The Medicago genome provides insight into the evolution of rhizobial symbioses

Nature - Tập 480 Số 7378 - Trang 520-524 - 2011
Nevin D. Young1, Jean‐Jacques Bono2, Giles Oldroyd3, René Geurts4, Steven B. Cannon5, Michael K. Udvardi6, Vagner A. Benedito7, Klaus Mayer8, Jérôme Gouzy2, Heiko Schoof9, Yves Van de Peer10, Sebastian Proost10, Douglas R. Cook11, Blake C. Meyers12, M. Spannagl8, Foo Cheung13, Stéphane De Mita4, Vivek Krishnakumar13, Heidrun Gundlach8, Shiguo Zhou14, Joann Mudge15, Arvind K. Bharti15, Jeremy D. Murray3, Marina Naoumkina6, Benjamin D. Rosen11, Kevin A.T. Silverstein16, Haibao Tang13, Stéphane Rombauts10, Patrick X. Zhao6, Peng Zhou1, Valérie Barbe17, Philippe Bardou18, Michael Bechner14, Arnaud Bellec19, Anne Berger17, Hélène Berges19, Shelby Bidwell13, Ton Bisseling4, Nathalie Choisne17, Arnaud Couloux17, Roxanne Denny1, Shweta Deshpande20, Xinbin Dai6, Jeff J. Doyle21, Anne-Marie Dudez18, Andrew Farmer15, Stéphanie Fouteau17, Carolien Franken4, Chrystel Gibelin18, John Gish11, Steven Goldstein14, Álvaro González22, Pamela J. Green12, Asis Hallab23, Marijke Hartog4, Axin Hua20, Sean Humphray24, Dong Hoon Jeong12, Yi Jing20, Anika Jöcker23, Steve Kenton20, Dong-Jin Kim11, Kathrin Klee23, Hongshing Lai20, Chunting Lang4, Shaoping Lin20, Simone L. Cree20, Anton Lavrinienko17, Lucy Matthews24, Jamison McCorrison13, Erin L. Monaghan13, Jeong-Hwan Mun11, Fares Z. Najar20, Christine Nicholson24, Céline Noirot25, Majesta O’Bleness20, C R Paule1, Julie Poulain17, Florent Prion18, Baifang Qin20, Chunmei Qu20, Ernest F. Retzel15, Claire Riddle24, Erika Sallet18, Sylvie Samain17, Nicolas Samson18, Iryna Sanders20, Olivier Saurat18, Claude Scarpelli17, Béatrice Ségurens17, Andrew Severin26, D. Janine Sherrier12, Ruihua Shi20, Sarah Sims24, Susan R. Singer27, Senjuti Sinharoy6, Lieven Sterck10, Agnès Viollet17, Bing Bing Wang1, Keqin Wang20, Mingyi Wang6, Xiaohong Wang1, Jens Warfsmann23, Jean Weissenbach17, Doug D. White20, Jim White20, Graham B. Wiley20, Patrick Wincker17, Yanbo Xing20, Limei Yang20, Ziyun Yao20, Ying Fu20, Jixian Zhai12, Liping Zhou20, Antoine Zuber18, Jean Denarié18, Richard A. Dixon6, Gregory D. May15, David C. Schwartz14, Jane Rogers28, Françis Quétier17, Christopher D. Town13, Bruce A. Roe20
1Departments of Plant Pathology and Plant Biology, University of Minnesota, St Paul, 55108, Minnesota, USA
2INRA, Laboratoire des Intéractions Plantes-Microorganismes (LIPM), UMR441, BP 52627, F-31326 Castanet-Tolosan CEDEX, France,
3Department of Disease and Stress Biology, John Innes Centre, NR4 7UH, Norwich, UK
4Department of Plant Science, Laboratory of Molecular Biology, Wageningen University, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands,
5USDA-ARS Corn Insects and Crop Genetics Research Unit, Ames, 50011, Iowa, USA
6Plant Biology Division, Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, Oklahoma 73401, USA
7Department of Genetics and Developmental Biology, Plant and Soil Science Division, West Virginia University, Morgantown, 26506, West Virginia, USA
8MIPS/Institute for Bioinformatics and Systems Biology, Helmholtz Center Munich, Ingolstädter Landstrasse 1, Neuherberg, Germany,
9University of Bonn, INRES Crop Bioinformatics, Katzenburgweg 2, 53115 Bonn, Germany,
10Department of Plant Systems Biology, VIB, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium,
11Department of Plant Pathology, University of California, Davis, 95616, California, USA
12Department of Plant & Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, 19711, Delaware, USA
13J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, 20850, Maryland, USA
14Laboratory for Molecular and Computational Genomics, University of Wisconsin-Madison, Wisconsin, 53706, USA
15National Center for Genome Resources, 2935 Rodeo Park Drive East, Santa Fe, 87505, New Mexico, USA
16Masonic Cancer Center, Biostatistics and Bioinformatics Group, University of Minnesota, Minneapolis, 55455, Minnesota, USA
17GENOSCOPE, Centre National de Séquençage, 2 rue Gaston Crémieux, CP 5706, 91057 Evry Cedex, France
18CNRS, Laboratoire des Intéractions Plantes-Microorganismes (LIPM), UMR2594, BP 52627, F-31326 Castanet-Tolosan CEDEX, France,
19INRA, Centre National de Ressources Génomiques Végétales (CNRGV), BP 52627, F-31326 Castanet-Tolosan CEDEX, France,
20Department of Chemistry and Biochemistry, Advanced Center for Genome Technology, Stephenson Research and Technology Center, University of Oklahoma, Norman, 73019, Oklahoma, USA
21Department of Plant Biology, Cornell University, Ithaca, New York 14853, USA
22Department of Computer & Information Sciences, and Delaware Biotechnology Institute, University of Delaware, Newark, 19711, Delaware, USA
23Max Planck Institute for Plant Breeding Research, Plant Computational Biology, Carl von Linné Weg 10, 50829 Köln, Germany,
24Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK,
25INRA, Unité de Biométrie et d'Intelligence Artificielle (UBIA), UR875, BP 52627, F-31326 Castanet-Tolosan CEDEX, France,
26Department of Agronomy, Iowa State University Ames, 50011, Iowa, USA
27Department of Biology, Carleton College, Northfield, 55057, Minnesota, USA
28The Genome Analysis Centre, Norwich Research Park, Norwich, NR4 7UH, Norfolk, UK

