1. The genome of the mesopolyploid crop species Brassica rapa
- Author
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Binghang Liu, Wei Hua, Zhenyu Li, Chunfang Peng, Jeong-Sun Kim, J. Chris Pires, Beom-Seok Park, Shengyi Liu, Shu Zhang, Ye Yin, Chaobo Tong, Tae-Ho Lee, Yang Qiu, Di Shen, Sanwen Huang, Qingle Cai, Jin A Kim, Shunmou Huang, Lu Fang, Graham J.W. King, Nizar Drou, Bo Li, Gavin C. Conant, Bernd Weisshaar, Jiaohui Xu, Jun Wang, Zhiyong Xiong, Fei Li, Chi Song, Zhonghua Zhang, Matthew G. Links, Rifei Sun, Jinpeng Wang, Fiona Fraser, Chuyu Lin, Yongcui Liao, Chushin Koh, Wei Fan, Su-Ryun Choi, Shusei Sato, Shifeng Cheng, Xiang Zhao, Jeong-Hwan Mun, Hideki Hirakawa, Harry Belcram, Zhiwen Wang, Martin Trick, Alice Hayward, Xixiang Li, Shujiang Zhang, Desheng Mu, Satoshi Tabata, Silong Sun, Isobel A. P. Parkin, Bo Liu, Xu Tan, Nirala Ramchiary, Guusje Bonnema, Yinqi Bai, Yoshihiro Narusaka, Yongchen Du, Hui Wang, Julie Poulain, Xun Xu, Yupeng Wang, Yan Wang, Haibao Tang, Zhenyi Wang, Meixia Zhao, David Edwards, Jinling Meng, Chris Duran, Andrew H. Paterson, Soo-Jin Kwon, Hanzhong Wang, Feng Cheng, Heling Zhou, Geng Chunyu, Jacqueline Batley, Bo Wang, Yingrui Li, Junyi Wang, Gilles Lassalle, Boulos Chalhoub, Jianwen Li, Yong Pyo Lim, Quanfei Huang, Eleni Soumpourou, Jian Wu, Katsunori Hatakeyama, Xiaowu Wang, Paul J. Berkman, Ian Bancroft, Jérémy Just, Jingyin Yu, Hui Guo, Kui Wu, Li Wang, Ruiqiang Li, Xiyin Wang, Huizhe Jin, Haiping Wang, Andrew G. Sharpe, Michael Freeling, Hiroshi Abe, Mina Jin, Jie Deng, Jiumeng Min, Jingping Li, Institute of Vegetables and Flowers (IVF), Chinese Academy of Agricultural Sciences (CAAS), Zhejiang University, Oil Crops Research Institute, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture-Chinese Academy of Agricultural Sciences (CAAS), Department of Plant Pathology, University of Kentucky (UK), Rural Development Administration, Department of Biology, University of York [York, UK], Hasso Plattner Institute (HPI), University of Potsdam = Universität Potsdam, Institute of Vegetable sand Flowers, Key Laboratory for Ultrafine Materials, East China University of Science and Technology, Beijing Genom Inst Shenzhen, University of Georgia [USA], School of Life Sciences, Center of Genomics and Computational Biology, Hebei United University, University of California [Berkeley] (UC Berkeley), University of California (UC), The Hospital for sick children [Toronto] (SickKids), University of Toronto, Unité de recherche en génomique végétale (URGV), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), State Key Laboratory for Mineral Deposits Research, Nanjing University (NJU), Amélioration des Plantes et Biotechnologies Végétales (APBV), and Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST
- Subjects
Genome evolution ,Chromosomes, Artificial, Bacterial ,lineages ,diversification ,[SDV]Life Sciences [q-bio] ,Molecular Sequence Data ,Arabidopsis ,Biology ,Genes, Plant ,Genome ,Chromosomes, Plant ,Evolution, Molecular ,Polyploidy ,Contig Mapping ,Laboratorium voor Plantenveredeling ,Gene density ,Gene Duplication ,Brassica rapa ,evolution ,genetics ,Gene ,Phylogeny ,Genetics ,Whole genome sequencing ,repressor ,EPS-3 ,fungi ,duplicated genes ,food and beverages ,Molecular Sequence Annotation ,alignment ,Genome project ,Sequence Analysis, DNA ,sequence ,Plant Breeding ,Paleopolyploidy ,plant arabidopsis-thaliana ,Genome, Plant ,triplication - Abstract
The Brassicaceae family which includes Arabidopsis thaliana, is a natural priority for reaching beyond botanical models to more deeply sample angiosperm genomic and functional diversity. Here we report the draft genome sequence and its annoation of Brassica rapa, one of the two ancestral species of oilseed rape. We modeled 41,174 protein-coding genes in the B. rapa genome. B. rapa has experienced only the second genome triplication reported to date, with its close relationship to A. thaliana providing a useful outgroup for investigating many consequences of triplication for its structural and functional evolution. The extent of gene loss (fractionation) among triplicated genome segments varies, with one copy containing a greater proportion of genes expected to have been present in its ancestor (70 percent) than the remaining two (46 percent and 36 percent). Both a generally rapid evolutionary rate, and specific copy number amplifications of particular gene families, may contribute to the remarkable propensity of Brassica species for the development of new morphological variants. The B. rapa genome provides a new resource for comparative and evolutionary analysis of the Brassicaceae genomes and also a platform for genetic improvement of Brassica oil and vegetable crops.
- Published
- 2011
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