The genome of the mesopolyploid crop species Brassica rapa

Nature Genetics - Tập 43 Số 10 - Trang 1035-1039 - 2011
Xiaowu Wang1, Hanzhong Wang2, Jun Wang3, Rifei Sun1, Jian Wu1, Shengyi Liu2, Yinqi Bai3, Jeong‐Hwan Mun4, Ian Bancroft5, Feng Cheng1, Sanwen Huang1, Xixiang Li1, Wei Hua2, Junyi Wang3, Xiyin Wang6, Michael Freeling7, J. Chris Pires8, Andrew H. Paterson9, Boulos Chalhoub10, Bo Wang3, Alice Hayward11, Andrew Sharpe12, Beom‐Seok Park4, Bernd Weißhaar13, Binghang Liu3, Bo Li3, Bo Liu1, Chaobo Tong2, Chi Song3, Christopher Duran11, Chunfang Peng3, Chunyu Geng3, ChuShin Koh12, Chuyu Lin3, David Edwards11, Desheng Mu3, Di Shen1, Eleni Soumpourou5, Fei Li1, F C Fraser5, Gavin C. Conant14, Gilles Lassalle15, Graham J.W. King16, Guusje Bonnema17, Haibao Tang7, Haiping Wang1, Harry Belcram10, Heling Zhou3, Hideki Hirakawa18, Hiroshi Abe19, Hui Guo9, Hui Wang1, Huizhe Jin9, Isobel A. P. Parkin20, Jacqueline Batley11, Jeong‐Sun Kim4, Jérémy Just10, Jianwen Li3, Jiaohui Xü3, Jie Deng1, Jin A Kim4, Jingping Li9, Jingyin Yu2, Jinling Meng21, Jinpeng Wang6, Jiumeng Min3, Julie Poulain22, Katsunori Hatakeyama23, Kui Wu3, Li Wang24, Fang Lü1, Martin Trick5, Matthew G. Links20, Meixia Zhao2, Mina Jin4, Nirala Ramchiary25, Nizar Drou5, Paul J. Berkman11, Qingle Cai3, Quanfei Huang3, Ruiqiang Li3, Satoshi Tabata18, Shifeng Cheng3, Shu Zhang3, Shujiang Zhang1, Shunmou Huang2, Shusei Sato18, Silong Sun1, Soo-Jin Kwon4, Su-Ryun Choi25, Tae‐Ho Lee9, Wei Fan3, Xiang Zhao3, Xu Tan9, Xun Xu3, Yan Wang1, Yang Qiu1, Ye Yin3, Yingrui Li3, Yongchen Du1, Yongcui Liao1, Yong-Pyo Lim25, Yoshihiro Narusaka26, Yupeng Wang27, Zhenyi Wang27, Zhenyu Li3, Zhiwen Wang3, Zhiyong Xiong8, Zhonghua Zhang1
1Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences (IVF, CAAS), Beijing, China
2Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
3BGI-Shenzhen, Shenzhen, China
4Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, Suwon, Korea
5John Innes Centre. Norwich Research Park, Colney, Norwich, UK
6Center for Genomics and Computational Biology, School of Life Sciences, Hebei United University, Tangshan, Hebei, China
7Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
8Division of Biological Sciences, Bond Life Sciences Center, University of Missouri, Columbia, Missouri, USA
9Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia, USA
10Organization and Evolution of Plant Genomes, Unité de Recherche en Génomique Végétale, Unité Mixte de Recherché 1165, (Inland Northwest Research Alliance-Centre National de la Recherche Scientifique, Université Evry Val d'Essonne), Evry, France
11University of Queensland, School of Agriculture and Food Sciences, Brisbane, Queensland, Australia
12National Research Council-Plant Biotechnology Institute, Saskatoon, Saskatchewan, Canada
13Center for Biotechnology, Bielefeld University, Bielefeld, Germany
14Division of Animal Sciences, University of Missouri, Columbia, Missouri, USA
15Inland Northwest Research Alliance-Agrocampus Rennes–University of Rennes 1, Unité Mixte de Recherché 118 Amélioration des Plantes et Biotechnologies Végétales, Le Rheu Cedex, France
16Centre for Crop Genetic Improvement, Rothamsted Research, West Common, Harpenden, UK
17Droevendaalsesteeg 1, Wageningen University, Wageningen, The Netherlands
18Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, Japan
19Experimental Plant Division, RIKEN BioResource Center, Tsukuba, Japan
20Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
21National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
22Genoscope, Institut de Génomique du Commissariat à l'Energie Atomique, 2 rue Gaston Crémieux, Evry, France
23National Institute of Vegetable and Tea Science, Tsu, Japan
24School of Sciences, Hebei United University, Tangshan, Hebei
25Department of Horticulture, Molecular Genetics and Genomics Lab, Chungnam National University, Daejeon, Republic of Korea
26Research Institute for Biological Sciences, Okayama, Japan
27China

