Publications related to legume symbioses

Peiter, E, Sun, J, Heckmann,  AB, Venkateshwaran, M, Riley,  BK, Otegui, MJ, Edwards, A, Freshour,  G, Hahn, MG, Cook, DR, Sanders, D, Oldroyd, GED, Downie, JA, AnŽ, JM (2007) The Medicago truncatula DMI1 Protein Modulates Cytosolic Calcium Signaling. Plant Physiol, in press.

Messinese, E., Mun, J.H., Yeun, L.H., Jayaraman, D., Lougnon, G., RougŽ, P., Barre, A., Bono, J.J., Cook, D.R., and AnŽ, J.M. (2007) A novel nuclear protein interacting with the symbiotic DMI3 CCaMK.  MPMI, in press.

Middleton, P., Jakab, J., Penmetsa, R.V., Starker, C., Doll, J., Kalo, P., Prabu, R., Marsh, J., Mitra, R., Kereszt, A., Dudas, B., VandenBosch, K., Long, S., Cook, D., Kiss, G., and Oldroyd, G. (2007) An ERF transcription factor in Medicago truncatula that is essential for Nod factor signal transduction.  The Plant Cell 19:1-14.

Javot, H., Penmetsa, R.V., Terzaghi, N., Cook, D.R., and Harrison, M.J. (2007) Phosphate delivery by MtPT4 is indispensable for the arbuscular mycorrhizal symbiosis. Proc. Natl. Acad. Sci. USA Proc. Natl. Acad. Sci. USA 104:1720-1725.

Riely, B.K., Lougnon, G., AnŽ, J.-M., Cook, D.R. (2007) The symbiotic ion channel homolog DMI1 functions in the nuclear membrane of Medicago truncatula roots.  The Plant Journal 49:208-216.

Veereshlingam, H., Haynes, J.G., Sherrier, D.J., Penmetsa, R.V., Cook, D.R., and Rebecca Dickstein (2004) nip, a symbiotic Medicago truncatula mutant that forms root nodules with aberrant infection threads and exhibits an altered defense response. Plant Physiology 136:3692-3702.

Kuppusamy,  K.T., Endre, G., Prabhu, R., Penmetsa, R.V., Veereshlingam, H., Cook, D.R., Dickstein, R., and VandenBosch, K.A. (2004) LIN, a Medicago truncatula gene required for nodule differentiation and persistence of rhizobial infections. Plant Physiology 136:3682-3691.

Riely, B., Ane, J-M., Penmetsa, R.V., and Cook, D.R. (2004) Genetic and genomic analysis in model legume systems bring Nod factor signaling to center stage.  Current Opinion in Plant Biology 7:408-413.

Cook, D.R. (2004) Unraveling the mystery of Nod factor signaling by a genomic approach in Medicago trunactula. Proc. Natl. Acad. Sci. USA 101:4339-4340.

AnŽ, J.M., Kiss, G.B., Riely, B.K., Penmetsa, R.V., Ayax, C., LŽvy, J., DebellŽ, F., Baek, J.M., Kalo, P., Roseberg, C., Roe, B.A., Long, S.R., DŽnariŽ, J., and Cook, D.R. (2004). Medicago truncatula DMI1 required for bacterial and fungal symbioses in legumes. Science 303:1364-1367.

Schnabel, E., Kulikova, O., Penmetsa, R.V., Bisseling, T., Cook, D., Frugoli, J. (2003) An integrated physical, genetic and cytogenetic map around the sunn locus of M. truncatula.  Genome 46: 665-672.

Ben Amor, B., Shaw, S.L. Oldroyd, G.E.D., Maillet, F., Penmetsa, R.V., Cook, D., Long, S.R., DŽnariŽ, J., and Gough, C. (2003) The NFP locus of Medicago truncatula controls an early step of Nod factor signal transduction upstream of a rapid calcium flux and root hair deformation. The Plant J. 34: 495-506.

