</xref> followed by
massive gene loss and frequent reshuffling of triplicated genomic blocks. Analysis
of retained or lost genes following triplication identified over-retention of genes
for metabolic pathways such as oxidative phosphorylation, carbon fixation,
photosynthesis and circadian rhythm<xref ref-type="bibr" rid="b32">32</xref>, which may contribute to
polyploid vigour<xref ref-type="bibr" rid="b45">45</xref>. Fewer lost genes were observed in the
less-fractionated subgenome, possibly due to expression dominance as reported in
maize<xref ref-type="bibr" rid="b46">46</xref>.</p><p>Gene expression analysis revealed extensive divergence and AS variants between
duplicate genes. This subfunctionalization or neofunctionalization of duplicated
genes provides genetic novelty and a basis for species evolution and new species
formation. For example, TF genes that are considered to be conserved still have more
than 38% of paralogous pairs showing differential expression across tissues although
this percentage is lower than the average from all duplicated genes. Gene expression
variation may contribute to an increased complexity of regulatory networks after
polyploidization.</p><p>The multi-layered asymmetrical evolution of the <italic>Brassica</italic> genomes revealed in
this study suggests mechanisms of polyploid genome evolution underlying speciation.
Asymmetrical gene loss between the <italic>Brassica</italic> subgenomes, the asymmetrical
amplification of TEs and tandem duplications, preferential enrichment of genes for
certain pathways or functional categories, and divergence in DNA sequence and
expression, including alternative splicing among a large number of paralogous and
orthologous genes, together shape a route for genome evolution after
polyploidization. A molecular model of polyploid genome evolution through these
asymmetrical mechanisms is summarized in <xref ref-type="supplementary-material" rid="S1">Supplementary Fig. 2</xref>. The additional information of accessible large
datasets and resource was provided in <xref ref-type="supplementary-material" rid="S1">Supplementary Table 49</xref>.</p><p>In summary, the <italic>B. oleracea</italic> genomic sequence, its features in comparison with
its relatives, and the genome evolution mechanisms revealed, provide a fundamental
resource for the genetic improvement of important traits, including components of
GSLs for anticancer pharmaceuticals. The genome sequence has also laid a foundation
for investigation of the tremendous range of morphological variation in <italic>B.
oleracea</italic> as well as supporting genome analysis of the important
allotetraploid crop <italic>B. napus</italic> (canola or rapeseed).</p></sec><sec disp-level="1" sec-type="methods"><title>Methods</title><sec disp-level="2"><title>Sample preparation and genome sequencing</title><p>A <italic>B. oleracea</italic> sp. <italic>capitata</italic> homozygous line 02–12 with
elite agronomic characters and widely used as a parent in hybrid breeding was
used for the reference genome sequencing (<xref ref-type="supplementary-material" rid="S1">Supplementary Methods</xref>). The seedlings of plants were collected and
genomic DNA was extracted from leaves with a standard CTAB extraction method.
Illumina Genome Analyser whole-genome shotgun sequencing combined with GS FLX
Titanium sequencing technology was used to achieve a <italic>B. oleracea</italic> draft
genome. We constructed a total of 35 paired-end sequencing libraries with
insertion sizes of 180 base pairs (bp), 200 bp, 350 bp,
500 bp, 650 bp, 800 bp, 2 kb,
5 kb, 10 kb and 20 kb following a standard
protocol provided by Illumina (<xref ref-type="supplementary-material" rid="S1">Supplementary Methods</xref>). Sequencing was performed using Illumina
Genome Analyser II according to the manufacturer’s standard
protocol.</p></sec><sec disp-level="2"><title>Genome assembly and validation</title><p>We took a series of checking and filtering measures on reads following the
Illumina-Pipeline, and low-quality reads, adaptor sequences and duplicates were
removed (<xref ref-type="supplementary-material" rid="S1">Supplementary Methods</xref>).