Tóm tắt

Từ khóa


Tài liệu tham khảo

Tang, H. et al. Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps. Genome Res. 18, 1944–1954 (2008).

Johnston, J.S. et al. Evolution of genome size in Brassicaceae. Ann. Bot. 95, 229–235 (2005).

Koch, M.A. & Kiefer, M. Genome evolution among cruciferous plants: a lecture from the comparison of the genetic maps of three diploid species—Capsella rubella, Arabidopsis lyrata subsp Petraea, and A. thaliana. Am. J. Bot. 92, 761–767 (2005).

Yogeeswaran, K. et al. Comparative genome analyses of Arabidopsis spp.: inferring chromosomal rearrangement events in the evolutionary history of A. thaliana. Genome Res. 15, 505–515 (2005).

Bowers, J.E., Chapman, B.A., Rong, J. & Paterson, A.H. Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 422, 433–438 (2003).

Yang, Y.W., Lai, K.N., Tai, P.Y. & Li, W.H. Rates of nucleotide substitution in angiosperm mitochondrial DNA sequences and dates of divergence between Brassica and other angiosperm lineages. J. Mol. Evol. 48, 597–604 (1999).

Town, C.D. et al. Comparative genomics of Brassica oleracea and Arabidopsis thaliana reveal gene loss, fragmentation, and dispersal after polyploidy. Plant Cell 18, 1348–1359 (2006).

Lysak, M.A., Koch, M.A., Pecinka, A. & Schubert, I. Chromosome triplication found across the tribe Brassiceae. Genome Res. 15, 516–525 (2005).

Labana, K.S. & Gupta, M.L. Importance and origin. in Breeding Oilseed Brassicas (eds. Labana, K.S., Banga, S.S. & Banga, S.K.) 1–20 (Springer-Verlag, Berlin, Germany, 1993).

Nagaharu, U. Genome analysis in Brassica with special reference to the experimental formation of B. napus and peculiar mode of fertilization. Jap. J. Bot. 7, 389–452 (1935).

O'Neill, C.M. & Bancroft, I. Comparative physical mapping of segments of the genome of Brassica oleracea var. alboglabra that are homoeologous to sequenced regions of chromosomes 4 and 5 of Arabidopsis thaliana. Plant J. 23, 233–243 (2000).

Park, J.Y. et al. Physical mapping and microsynteny of Brassica rapa ssp. pekinensis genome corresponding to a 222 kbp gene-rich region of Arabidopsis chromosome 4 and partially duplicated on chromosome 5. Mol. Genet. Genomics 274, 579–588 (2005).

Beilstein, M.A., Nagalingum, N.S., Clements, M.D., Manchester, S.R. & Mathews, S. Dated molecular phylogenies indicate a Miocene origin for Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA 107, 18724–18728 (2010).

Mun, J.H. et al. Genome-wide comparative analysis of the Brassica rapa gene space reveals genome shrinkage and differential loss of duplicated genes after whole genome triplication. Genome Biol. 10, R111 (2009).

Mun, J.H. et al. Sequence and structure of Brassica rapa chromosome A3. Genome Biol. 11, R94 (2010).

Arabidopsis Genome Initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796–815 (2000).

Ming, R. et al. The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature 452, 991–996 (2008).

Jaillon, O. et al. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449, 463–467 (2007).

Sankoff, D., Zheng, C. & Zhu, Q. The collapse of gene complement following whole genome duplication. BMC Genomics 11, 313 (2010).

Messing, J. et al. Sequence composition and genome organization of maize. Proc. Natl. Acad. Sci. USA 101, 14349–14354 (2004).

Schnable, J.C., Springer, N.M. & Freeling, M. Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss. Proc. Natl. Acad. Sci. USA 108, 4069–4074 (2011).