Penmetsa, R.V., Frugoli, J.A., Smith, L., Long, S.R., and Cook, D.R. (2003). Dual Genetic Pathways Controlling Nodule Number In Medicago truncatula.  Plant Physiology 131:998-1008.

AnŽ, J-M., LŽvy, J., Thoquet, P., Kulikova, O., de Billy, F., Penmetsa, V., DebellŽ, F., Rosenberg, C., Kim, D.J., Cook, D., Bisseling, T., Huguet, T., and DŽnariŽ, J. (2002). Genetic and cytogenetic mapping of dmi1, dmi2 and dmi3 genes of Medicago truncatula involved in Nod factor transduction, nodulation and mycorrhization.  MPMI 15: 1108-1118.

Dickstein, R., Hu, X., Yang, J., Ba, L., Coque, L., Kim, D.J., Cook, D.R., Yeung, A. (2002). Differential expression of tandemly duplicated ENOD8 genes in Medicago truncatula. Plant Science 163, 333-343.

Ramu, S.R., Peng, H., and Cook, D.R. (2002). Nod factor induction of reactive oxygen species production is correlated with early nodulin gene expression.  MPMI 15: 522-528.

Catoira, R., Timmer, A.C.J., Maillet, F., Galear, C., Penmetsa, R.V., Cook, D.R., Gough, C., and Denarie, J.  (2001).  The HCL gene of Medicago truncatula controls Rhizobium-induced root hair curling. Development 128, 1507-1518.

Cohn, J., Ramu, S., Uhm, T., Nam, Y.W., Kim, D.J., Penmetsa, V., Wood, T., Cook, D., and Stacey, G. (2001).  Differential regulation of a family of apyrase genes from Medicago truncatula. Plant Physiology 125, 2104-2119.

Wais, R.J., Galera, C., Catoira^, R., Penmetsa^, R.V., Cook, D., Gough, C., DŽnariŽ, J., and Long, S.R. (2000). Early symbiosis mutants of Medicago truncatula show a block in Ca++ spiking. Proc. Natl. Acad. Sci. USA, 97: 13407-13412.

Catoira, R., Galera C., de Billy F., Journet E.P., Maillet F., Penmetsa, V., Rosenberg C., Gough, C., Cook D., and Denarie J. (2000). Identification of four genes of Medicago truncatula controlling steps in Nod factor transduction. Plant Cell 12, 1647-1665.

Penmetsa, R.V. and Cook, D.R. (2000). Production and Characterization of Diverse Developmental Mutants of Medicago truncatula.  Plant Physiology 123, 1387-1397.

Salzer, P., Bonanomi, A., Beyer, K., Všgeli-Lange, R., Aeschbacher, R.A., Lange, J., Wiemken, A., Kim, D., Cook, D.R., and Boller, T. (2000).  Differential Expression of Eight Chitinase Genes in Medicago truncatula Roots During Mycorrhiza Formation, Nodulation, and Pathogen Infection".  MPMI, 13 763-777.

Satcey, G., Day, R.B., Chon, J., Okada, M., Ito, Y., Koh, S., Ramu, S., Uhm, T., Kim, D., Cook, D., and Shibyua, N. (2000). Nod Factor Perception.  In, Nitrogen fixation: from molecules to crop productivity, pp. 227-230.

Geurts, R. Gualtieri, G., Kulikova, O., Kim, D-J., Cook, D.R., and Bisseling, T.  (2000). A region on the upper arm of chromosome 5 of Medicago truncatula is highly syntenic to the sym2 reion of pea. In, Nitrogen fixation: from molecules to crop productivity, pp 309-310.

Peng, H.-M., Dreyer, D.A., VandenBosch, K.A., and Cook, D. (1996).  Gene structure and differential regulation of the Rhizobium-induced peroxidase gene rip1. Plant Physiology 112, 1437-1446.

Cook, D., Dreyer, D. A., Bonnet, D., Howell, M., Nony, E., and VandenBosch, K.A. (1995).  Transient induction of a peroxidase gene in Medicago truncatula precedes infection by Rhizobium meliloti.  Plant Cell 7:43-55.

