ARS | Publication request: The medicago genome provides insight into evolution of rhizobial symbiosis

Submitted to: Nature
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: October 13, 2011
Publication Date: November 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.