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Title: The medicago genome provides insight into evolution of rhizobial symbiosis

Author
item Young, Nevin - University Of Minnesota
item Debelle, Frederic - Institut National De La Recherche Agronomique (INRA)
item Oldroyd, Giles - John Innes Center
item Geurts, Rene - University Of Wageningen
item Cannon, Steven
item Mayer, Klaus - Institute For Bioinformatics - Germany
item Gouzy, Jerome - Institut National De La Recherche Agronomique (INRA)
item Van De Peer, Yves - Ghent University
item Schoof, Heiko - Institute For Bioinformatics - Germany
item Udvardi, Michael - Samuel Roberts Noble Foundation, Inc
item Cook, Douglas - University Of California
item Meyers, Blake - University Of Delaware
item Spannagl, Manuel - Institute For Bioinformatics - Germany
item Cheung, Foo - J Craig Venter Institute
item De Mita, Stephane - University Of Wageningen
item Proost, Sebastian - Ghent University
item Krishnakumar, Vivek - J Craig Venter Institute
item Gundlach, Heidrun - Institute For Bioinformatics - Germany
item Zhou, Shinguo - University Of Wisconsin
item Mudge, Joann - National Center For Genome Resources
item Bharti, Arvind - National Center For Genome Resources
item Benedito, Vagner - Samuel Roberts Noble Foundation, Inc
item Murray, Jeremy - Samuel Roberts Noble Foundation, Inc
item Naoumkina, Marina
item Rosen, Benjamin - University Of California
item Silverstein, Kevin - University Of Minnesota
item Tang, Haibao - J Craig Venter Institute
item Rombauts, Stephane - Ghent University
item Zhao, Patrick - Samuel Roberts Noble Foundation, Inc
item Zhou, Peng - University Of Minnesota
item Barbe, Valerie - Genoscope
item Bardou, Philippe - Institut National De La Recherche Agronomique (INRA)
item Bechner, Michael - University Of Wisconsin
item Bellec, Arnaud - Institut National De La Recherche Agronomique (INRA)
item Berger, Anne - Genoscope
item Berges, Helene - Institut National De La Recherche Agronomique (INRA)
item Bidwell, Shelby - J Craig Venter Institute
item Bisseling, Ton - University Of Wageningen
item Choisne, Nathalie - Genoscope
item Couloux, Arnaud - Genoscope
item Denny, Roxanne - University Of Minnesota
item Deshpande, Shweta - University Of Oklahoma
item Doyle, Jeffrey - Cornell University - New York
item Dudez, Anne-marie - Institut National De La Recherche Agronomique (INRA)
item Farmer, Andrew - National Center For Genome Resources
item Fouteau, Stephanie - Genoscope
item Franken, Carolien - University Of Wageningen
item Gibelin, Chrystel - Institut National De La Recherche Agronomique (INRA)
item Gish, John - University Of California
item Gonzalez, Alvaro - University Of Delaware
item Green, Pamela - University Of Delaware
item Hallab, Asis - Max Planck Society
item Hartog, Marijke - University Of Wageningen
item Hua, Axin - University Of Oklahoma
item Humphray, Sean - Wellcome Trust Sanger Institute
item Jeong, Dong-hoon - University Of Delaware
item Jing, Yi - University Of Oklahoma
item Jocker, Anika - Max Planck Society
item Kenton, Steve - University Of Oklahoma
item Kim, Dong-jin - University Of California
item Klee, Kathrin - Max Planck Society
item Lai, Hongshing - University Of Oklahoma
item Lang, Chunting - University Of Wageningen
item Lin, Shaoping - University Of Oklahoma
item Macmill, Simone - University Of Oklahoma
item Magdelenat, Ghislaine - Genoscope
item Matthews, Lucy - Wellcome Trust Sanger Institute
item Mccorrison, Jamison - J Craig Venter Institute
item Monaghan, Erin - J Craig Venter Institute
item Mun, Jeong-hwan - University Of California
item Najar, Fares - University Of Oklahoma
item Nicholson, Christine - Wellcome Trust Sanger Institute
item Noirot, Celine - Institut National De La Recherche Agronomique (INRA)
item Paule, Charles - University Of Minnesota
item Poulain, Julie - Genoscope
item Prion, Florent - Institut National De La Recherche Agronomique (INRA)
item Qin, Baifang - University Of Oklahoma
item Qu, Chunmei - University Of Oklahoma
item Retzel, Ernest - National Center For Genome Resources
item Riddle, Clare - Wellcome Trust Sanger Institute
item Sallet, Erika - Institut National De La Recherche Agronomique (INRA)
item Samain, Sylvie - Genoscope
item Samson, Nicolas - Institut National De La Recherche Agronomique (INRA)
item Saurat, Olivier - Institut National De La Recherche Agronomique (INRA)
item Scarpelli, Claude - Genoscope
item Schiex, Thomas - Institut National De La Recherche Agronomique (INRA)
item Segurens, Beatrice - Genoscope
item Seigfried, Majesta - University Of Oklahoma
item Severin, Andrew - Iowa State University
item Sherrier, Janine - University Of Delaware
item Shi, Ruihua - University Of Oklahoma
item Sims, Sarah - Wellcome Trust Sanger Institute
item Sinharoy, Senjuti - Ghent University
item Sterck, Lieven - Ghent University
item Vasylenko, Iryna - University Of Oklahoma
item Viollet, Agnes - Genoscope
item Wang, Keqin - University Of Oklahoma
item Wang, Bing-bing - University Of Minnesota
item Wang, Xiaohong - University Of Minnesota