Cook, D. (1995). Surprising developments in the legume root nodule.  BioEssays 17(3), 191-194.

Penmetsa, R.V. and Cook, D. (1997).  A legume ethylene-insensitive mutant hyperinfected by its rhizobial symbiont.  Science 275, 527-530

Publications related to legume genomics

Cannon, SB, Sterck, L, Rombauts, S, Sato, S, Wang, X, Mudge, J, Vasdewani, J, Cheung, F, Gouzy, JP, Schiex, T, Spanngl, M, Schoof, H, Nicholson, C, Humphays, S, Mayer, K, Rogers, J, Quetier, F, Oldroyd, GE, Debelle, F, Cook, DR, Town, CD, Roe, BA, Tabata, S, Van de Peer, Y, Young, ND (2006) Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes. Proc. Natl. Acad. Sci. USA Proc. Natl. Acad. Sci. USA 103:14959-14964.

Choi, H.K., Luckow, M.A., Doyle, J., and Cook, D.R. (2006) Development of nuclear gene-derived molecular markers linked to legume genetic maps.  Molecular Genetics and Genomics. 276:56-70.

Mun, JH, Kim, DJ, Choi, HK, Gish, J, DebellŽ, F, Mudge, J., Denny, R., EndrŽ, G, DŽnariŽ, J, Kiss, GB, Roe, B, Young, ND, and Cook , DR (2006) Distribution of microsatellites in the genome of Medicago truncatula: A resource of genetic markers that integrate genetic and physical maps. Genetics 172: 2541-2555.

Scherson, R., Choi, H-K., Cook, D. R., and Sanderson, M. (2005). Phylogenetics of New World Astragalus: screening of novel nuclear loci for the reconstruction of phylogenies at low taxonomic levels.  Brittonia  57: 56-66.

Nevin D. Young, Steven B. Cannon, Shusei Sato, Dongjin Kim, Douglas R. Cook, Chris D. Town, Bruce A. Roe, and Satoshi Tabata (2005) Sequencing the Genespaces of Medicago truncatula and Lotus japonicus. Plant Physiol. 137: 1174-1181.

Steven B. Cannon, John A. Crow, Michael L. Heuer, Xiaohong Wang, Ethalinda K.S. Cannon, Christopher Dwan, Anne-Francoise Lamblin, Jayprakash Vasdewani, Joann Mudge, Andrew Cook, John Gish, Foo Cheung, Steve Kenton, Timothy M. Kunau, Douglas Brown, Gregory D. May, Dongjin Kim, Douglas R. Cook, Bruce A. Roe, Chris D. Town, Nevin D. Young, and Ernest F. Retzel. (2005). Databases and Information Integration for the Medicago truncatula Genome and Transcriptome. Plant Physiol. 138: 38-46.

Zhu, H., Choi, H-K., Cook, D.R. and Shoemaker, R.C. (2005). Bridging Model and Crop Legumes through Comparative Genomics. Plant Physiology 137: 1189-1196.

Kulikova, O., Geurts, R., Lamine, M., Kim, D.J., Cook D.R., Leunissen, J., de Hong, H., Roe, B.A. and Bisseling, T. (2004) Satellite repeats in the functional centromere and pericentromeric heterochromatin of Medicago truncatula. Chromosoma 113:276-283.

Choi, H.-K., Mun, J.-H., Kim, D.-J., Zhu, H., Baek, J.-M., Mudge, J., Roe, B., Ellis, T.H.N., Doyle, J., Kiss, G.B., Young, N.D., and Cook, D.R. (2004) Estimating genome conservation between crop and model legume species.  Proc. Natl. Acad. Sci. USA 101:15289-15294.