The reads after the above filtering and correction steps were used to perform
assembly including contig construction, scaffold construction and gap filling
using SOAPdenovo1.04 ( <ext-link ext-link-type="uri" xlink:href="http://soap.genomics.org.cn/">http://soap.genomics.org.cn/</ext-link>) (<xref ref-type="supplementary-material" rid="S1">Supplementary Methods</xref>). Finally, we used
20-kb-span paired-end data generated from the 454 platform and 105-kb-span
BAC-end data downloaded from NCBI ( <ext-link ext-link-type="uri" xlink:href="http://www.ncbi.nlm.nih.gov/nucgss?term=BOT01">http://www.ncbi.nlm.nih.gov/nucgss?term=BOT01</ext-link>) to extend scaffold
length (<xref ref-type="supplementary-material" rid="S1">Supplementary Methods</xref>). The
<italic>B. oleracea</italic> genome size was estimated using the distribution curve of
17-mer frequency (<xref ref-type="supplementary-material" rid="S1">Supplementary
Methods</xref>).</p><p>To anchor the assembled scaffolds onto pseudo-chromosomes, we developed a genetic
map using a double haploid population with 165 lines derived from a F1 cross
between two homozygous lines 02–12 (sequenced) and 0188
(re-sequenced). The genetic map contains 1,227 simple sequence repeat markers
and single nucleotide polymorphism markers in nine linkage groups, which span a
total of 1,180.2 cM with an average of 0.96 cM between the
adjacent loci<xref ref-type="bibr" rid="b16">16</xref>. To position these markers to the scaffolds,
marker primers were compared with the scaffold sequences using e-PCR (parameters
-n2 -g1 –d 400–800), with the best-scoring match chosen in
case of multiple matches.</p><p>We validated the <italic>B. oleracea</italic> genome assembly by comparing it with the
published physical map constructed using 73,728 BAC clones ( <ext-link ext-link-type="uri" xlink:href="http://lulu.pgml.uga.edu/fpc/WebAGCoL/%20brassica/WebFPC/">http://lulu.pgml.uga.edu/fpc/WebAGCoL/brassica/WebFPC/</ext-link>)<xref ref-type="bibr" rid="b17">17</xref> and a genetic map from <italic>B. napus</italic><xref ref-type="bibr" rid="b18">18</xref> (<xref ref-type="supplementary-material" rid="S1">Supplementary Methods</xref>). Eleven
Sanger-sequenced <italic>B. oleracea</italic> BAC sequences were used to assess the
assembled genome using MUMmer-3.22 ( <ext-link ext-link-type="uri" xlink:href="http://mummer.sourceforge.net/">http://mummer.sourceforge.net/</ext-link>) (<xref ref-type="supplementary-material" rid="S1">Supplementary Methods</xref>).</p></sec><sec disp-level="2"><title>Gene prediction and annotation</title><p>Gene prediction was performed on the genome sequence after pre-masking for TEs
(<xref ref-type="supplementary-material" rid="S1">Supplementary Methods</xref>). Gene
prediction was processed with the following steps: (i) <italic>De novo</italic> gene
prediction used AUGUSTUS<xref ref-type="bibr" rid="b47">47</xref> and GlimmerHMM<xref ref-type="bibr" rid="b48">48</xref> with
parameters trained from <italic>A. thaliana</italic> genes. (ii) For homologue prediction,
we mapped the protein sequences from <italic>A. thaliana</italic>, <italic>O. sativa</italic>, <italic>C.
papaya</italic>, <italic>V. vinifera</italic> and <italic>P. trichocarpa</italic> to the <italic>B.
oleracea</italic> genome using tblastn with an <italic>E</italic>-value cutoff of
10<sup>−5</sup>, and used GeneWise (Version 2.2.0)<xref ref-type="bibr" rid="b49">49</xref> for gene annotation. (iii) For EST-aided annotation, the
<italic>Brassica</italic> ESTs from NCBI were aligned to the <italic>B. oleracea</italic> genome
using BLAT (identity ≥0.95, coverage ≥0.90) and further
assembled using PASA<xref ref-type="bibr" rid="b50">50</xref>. Finally, all the predictions were
combined using GLEAN<xref ref-type="bibr" rid="b51">51</xref> to produce the consensus gene sets.</p><p>Functional annotation of <italic>B. oleracea</italic> genes was based on comparison with
SwissProt, TrEMBL, Interproscan and KEGG proteins databases. The tRNA genes were
identified by tRNAscan-SE using default parameters<xref ref-type="bibr" rid="b52">52</xref>. Then rRNAs
were compared with the genome using blastn. Other non-coding RNAs, including
miRNA, snRNA, were identified using INFERNAL<xref ref-type="bibr" rid="b53">53</xref> by comparison with
the Rfam database.</p></sec><sec disp-level="2"><title>TE annotation</title><p>LTR-RTs were initially identified using the LTR_STRUC<xref ref-type="bibr" rid="b54">54</xref> programme,
and then manually annotated and checked based on structure characteristics and
sequence homology. Refined intact elements were then used to identify other
intact elements and solo LTRs<xref ref-type="bibr" rid="b55">55</xref>. All the LTR-RTs with clear
boundaries and insertion sites were classified into superfamilies
(<italic>Copia</italic>-like, <italic>Gypsy</italic>-like and Unclassified retroelements) and
families relying on the internal protein sequence, 5′, 3′
LTRs, primer-binding site and polypurine tracts. Non-LTR-RTs (Long interspersed
nuclear element, LINE and Short interspersed nuclear element, SINE) and DNA
transposons (<italic>Tc1-Mariner</italic>, <italic>hAT</italic>, <italic>Mutator</italic>, <italic>Pong</italic>,
<italic>PIF-Harbinger</italic>, CACTA and miniature inverted repeat TE) were
identified using conserved protein domains of reverse transposase or transposase
as queries to search against the assembled genome using tblastn. Further
upstream and downstream sequences of the candidate matches were compared with
each other to define their boundaries and structure<xref ref-type="bibr" rid="b56">56</xref>.
<italic>Helitron</italic> elements were identified by the HelSearch 1.0 programme<xref ref-type="bibr" rid="b57">57</xref> and manually inspected. All the TE categories were identified
according to the criteria described previously<xref ref-type="bibr" rid="b58">58</xref>. Typical
elements of each category were selected and mixed together as a database for
RepeatMasker<xref ref-type="bibr" rid="b59">59</xref> analysis. Around 20 × coverage of
shotgun reads randomly sampled from the two <italic>Brassica</italic> genomes were masked
by the same TE data set to confirm the different accumulation of TEs between the
two genomes.</p></sec><sec disp-level="2"><title>Syntenic block construction of <italic>B. oleracea</italic> and its
relatives</title><p>We used the same strategy as described in the <italic>B. rapa</italic> genome paper<xref ref-type="bibr" rid="b11">11</xref> to construct syntenic blocks between species (<xref ref-type="supplementary-material" rid="S1">Supplementary Methods</xref>). The all-against-all
blastp comparison (<italic>E</italic>-value ≤ 1e–5) provided the
gene pairs for syntenic clustering determined by MCScan (MATCH_SCORE: 50,
MATCH_SIZE: 5, GAP_SCORE: –3, E_VALUE: 1E–05). As applied
in <italic>B. rapa</italic><xref ref-type="bibr" rid="b11">11</xref>, we assigned and partitioned multiple <italic>B.