Submitted to: Nature
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/13/2011
Publication Date: 11/16/2011
Citation: Young, N.D., Debelle, F., Oldroyd, G., Geurts, R., Cannon, S.B., Mayer, K.F., Gouzy, J., Van De Peer, Y., Schoof, H., Udvardi, M.K., Cook, D.R., Meyers, B.C., Spannagl, M., Cheung, F., De Mita, S., Proost, S., Krishnakumar, V., Gundlach, H., Zhou, S., Mudge, J., Bharti, A.K., Benedito, V.A., Murray, J.D., Naoumkina, M.A., Rosen, B., Silverstein, K.A., Tang, H., Rombauts, S., Zhao, P.X., Zhou, P., Barbe, V., Bardou, P., Bechner, M., Bellec, A., Berger, A., Berges, H., Bidwell, S., Bisseling, T., Choisne, N., Couloux, A., Denny, R., Deshpande, S., Doyle, J.J., Dudez, A., Farmer, A.D., Fouteau, S., Franken, C., Gibelin, C., Gish, J., Gonzalez, A.J., Green, P.J., Hallab, A., Hartog, M., Hua, A., Humphray, S., Jeong, D., Jing, Y., Jocker, A., Kenton, S.M., Kim, D., Klee, K., Lai, H., Lang, C., Lin, S., Macmill, S.L., Magdelenat, G., Matthews, L., Mccorrison, J., Monaghan, E.L., Mun, J., Najar, F.Z., Nicholson, C., Noirot, C., Paule, C.R., Poulain, J., Prion, F., Qin, B., Qu, C., Retzel, E.F., Riddle, C., Sallet, E., Samain, S., Samson, N., Saurat, O., Scarpelli, C., Schiex, T., Segurens, B., Seigfried, M., Severin, A., Sherrier, J.D., Shi, R., Sims, S., Sinharoy, S., Sterck, L., Vasylenko, I., Viollet, A., Wang, K., Wang, B., Wang, X. 2011. The medicago genome provides insight into evolution of rhizobial symbiosis. Nature. 480(7378):520-524.

Interpretive Summary: Many crop species have characteristics that make them difficult to use in experiments about fundamental questions in plant biochemistry, genetics, physiology, or development. "Model" species are used to partially bypass these difficulties and general findings about the models are then applied to other related crop species. Medicago truncatula, a close relative of alfalfa and a more distant relative of soybean and other beans, is used as a model because of characteristics such as its small size, short generation time, and relatively simple genetics. Medicago also shares, with many other species in the legume plant family, an association with "rhizobial" bacteria that are able to convert inert atmospheric nitrogen into a form of nitrogen fertilizer that the plants can use. This capacity, called nitrogen fixation, is extremely valuable in crop plants, because these species don't need supplemental nitrogen fertilizer. This paper reports the essentially complete genome sequence (the set of all DNA letters in the chromosomes) of M. truncatula. Analysis of the genome sequence and the contained genes shows that although the M. truncatula genome is less than half the size of the soybean genome and has not undergone a genome-doubling experienced by soybean, it nevertheless has nearly as many genes as soybean, and has accumulated more changes (large and small) since the two species diverged from their common ancestor. Analysis of genes involved in nitrogen fixation shows that this capacity probably evolved from older genes that were involved in plant-fungal interactions, and that the evolution was spurred by a genome doubling that occurred near the origin of the legume family, around 60 million years ago. The genome sequence and other findings are expected to have large impacts on crop plants in the legume family. The basic knowledge from M. truncatula may help plant breeders and biotechnologists develop crop varieties that are able to more efficiently "fix" and use their own nitrogen fertilizer.

Technical Abstract: Medicago truncatula is an excellent model for the study of legume-specific biology, especially endosymbiotic interactions with bacteria and fungi. This paper describes the sequence of the euchromatic portion of the M. truncatula genome based on a recently completed BAC-based assembly supplemented by Illumina-shotgun sequence, together capturing ~94% of all M. truncatula genes. A whole-genome duplication (WGD) that occurred approximately 58 million years ago contributed significantly to the genome we see today and supported the evolution of nodulation and symbiotic nitrogen fixation. Compared to soybean or Lotus japonicus, the M. truncatula genome experienced higher levels of genome rearrangement subsequent to the WGD. Our work provides evidence that this WGD and perhaps also a more ancient whole genome triploidization event gave rise to key components in the perception of rhizobial signals and formation of nitrogen fixing nodules, traits instrumental to the success of legumes and major drivers for their importance in natural and agricultural systems.