Thomas, B.C., Pedersen, B. & Freeling, M. Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes. Genome Res. 16, 934–946 (2006).

Woodhouse, M.R. et al. Following tetraploidy in maize, a short deletion mechanism removed genes preferentially from one of the two homologs. PLoS Biol. 8, e1000409 (2010).

Wang, X., Tang, H., Bowers, J.E. & Paterson, A.H. Comparative inference of illegitimate recombination between rice and sorghum duplicated genes produced by polyploidization. Genome Res. 19, 1026–1032 (2009).

Wang, X.Y., Tang, H.B. & Paterson, A.H. Seventy million years of concerted evolution of a homoeologous chromosome pair, in parallel, in major poaceae lineages. Plant Cell 23, 27–37 (2011).

Birchler, J.A. & Veitia, R.A. The gene balance hypothesis: from classical genetics to modern genomics. Plant Cell 19, 395–402 (2007).

Ha, M., Kim, E.D. & Chen, Z.J. Duplicate genes increase expression diversity in closely related species and allopolyploids. Proc. Natl. Acad. Sci. USA 106, 2295–2300 (2009).

Paterson, A.H., Lan, T.H., Amasino, R., Osborn, T.C. & Quiros, C. Brassica genomics: a complement to, and early beneficiary of, the Arabidopsis sequence. Genome Biol. 2, R1011 (2001).

Teale, W.D., Paponov, I.A. & Palme, K. Auxin in action: signalling, transport and the control of plant growth and development. Nat. Rev. Mol. Cell Biol. 7, 847–859 (2006).

Theologis, A. et al. Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana. Nature 408, 816–820 (2000).

Vanneste, S. & Friml, J. Auxin: a trigger for change in plant development. Cell 136, 1005–1016 (2009).

Reeves, P.A. & Olmstead, R.G. Evolution of the TCP gene family in Asteridae: cladistic and network approaches to understanding regulatory gene family diversification and its impact on morphological evolution. Mol. Biol. Evol. 20, 1997–2009 (2003).

Michaels, S.D. & Amasino, R.M. FLOWERING LOCUS C encodes a novel MADS domain protein that acts as a repressor of flowering. Plant Cell 11, 949–956 (1999).

Levy, Y.Y., Mesnage, S., Mylne, J.S., Gendall, A.R. & Dean, C. Multiple roles of Arabidopsis VRN1 in vernalization and flowering time control. Science 297, 243–246 (2002).

Günl, M., Liew, E.F., David, K. & Putterill, J. Analysis of a post-translational steroid induction system for GIGANTEA in Arabidopsis. BMC Plant Biol. 9, 141 (2009).

Li, D. et al. A repressor complex governs the integration of flowering signals in Arabidopsis. Dev. Cell 15, 110–120 (2008).

Ledger, S., Strayer, C., Ashton, F., Kay, S.A. & Putterill, J. Analysis of the function of two circadian-regulated CONSTANS-LIKE genes. Plant J. 26, 15–22 (2001).

Paterson, A.H. et al. The Sorghum bicolor genome and the diversification of grasses. Nature 457, 551–556 (2009).

Li, R. et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 20, 265–272 (2010).

Li, R. et al. The sequence and de novo assembly of the giant panda genome. Nature 463, 311–317 (2010).

Delcher, A.L., Phillippy, A., Carlton, J. & Salzberg, S.L. Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Res. 30, 2478–2483 (2002).

Parkin, I.A. et al. Segmental structure of the Brassica napus genome based on comparative analysis with Arabidopsis thaliana. Genetics 171, 765–781 (2005).

Birney, E., Clamp, M. & Durbin, R. GeneWise and Genomewise. Genome Res. 14, 988–995 (2004).

Haas, B.J. et al. Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res. 31, 5654–5666 (2003).

Elsik, C.G. et al. Creating a honey bee consensus gene set. Genome Biol. 8, R13 (2007).

Li, L., Stoeckert, C.J. & Roos, D.S. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 13, 2178–2189 (2003).

Tamura, K., Dudley, J., Nei, M. & Kumar, S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24, 1596–1599 (2007).

Thông tin
Thông tin xuất bản

Nature Genetics

Tập 43 Số 10

1035-1039

Thông tin tác giả