oleracea</italic> or <italic>B. rapa</italic> chromosomal segments that matched the same
<italic>A. thaliana</italic> segment (‘A to X’ numbering system
in <italic>A. thaliana</italic><xref ref-type="bibr" rid="b22">22</xref>) into three subgenomes: LF, MF1 and
MF2.</p></sec><sec disp-level="2"><title>OrthoMCL clustering</title><p>To identify and estimate the number of potential orthologous gene families
between <italic>B. oleracea</italic>, <italic>B. rapa</italic>, <italic>A. thaliana</italic>, <italic>C.
papaya</italic>, <italic>P. trichocarpa</italic>, <italic>V. vinifera</italic>, <italic>S. bicolor</italic> and
<italic>O. sativa</italic>, and also between <italic>B. oleracea</italic> and <italic>B. rapa</italic>, we
applied the OrthoMCL pipeline<xref ref-type="bibr" rid="b60">60</xref> using standard settings (blastp
<italic>E</italic> value <1 × 10<sup>−5</sup> and
inflation factor =1.5) to compute the all-against-all similarities.</p></sec><sec disp-level="2"><title>Phylogenetic analysis of gene families</title><p>We performed comparative analysis of trait-related gene families. Genes from
grape, papaya and <italic>Arabidopsis</italic> were downloaded from the GenoScope database
( <ext-link ext-link-type="uri" xlink:href="http://www.genoscope.cns.fr/externe/GenomeBrowser/Vitis/">http://www.genoscope.cns.fr/externe/GenomeBrowser/Vitis/</ext-link>), the
Hawaii Papaya Genome Project ( <ext-link ext-link-type="uri" xlink:href="http://asgpb.mhpcc.hawaii.edu/papaya/">http://asgpb.mhpcc.hawaii.edu/papaya/</ext-link>), and the Arabidopsis
Information Resource ( <ext-link ext-link-type="uri" xlink:href="http://www.arabidopsis.org/">http://www.arabidopsis.org/</ext-link>). Previously reported
<italic>Arabidopsis</italic> and <italic>Brassica</italic> gene sequences were downloaded from
TAIR ( <ext-link ext-link-type="uri" xlink:href="http://www.arabidopsis.org/">http://www.arabidopsis.org/</ext-link>) and BRAD ( <ext-link ext-link-type="uri" xlink:href="http://brassicadb.org/brad/">http://brassicadb.org/brad/</ext-link>).
The protein sequences of the genes were used to determine homologues in grape,
papaya, <italic>Arabidopsis</italic>, <italic>B. oleracea</italic> and <italic>B. rapa</italic> by performing
blast comparisons with an <italic>E</italic>-value 1e–10. The Clustal<xref ref-type="bibr" rid="b61">61</xref> programs were used for multiple sequence alignment. Alignment of
the small family of GI genes was performed using MEGA5<xref ref-type="bibr" rid="b62">62</xref> to
conduct neighbour-joining analysis with default parameters and subjected to
careful manual checks to remove highly divergent sequences from further
analysis. While for other genes, often found in families of tens of genes, the
phylogenetic analysis were performed by PhyML<xref ref-type="bibr" rid="b63">63</xref>, which can
accommodate quite divergent sequences by implementing a maximal likelihood
approach with initial analysis based on neighbour-joining method. During these
analyses, we constructed trees using both CDS and protein sequence, and the
protein-derived tree was used to show the phylogeny if not much incongruity was
found. Bootstrapping was performed using 100 repetitive samplings for each gene
family. All the inferred trees were displayed using MEGA5 (ref. <xref ref-type="bibr" rid="b62">62</xref>). The multiple sequence alignment of these families
was provided as <xref ref-type="supplementary-material" rid="S1">Supplementary Data
3</xref>.</p></sec><sec disp-level="2"><title>Differential expression of duplicated genes across tissues</title><p>RNA-seq reads were mapped to their respective locations on the reference genome
using Tophat<xref ref-type="bibr" rid="b64">64</xref>. Uniquely aligned read counts were calculated for
each gene for each tissue sample. We performed the exact conditional test of two
Poisson rates on read counts of duplicated genes to test the differential
expression of duplicated genes, according to the method applied in soybean<xref ref-type="bibr" rid="b65">65</xref><xref ref-type="bibr" rid="b66">66</xref>. For each duplicated gene pair (for example, genes A and B),