Choi, H.K., Kim, D., Uhm, T., Limpens, E., Lim, H., Mun, J.H., Kalo, P., Penmetsa, R.V., Seres, A., Kulikova, O., Bisseling, T., Kiss, G.B., and Cook, D.R. (2004). A Sequence-based Genetic Map of Medicago truncatula and comparison of marker co-linearity with Medicago sativa. Genetics 166:1463-1502.

Yan, H.H., Mudge, J., Kim, D.J., Larsen, D., Denny, R., Shoemaker, R.C., Cook, D.R., Young, N.D. (2004) Comparative physical mapping reveals features of microsynteny between Glycine max, Medicago truncatula, and Arabidopsis thaliana. Genome 47:141-155.

Ecker, J. and Cook, D. (2004) Genome studies and molecular genetics: Unwrapping new layers of complexity in plant genomes.  Current Opinion in Plant Biology 7:99-101.

Zhu, HY, Kim, DJ,  Baek, JM, Choi, HK, Ellis, L., Kuester, H., McCombie, W.R., Peng, H.M. and Cook, D.R. (2003). Syntenic Relationships between Medicago truncatula and Arabidopsis thaliana Reveal Extensive Divergence of Genome Organization. Plant Physiology, 131:1018-1026.

Yan, H., Mudge, J., Kim, D.J., Shoemaker, R.C., Cook, D.R., and Young, N.D. (2003). Global estimates of conserved microsynteny among the genomes of soybean, Medicago truncatula, and Arabidopsis thaliana. Theoretical and Applied Genetics. 106:1256-1265.

Lamblin, AJ, Crow, JA, Johnson, JE, Silverstein, KAT, Kunau, TM, Endre, G, Stromvik, M, VandenBosch, KA, Cook, DR, and Retzel, EF (2003)  MtDB: A database for personalized data mining of the model legume Medicago truncatula transcriptome. NAR 31:196-201.

Zhu, H.Y., Cannon, S., Young, N.D., and Cook, D.R. (2002). Phylogeny and Genomic Organization of the TIR and non-TIR NBS-LRR Resistance Gene Family in Medicago truncatula, MPMI 15:529-539.

Gualtieri, G., Kulikova, O., Limpens, E., Kim, DJ, Cook, DR, Bisseling, T., Geurts, R. (2002). Microsynteny between pea and Medicago truncatula in the SYM2 region. Plant Molecular Biology 50: 225-235.

Cannon, S.B., Zhu, H.Y., Baumgarten, A., Spangler, R., May, G., Cook, D.R., and Young, N.D. (2002).  Diversity, distribution and ancient taxonomic relationships within the TIR and non-TIR NBS-LRR resistance gene subfamilies. Journal of Molecular Evolution 54:548-562.

Kulikova, O, Gualtieri, G., Geurts, R., Kim, DJ, Cook, DR, Huguet, T., de Jong, J.H., Fransz, P.F., and Bisseling, T. (2001). Integration of the Fish-pachytene and genetic maps of Medicago truncatula. Plant Journal 27, 49-58.

Nam. Y-W, Penmetsa, R.V., Endre, G., Kim, D., and Cook, D.R. (1999). Construction of a bacterial artificial chromosome library of Medicago truncatula and identification of clones containing ethylene response genes.  Theor Appl Genet 98: 638-646.

Publications related to grape genomics

Debolt, S, Cook, DR, and Ford, CM (2006) L-Tartaric acid synthesis from vitamin C in higher plants. Proc. Natl. Acad. Sci. USA 103:5608-5613.

Goes da Silva, F., Iandolino, A., Al-Kayal, F., Bohlmann, M.C., Cushman, M.A., Lim, H., Figueroa, R., Leslie, A., Xu, J., Kabuloglu, E.K., Tattersall, E., Ergul, A., Baek, J.M., Cramer, G.R., Cushman, J.C.,Cook, D.R. (2005) Characterizing the grape transcriptome. Analysis of expressed sequence tags from multiple Vitis species and development of a compendium of expression during berry development. Plant Physiology 139: 574-597.