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Tài liệu tham khảo

Wang, H. et al. Rosid radiation and the rapid rise of angiosperm-dominated forests. Proc. Natl Acad. Sci. USA 106, 3853–3858 (2009)

Lavin, M., Herendeen, P. S. & Wojciechowski, M. F. Evolutionary rates analysis of Leguminosae implicates a rapid diversification of lineages during the tertiary. Syst. Biol. 54, 575–594 (2005)

Kulikova, O. et al. Integration of the FISH pachytene and genetic maps of Medicago truncatula. Plant J. 27, 49–58 (2001)

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

International Rice Genome Sequencing Project. The map-based sequence of the rice genome. Nature 436, 793–800 (2005)

Tuskan, G. A. et al. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313, 1596–1604 (2006)

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

Pfeil, B. E., Schlueter, J. A., Shoemaker, R. C. & Doyle, J. J. Placing paleopolyploidy in relation to taxon divergence: a phylogenetic analysis in legumes using 39 gene families. Syst. Biol. 54, 441–454 (2005)

Cannon, S. B. et al. Polyploidy did not predate the evolution of nodulation in all legumes. PLoS ONE 5, e11630 (2010)

Schmutz, J. et al. Genome sequence of the palaeopolyploid soybean. Nature 463, 178–183 (2010)

Lynch, M. & Conery, J. S. The evolutionary fate and consequences of duplicate genes. Science 290, 1151–1155 (2000)

Soltis, D. E. et al. Chloroplast gene sequence data suggest a single origin of the predisposition for symbiotic nitrogen fixation in angiosperms. Proc. Natl Acad. Sci. USA 92, 2647–2651 (1995)

Doyle, J. J. & Luckow, M. A. The rest of the iceberg. Legume diversity and evolution in a phylogenetic context. Plant Physiol. 131, 900–910 (2003)

Freeling, M. & Thomas, B. C. Gene-balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexity. Genome Res. 16, 805–814 (2006)

Oldroyd, G. E. & Downie, J. A. Coordinating nodule morphogenesis with rhizobial infection in legumes. Annu. Rev. Plant Biol. 59, 519–546 (2008)

Arrighi, J. F. et al. The Medicago truncatula lysine motif-receptor-like kinase gene family includes NFP and new nodule-expressed genes. Plant Physiol. 142, 265–279 (2006)

Middleton, P. H. et al. An ERF transcription factor in Medicago truncatula that is essential for Nod factor signal transduction. Plant Cell 19, 1221–1234 (2007)

Op den Camp, R. et al. LysM-type mycorrhizal receptor recruited for rhizobium symbiosis in nonlegume Parasponia. Science 331, 909–912 (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)

Kistner, C. & Parniske, M. Evolution of signal transduction in intracellular symbiosis. Trends Plant Sci. 7, 511–518 (2002)

Kato, T. et al. Expression of genes encoding late nodulins characterized by a putative signal peptide and conserved cysteine residues is reduced in ineffective pea nodules. Mol. Plant Microbe Interact. 15, 129–137 (2002)

Van de Velde, W. et al. Plant peptides govern terminal differentiation of bacteria in symbiosis. Science 327, 1122–1126 (2010)

Meyers, B. C., Kozik, A., Griego, A., Kuang, H. & Michelmore, R. W. Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis. Plant Cell 15, 809–834 (2003)

Yang, S., Zhang, X., Yue, J. X., Tian, D. & Chen, J. Q. Recent duplications dominate NBS-encoding gene expansion in two woody species. Mol. Genet. Genomics 280, 187–198 (2008)

Zhou, T. et al. Genome-wide identification of NBS genes in japonica rice reveals significant expansion of divergent non-TIR NBS-LRR genes. Mol. Genet. Genomics 271, 402–415 (2004)

Peters, N. K., Frost, J. W. & Long, S. R. A plant flavone, luteolin, induces expression of Rhizobium meliloti nodulation genes. Science 233, 977–980 (1986)

Winkel-Shirley, B. Flavonoid biosynthesis. A colorful model for genetics, biochemistry, cell biology, and biotechnology. Plant Physiol. 126, 485–493 (2001)

Hegnauer, R. Relevance of seed polysaccharides and flavonoids for the classification of the leguminosae: a chemotaxonomic approach. Phytochemistry 34, 3–16 (1993)

Shirley, B. W. et al. Analysis of Arabidopsis mutants deficient in flavonoid biosynthesis. Plant J. 8, 659–671 (1995)

Singer, S. R. et al. Venturing beyond beans and peas: what can we learn from Chamaecrista? Plant Physiol. 151, 1041–1047 (2009)