read counts and gene length were denoted as Ea and La for gene A, and Eb and Lb
for gene B, respectively. The read counts of the genes A and B were assumed to
follow the Poisson distributions with rates <italic>λA</italic>=Ra × La
and <italic>λB</italic>=Rb × Lb. Under the null hypothesis of equal
expression of the genes A and B, that is, Ra=Rb, the conditional distribution of
Ea given Ea+Eb=<italic>k</italic> follows a binomial distribution with success probability
<italic>P</italic>=λa/(λa+λb)=La/(La+Lb). The <italic>P</italic>values were computed and further adjusted to maintain the false discovery rate
at 0.05 across gene pairs using the Benjamini–Hochberg method<xref ref-type="bibr" rid="b67">67</xref>.</p></sec><sec disp-level="2"><title>Statistical analysis</title><p>The average number of all retained orthologues in the three subgenomes was used
to estimate the expected retained gene number in each block, and used together
with the observed retained gene number, for the gene retention disparity
statistics using the <italic>χ</italic><sup>2</sup> test. In the GO, IPR
(Interproscan) or KEGG enrichment analyses of WGT or tandem genes, the
<italic>χ</italic><sup>2</sup> test (<italic>N</italic>>5) or the
Fisher’s exact test (<italic>N</italic>≤5) was used to detect
significant differences between the proportion of (WGT or tandem) genes observed
in each child GO, IPR or KEGG categories, and the expected overall proportion of
(WGT or tandem) genes in the whole genome. Correlation of the gene numbers of
WGT-derived paralogous genes with tandem genes in 938 GO terms was tested by
Pearson correlation coefficients (<xref ref-type="supplementary-material" rid="S1">Supplementary Figure 68</xref>). The Benjamini–Hochberg false
discovery rate was performed to adjust the <italic>P</italic> values<xref ref-type="bibr" rid="b67">67</xref>.</p></sec></sec><sec disp-level="1"><title>Author contributions</title><p>I.B., B.C., D.E., Q.H., W.H., G.J.K., S.L., Y.L., J. Ma, A.H.P., J.C.P., I.A.P.P.,
JunW., XiaowuW., XiyinW. and T.-J.Y. are principal investigators (alphabetic order).
B.C., W.H., A.H.P., JunW. and XiaowuW. are equally contributing senior authors.
S.L., J.W., W.H., X.X. and Z.Y. planned and managed the project. S.L., C.T., A.H.P.
and D.E., X.Y. and M.Z. wrote this manuscript and I.B., J. Ma., G.J.K., J.C.P.,
B.C., T.-J.Y., I.A.P.P., XiyinW., XiaowuW., K.L., Y.L., J.B. and A.G.S. made
revision or edits or comments. J.W. (leader), W.H. (co-leader), JunW., L.Y., and
Z.Y. performed DNA sequencing. L.Y. (leader), W.H. (co-leader), S.H., J.W., S.L. and
J.Y. conducted genomic sequence assembly. S.H. (leader), XiyinW. (co-leader), J.Min,
I.B., W.H., J.B., D.E., P.R., S.L., J.S., Y.L. and W.W. conducted scaffold anchoring
to linkage maps and assembly validation. X.Y. (leader), J.Y. (co-leader), S.L.,
Q.Z., S.H. and J. Min performed annotation. C.T. (leader), Wanshun L., W.H., Y.L.,
C.L., W.W., J. Wu, S.L., C.D. and M.Z. performed transcriptome sequencing. S.L.
conceived analysis of comparison and evolution. S.L. (leader), C.T., X.Y.,
ZhangyanW., C.L., S.H., J. Ma, J.Y., M.Z., Zhuo W., Q.Z., S.P., I.A.P.P., A.G.S.,
L.Y., I.B., G.J.K., J.C.P., XiaowuW., B.C., F.C., YinH., WenbinL. and X.Liang
performed analysis of comparative genomics and evolution. J. Ma (leader), M.Z.,
Q.Z., C.T., S.L., B.C., S.H., H.B., C.L. and JianaL. conducted TE analysis. XiyinW.
(leader), J.Y., T.-J.Y., ZhangyanW., L.W., J. Li, T.-H.L., JinpengW., H.J., X.T.,
X.L., M.G. and L.J. conducted gene family analysis. K.L. (leader), J.Y., S.L., C.T.,
H.L., H.G., S.P., D.Z., Z.F., Q.H., Xnfa W., C.Q., D.D., Z.H., Y.H., J.H., D.M.,
J.L., Z. Li, J.Z., L.X., Y.Zhou., Z.L. and Y.Zhang conducted trait-related gene
analysis. A.H.P. (leader), XiyinW., D.J., Y.W. and T.-H.L. conducted gene conversion
analysis. T.-J. Y. (leader), M.Z., P.S., B.-S.P., J.Ma, N.E.W., R.Q., X.L., J.Lee
and H.H.K. conducted centromere analysis. C.T. (leader), S.L., X.Y., S.H., C.L.,
Zhangyan W., Q.Z., J.Y., J.T. and J.B. conducted tandemly duplicated gene analysis.
ZhangyanW. and J.Y. performed data submission.</p></sec><sec disp-level="1"><title>Additional information</title><p><bold>Accession codes:</bold> Genome sequence data for <italic>B. oleracea</italic> have been
deposited in the DDBJ/EMBL/GenBank nucleotide core database under the accession code
AOIX00000000. Transcriptome sequence data for <italic>B. rapa and B. oleracea</italic> have
been deposited in the DDBJ/EMBL/GenBank Sequence Read Archive (SRA) under the
accession codes GSE<ext-link ext-link-type="DDBJ/EMBL/GenBank" xlink:href="43245">43245</ext-link> and GSE<ext-link ext-link-type="DDBJ/EMBL/GenBank" xlink:href="42891">42891</ext-link> respectively.</p><p><bold>How to cite this article:</bold> Liu, S. <italic>et al</italic>. The <italic>Brassica oleracea</italic>genome reveals the asymmetrical evolution of polyploid genomes. <italic>Nat. Commun.</italic>5:3930 doi: 10.1038/ncomms4930 (2014).</p></sec><sec sec-type="supplementary-material" id="S1"><title>Supplementary Material</title><supplementary-material id="d33e19" content-type="local-data"><caption><title>Supplementary Figures, Tables, Methods and References</title><p>Supplementary Figures 1-68, Supplementary Tables 1-49, Supplementary Methods
and Supplementary References</p></caption><media xlink:href="ncomms4930-s1.pdf"></media></supplementary-material><supplementary-material id="d33e25" content-type="local-data"><caption><title>Supplementary Data 1</title><p>The 23,823 <italic>Brassica oleracea-B. rapa</italic> orthologous gene pairs and those
with different exon numbers</p></caption><media xlink:href="ncomms4930-s2.xls"></media></supplementary-material><supplementary-material id="d33e34" content-type="local-data"><caption><title>Supplementary Data 2</title><p>The genes for biosynthesis and breakdown of glucosinolates (GSL) in <italic>B.
rapa</italic> and <italic>B. oleracea</italic>.</p></caption><media xlink:href="ncomms4930-s3.xls"></media></supplementary-material><supplementary-material id="d33e46" content-type="local-data"><caption><title>Supplementary Data 3</title><p>The multiple sequence alignment of gene families corresponding to Figure 5
and Supplementary Figures 46-61.</p></caption><media xlink:href="ncomms4930-s4.xls"></media></supplementary-material></sec></body><back><ack><p>This work was supported by the National Basic Research Program of China
(2011CB109300, 2012CB113906, 2012CB723007 and 2006CB101600), the National Natural
Science Foundation of China (3067134, 30671119 and 31301039), the National High
Technology Research and Development Program (2013AA102602, 2012AA100105 and
2012AA100104), the China Agriculture Research System (CARS-13 and CARS-25-A), the
Core Research Budget of the Non-profit Governmental Research Institution
(1610172010005), the Special Fund for Agro-scientific Research in the Public
Interest (201103016), China–Australia collaboration project
(2010DFA31730), UK Biotechnology and Biological Sciences Research Council
(BB/E017363/1), the Australian Research Council (LP0882095, LP0883462, DP0985953 and
LP110100200), the Next-Generation BioGreen 21 Program (PJ008944 and PJ008202), and
the US National Science Foundation (IOS 0638418, DBI 0849896, MCB 1021718).</p></ack><ref-list><ref id="b1"><mixed-citation publication-type="other">U.S. Department of Agriculture, Agricultural Research Service. <article-title>USDA
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4.0</article-title>. <source>Mol. Biol. Evol.</source><volume>24</volume>, <fpage>1596</fpage>–<lpage>1599</lpage> (<year>2007</year>).<pub-id pub-id-type="pmid">17488738</pub-id></mixed-citation></ref></ref-list></back><floats-group><fig id="f1"><label>Figure 1</label><caption><title>Genomic structure and gene retention rates in syntenic regions of <italic>B.
oleracea</italic> and <italic>B. rapa</italic>.</title><p>(<bold>a</bold>) Segmental colinearity of the genomes of <italic>B. oleracea</italic>, <italic>B.
rapa</italic> and <italic>A. thaliana</italic>. Syntenic blocks are defined and
labelled from A to X (coloured) previously reported in <italic>A.
thaliana</italic><xref ref-type="bibr" rid="b20">20</xref>. (<bold>b</bold>) Time estimate of WGD and
subsequent two <italic>Brassica</italic> species divergence. (<bold>c</bold>) Pattern of
retention/loss of orthologous genes on each set of three subgenomic (LF, MF1
and MF2) blocks of <italic>B. oleracea</italic> and <italic>B. rapa</italic> corresponding to
<italic>A. thaliana</italic> A to X blocks. The <italic>x</italic> axis denotes the physical
position of each <italic>A. thaliana</italic> gene locus. The <italic>y</italic> axis denotes
the proportion of orthologous genes retained in the <italic>B. oleracea</italic> and
<italic>B. rapa</italic> subgenomic blocks around each <italic>A. thaliana</italic> gene,
where 500 genes flanking each side of a certain gene locus were analysed,
giving a total window size of 1,001 genes.</p></caption><graphic xlink:href="ncomms4930-f1"></graphic></fig><fig id="f2"><label>Figure 2</label><caption><title>TE comparison analyses in <italic>B. oleracea</italic> and <italic>B. rapa.</italic></title><p>(<bold>a</bold>) TE copy number and total length in each assembly and <italic>B.
oleracea–B. rapa</italic> syntenic blocks. (<bold>b</bold>) The number
of intact LTR (<italic>Copia</italic>-like and <italic>Gypsy</italic>-like) birthed at different
times (million years ago, MYA) in the syntenic regions of <italic>B. oleracea</italic>and <italic>B. rapa</italic>. (<bold>c</bold>) The comparison of TE distribution and
composition in <italic>B. oleracea–B. rapa</italic> syntenic blocks along
<italic>B. oleracea</italic> chromosomes. We divided <italic>B. oleracea–B.
rapa</italic> syntenic region into non-overlapping sliding 200 kb
windows to compare TE contents. For each window, the ratio
log<sub>10</sub>(<italic>B. oleracea/B. rapa</italic>) was calculated for total
syntenic block length (blue line), LTR length (purple line), gene length
(yellow point), exons length (red point) and intron length (green point). If
<italic>B. oleracea</italic> > <italic>B. rapa</italic> in absolute length of TE
composition in a compared window, the dot or line is above the line
<italic>y</italic>=0. The corresponding <italic>B. rapa</italic> chromosome segments along <italic>B.
oleracea</italic> C08 were indicated by coloured bars. All other <italic>B.
oleracea</italic> chromosomes are showed in <xref ref-type="supplementary-material" rid="S1">Supplementary Fig. 31</xref>. (<bold>d</bold>)
Phylogeny of the Copia-like elements as an example of LTR-RTs of the
syntenic regions in <italic>B. rapa</italic> and <italic>B. oleracea</italic>. The
neighbor-joining (<italic>NJ</italic>) trees were generated based on the conserved RT
domain nucleotide sequences using the Kimura two-parameter method<xref ref-type="bibr" rid="b68">68</xref> in MEGA4 (ref. <xref ref-type="bibr" rid="b69">69</xref>).</p></caption><graphic xlink:href="ncomms4930-f2"></graphic></fig><fig id="f3"><label>Figure 3</label><caption><title>The duplicated genes derived from tandem duplication and whole-genome
duplications in <italic>Brassica</italic> genomes.</title><p>(<bold>a</bold>) A Venn diagram showing shared and specific tandem duplication
events in <italic>A. thaliana</italic>, <italic>B. rapa</italic> and <italic>B. oleracea</italic>.
(<bold>b</bold>,<bold>c</bold>) Distribution of tandem genes and WGT/WGD-derived
paralogues in the KEGG pathway maps in <italic>B. oleracea</italic> (bol), <italic>B.
rapa</italic> (bra) and <italic>A. thaliana</italic> (ath). For each KEGG pathway map,
the proportion of the number of duplicated genes or paralogues to the total
genes was calculated (<italic>x</italic> axis) and the number of maps whose tandem
gene proportion fell in a range was shown on the <italic>y</italic> axis. (<bold>d</bold>)
Oxidative phosphorylation pathway enriched by WGT-derived paralogous genes
in the <italic>Brassica</italic> genomes. The gene copy number for each KO enzyme in
<italic>B. oleracea</italic>, <italic>B. rapa</italic> and <italic>A. thaliana</italic> were shown
(dash-connected) under the KO enzyme number.</p></caption><graphic xlink:href="ncomms4930-f3"></graphic></fig><fig id="f4"><label>Figure 4</label><caption><title>Divergence of <italic>Brassica</italic> paralogous and orthologous genes in <italic>B.
oleracea</italic> and <italic>B. rapa</italic>.</title><p>(<bold>a</bold>) Genome-wide gene conversion in <italic>B. oleracea</italic>. The conversion
in <italic>B. rapa</italic> is showed in <xref ref-type="supplementary-material" rid="S1">Supplementary Fig. 64</xref>. (<bold>b</bold>) The ratio of differentially
expressed duplicated gene pairs derived from different duplications: alpha
whole-genome duplication (α-WGD), <italic>Brassiceae</italic>-lineage WGT,
tandem duplication (TD). Bol, <italic>B. oleracea</italic>; Bra, <italic>B. rapa</italic>. C:
callus; R: root; St: stem; L: leaf; F: flower; Si: silique. The
differentially expressed duplicated gene pairs were defined as fold change
>2 and false discovery rate (FDR) <0.05 or gene pair where
expression was detected for only one gene within gene pairs (FDR
<0.05). (<bold>c</bold>) Box and whisker plots for differentiated
expression for three subgenomes (LF, MF1 and MF2) in flower tissue of <italic>B.
oleracea</italic> and <italic>B. rapa</italic>. For the other tissues, see <xref ref-type="supplementary-material" rid="S1">Supplementary Fig. 67</xref>.
(<bold>d</bold>) The duplicated gene pairs belonging to transcription factors
(TFs) and its related GO terms contain a significantly lower ratio of
differentially expressed duplicated gene pairs than the average at the
genome-wide level in leaf (values given) and other tissues (values not
presented) (<xref ref-type="supplementary-material" rid="S1">Supplementary Table
45</xref>). (<bold>e</bold>) The GO terms (left) in which the duplicated gene
pairs contain a significantly higher ratio of differentially expressed
duplicated gene pairs than the average ratio at the genome-wide level in
leaf and other tissues (<xref ref-type="supplementary-material" rid="S1">Supplementary
Table 46</xref>). Values from one tissue were presented and the other
tissues were indicated with abbreviated letters to the right if expression
in these tissues is significantly higher. (<bold>f</bold>) Expression variation
caused by divergence (either different variants or differential expression
of the same variants) of alternative splicing (AS) variants in WGT
paralogous gene pairs with identical numbers of exons and in
Bol–Bra orthologous gene pairs. IRES denotes types of intron
retention and exon skipping.</p></caption><graphic xlink:href="ncomms4930-f4"></graphic></fig><fig id="f5"><label>Figure 5</label><caption><title>Whole-genome-wide comparison of genes involved in glucosinolate metabolism
pathways in <italic>B. oleracea</italic> and its relatives.</title><p>(<bold>a</bold>) Aliphatic and indolic GSL biosynthesis and catabolism pathways in
<italic>A. thaliana</italic>, <italic>B. oleracea</italic> and <italic>B. rapa</italic>. The copy
number of GSL biosynthetic genes in <italic>A. thaliana</italic>, <italic>B. rapa</italic> and
<italic>B. oleracea</italic> are listed in square brackets, respectively.
Potential anticancer substances/precursors are highlighted in blue bold. Two
important amino acid chain elongation and side-chain modification loci
<italic>MAMs</italic> and <italic>AOP2</italic> are highlighted in red bold, within the
number in the green bracket representing the number of non-functional genes.
(<bold>b</bold>,<bold>c</bold>) The neighbour-joining (NJ) trees of MAM and AOP
genes were generated based on the aligned coding sequences and 100 bootstrap
repeats. The silenced genes are indicated by red hollow circle, expressed
functional genes are represented by red solid disc and green rectangle. In
<italic>A. thaliana</italic> ecotype Columbia there are just MAM1 and MAM3. (<bold>d</bold>) Three <italic>B.
oleracea AOP2</italic> loci among which are one functional <italic>AOP2</italic> and
two mutated <italic>AOP2</italic>. 1MOI3M: 1-methoxyindol-3-ylmethyl GSL; 1OHI3M:
1-hydroxyindol-3-ylmethyl GSL; 3MSOP: 3-methylsulfinylpropyl GSL; 3MTP: 3-methylthiopropyl GSL;
3PREY: 2-Propenyl GSL; 4BTEY: 3-butenyl GSL; 4MOI3M: 4-methoxyindol-3-ylmethyl GSL;
4OHB, 4-hydroxybutyl GSL; 4OHI3M: 4-hydroxyindol-3-ylmethyl GSL;
4MSOB: 4-methylsulfinylbutyl GSL;
4MTB, 4-methylthiobutyl GSL; AITC: allyl isothiocyanate; I3C: indole-3-carbinol; I3M: indolyl-3-methyl GSL; DIM: 3,3′-diindolymethane;
MAM: methylthioalkylmalate; AOP: 2-oxoglutarate-dependent dioxygenase.</p></caption><graphic xlink:href="ncomms4930-f5"></graphic></fig><table-wrap position="float" id="t1"><label>Table 1</label><caption><title>Summary of genome assembly and annotation of <italic>B. oleracea</italic>.</title></caption><table frame="hsides" rules="groups" border="1"><colgroup><col align="left"></col><col align="center"></col><col align="center"></col><col align="center"></col><col align="center"></col></colgroup><thead valign="bottom"><tr><th colspan="5" align="left" valign="top" charoff="50"><italic><bold>B. oleracea</bold></italic><bold>genome assembly</bold></th></tr></thead><tbody valign="top"><tr><td align="left" valign="top" charoff="50"> <hr></hr></td><td align="center" valign="top" charoff="50"><bold>N90</bold><hr></hr></td><td align="center" valign="top" charoff="50"><bold>N50</bold><hr></hr></td><td align="center" valign="top" charoff="50"><bold>Longest</bold><hr></hr></td><td align="center" valign="top" charoff="50"><bold>Total size</bold><hr></hr></td></tr><tr><td align="left" valign="top" charoff="50">Contig size (bp)</td><td align="center" valign="top" charoff="50">3,527</td><td align="center" valign="top" charoff="50">26,828</td><td align="center" valign="top" charoff="50">199,461</td><td align="center" valign="top" charoff="50">502,114,421</td></tr><tr><td align="left" valign="top" charoff="50">Contig number</td><td align="center" valign="top" charoff="50">22,669</td><td align="center" valign="top" charoff="50">5,425</td><td align="center" valign="top" charoff="50"> </td><td align="center" valign="top" charoff="50"> </td></tr><tr><td align="left" valign="top" charoff="50"> </td><td colspan="4" align="center" valign="top" charoff="50">Total number(>2 kb):
27,351</td></tr><tr><td align="left" valign="top" charoff="50">Scaffold size (bp)</td><td align="center" valign="top" charoff="50">258,906</td><td align="center" valign="top" charoff="50">1,457,055</td><td align="center" valign="top" charoff="50">8,788,225</td><td align="center" valign="top" charoff="50">539,907,250</td></tr><tr><td align="left" valign="top" charoff="50">Scaffold number</td><td align="center" valign="top" charoff="50">388</td><td align="center" valign="top" charoff="50">224</td><td align="center" valign="top" charoff="50">Anchored to chr. 72%</td><td align="center" valign="top" charoff="50"> </td></tr><tr><td align="left" valign="top" charoff="50"> </td><td colspan="4" align="center" valign="top" charoff="50">Total number(>2 kb):
1,809</td></tr></tbody></table><table frame="hsides" rules="groups" border="1"><colgroup><col align="left"></col><col align="center"></col><col align="center"></col><col align="char" char="."></col><col align="char" char="."></col></colgroup><thead valign="bottom"><tr><th colspan="5" align="left" valign="top" charoff="50"><italic><bold>B. oleracea</bold></italic><bold>genome annotation</bold><hr></hr></th></tr><tr><th align="left" valign="top" charoff="50"> </th><th colspan="4" align="center" valign="top" charoff="50"><italic><bold>B. oleracea</bold></italic><hr></hr></th></tr><tr><th align="left" valign="top" charoff="50"> </th><th colspan="3" align="center" valign="top" charoff="50"><bold>In the assembly</bold><hr></hr></th><th align="center" valign="top" char="." charoff="50"><bold>In WG short reads</bold><xref ref-type="fn" rid="t1-fn1">*</xref></th></tr><tr><th align="left" valign="top" charoff="50"> </th><th align="center" valign="top" charoff="50"><bold>Size (bp)</bold></th><th align="center" valign="top" charoff="50"><bold>Copy number<xref ref-type="fn" rid="t1-fn2">†</xref></bold></th><th align="center" valign="top" char="." charoff="50"><bold>% assembly</bold><xref ref-type="fn" rid="t1-fn3">‡
</xref></th><th align="char" valign="top" char="." charoff="50"> </th></tr></thead><tbody valign="top"><tr><td align="left" valign="top" charoff="50">Retrotransposon</td><td align="center" valign="top" charoff="50">105,755,173</td><td align="center" valign="top" charoff="50">108,948</td><td align="char" valign="top" char="." charoff="50">22.13</td><td align="char" valign="top" char="." charoff="50">23.60</td></tr><tr><td align="left" valign="top" charoff="50">DNA transposon</td><td align="center" valign="top" charoff="50">79,675,583</td><td align="center" valign="top" charoff="50">170,500</td><td align="char" valign="top" char="." charoff="50">16.67</td><td align="char" valign="top" char="." charoff="50">12.71</td></tr><tr><td align="left" valign="top" charoff="50">Total<hr></hr></td><td align="center" valign="top" charoff="50">185,430,756<hr></hr></td><td align="center" valign="top" charoff="50">279,448<hr></hr></td><td align="char" valign="top" char="." charoff="50">38.80<hr></hr></td><td align="char" valign="top" char="." charoff="50">36.31<hr></hr></td></tr><tr><td align="left" valign="top" charoff="50"> <hr></hr></td><td align="center" valign="top" charoff="50"><bold>Gene models</bold><hr></hr></td><td align="center" valign="top" charoff="50"><bold>Gene space covered<xref ref-type="fn" rid="t1-fn4">§</xref></bold><hr></hr></td><td align="center" valign="top" char="." charoff="50"><bold>Annotated</bold><hr></hr></td><td align="center" valign="top" char="." charoff="50"><bold>Supported by ESTs</bold><hr></hr></td></tr><tr><td align="left" valign="top" charoff="50">Protein-coding genes<hr></hr></td><td align="center" valign="top" charoff="50">45,758<hr></hr></td><td align="center" valign="top" charoff="50">98%<hr></hr></td><td align="center" valign="top" char="." charoff="50">91.6%<hr></hr></td><td align="center" valign="top" char="." charoff="50">99.0%<hr></hr></td></tr><tr><td align="left" valign="top" charoff="50"> <hr></hr></td><td align="center" valign="top" charoff="50"><bold>Average transcript length</bold><hr></hr></td><td align="center" valign="top" charoff="50"><bold>Average coding length</bold><hr></hr></td><td align="center" valign="top" char="." charoff="50"><bold>No. of average exons</bold><hr></hr></td><td align="center" valign="top" char="." charoff="50"><bold>No. of alternative splicing variants</bold><hr></hr></td></tr><tr><td align="left" valign="top" charoff="50"> <hr></hr></td><td align="center" valign="top" charoff="50">1,762 bp<hr></hr></td><td align="center" valign="top" charoff="50">1,037 bp<hr></hr></td><td align="center" valign="top" char="." charoff="50">4.6<hr></hr></td><td align="center" valign="top" char="." charoff="50">30,932<hr></hr></td></tr><tr><td align="left" valign="top" charoff="50"><bold>Non-coding RNA</bold><hr></hr></td><td align="center" valign="top" charoff="50"><bold>miRNA</bold><hr></hr></td><td align="center" valign="top" charoff="50"><bold>tRNA</bold><hr></hr></td><td align="center" valign="top" char="." charoff="50"><bold>rRNA</bold><hr></hr></td><td align="center" valign="top" char="." charoff="50"><bold>snRNA</bold><hr></hr></td></tr><tr><td align="left" valign="top" charoff="50">Copy number</td><td align="center" valign="top" charoff="50">336</td><td align="center" valign="top" charoff="50">1,425</td><td align="center" valign="top" char="." charoff="50">553</td><td align="center" valign="top" char="." charoff="50">1,442</td></tr><tr><td align="left" valign="top" charoff="50">Average length (bp)</td><td align="center" valign="top" charoff="50">119</td><td align="center" valign="top" charoff="50">75</td><td align="center" valign="top" char="." charoff="50">166</td><td align="center" valign="top" char="." charoff="50">110</td></tr></tbody></table><table-wrap-foot><fn id="t1-fn1"><p><sup>*</sup>WG, whole genome, 20 × coverage
reads were randomly sampled from all the genomic short reads
libraries.</p></fn><fn id="t1-fn2"><p><sup>†</sup>The copy number of TEs was from
the RepeatMasker results.</p></fn><fn id="t1-fn3"><p><sup>‡</sup>The ungapped regions were used to
detect the percentage of TEs in the assembly. TE sizes are
from the ungapped regions of B. oleracea 477,847,347 bp.</p></fn><fn id="t1-fn4"><p><sup>§</sup>Estimated by public <italic>Brassica</italic>ESTs and RNA-seq data.</p></fn></table-wrap-foot></table-wrap></floats-group></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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