Iandolino,  A.B., Goes da Silva, F., Lim, H.J., Choi, H.K., Williams, L.E., and Cook, D.R. (2004). A rapid and efficient protocol for the isolation of high-quality total RNA from grapevine (Vitis vinifera L.) tissues containing high concentrations of polylphenols, polysaccharides and proteins.    Plant Molecular Biology Reporter 22:269-278.

Other

Hunter-Cevera, J., Cantor, C.R., Chiu, W., Cook, D.R., Kaler, E.W., Kalil, T., Kingsbury, D.T., Neuhauser, C., Petsko, G.A., Sticklen, M., Walker, L.P., and Westpheling, J. (2006) Committee on review of the Department of Energy's Genomics:  GTL Program.  The National Academies Press, Washington, D.C.

Donald A. Phillips, Howard Ferris, Douglas R. Cook and Donald R. Strong. (2003) Rhizosphere control points: molecules to food webs. Ecology  84:816-826.

Dangl, J., Cook, D., Haselkorn, R., Kellog, E., Last, R., Martienssen, R., McCouch, S., Retzel, E. F., Somerville, C.R., Wessler, S., Yates, J. (2002) The National Plant Genome Initiative: Objectives for 2003-2008. The National Academies Press, Washington, D.C.

Kim, D., Baek, J-M, Kim, D., Kenerley, C.M., Cook, D.R.. (2002). Cloning and characterization of multiple chitinase genes from the mycoparasitic fungus, Trichoderma virens.  Current Genetics 40:374-384.

Cook, D.R., and DŽnariŽ, J.  (2000). Progress in the genomics of Medicago truncatula and the promise for application to grain legume crops. Grain Legumes Magazine, No. 28, 12-13.

Cook, D.R., Kim, D., Zhu, H., and Uribe, P.  (2000). Plant-Pathogen interactions in Medicago truncatula. Grain Legumes Magazine, No.28, 20.

Chory, J., Ecker, J.R., Briggs, S., Caboche, M., Coruzzi, G.M., Cook, D., Dangl, J., Grant, S., Guerinot, L., Henikoff, S., Martienssen, R., Okada, K., Raikhel, N.V., Somerville, C.R., and Weigel, D. (2000). Functional genomics and the virtual plant. A blueprint for understanding how plants are built and how to improve them. Plant Physiol. 123, 423-426.

Cook, D. (1999). Medicago truncatula - a model in the making!  Current Opinion in Plant Biology, 2 (4) 301-304.

Cook, D.R., VandenBosch, K.A., de Bruijn, F.J., and Huguet, T. (1997). Model legumes get the nod.  Plant Cell 9, 275-281.

Cook, D.R. and VandenBosch, K.A. (1997). International Research Efforts on Medicago truncatula: a model for legume biology. IS-MPMI Reporter May 1997, 10-15.

VandenBosch, K.A., Cook, D., deBruijn, F., and Huguet, T. (1996).  Emerging model legume systems: Tools and recent advances.  In: Biology of Plant-Microbe Interactions, G. Stacey, B. Mullin and P.M. Gresshoff, ed. ISMPMI. pp. 557-562.

Cook. D. and Sequeira, L. (1994). Strain Differentiation of Pseudomonas solanacearum by Molecular Genetic Methods.  In: Bacterial Wilt (Pseudomonas solanacearum) A.C. Hayward and G.L. Hartman, ed. CAB International. pp. 77-93.

Raina, R., Cook, D., and Fedoroff, N. (1993). The Maize Spm transposable element has an enhancer-insensitive promoter. PNAS 90:6355-6359.

Cook, D. and Fedoroff, N. (1992). Regulation of Spm promoter activity by the Spm encoded tnpA gene product and DNA methylation. Maize Gen. Coop. Newslet. 66:11-12.

Fedoroff, N., Schlappi, M., Cook, D., and Kolosha, V. (1992). Regulation of the maize Spm transposable element: an hypothesis.  Maize Gen. Coop. Newslet. 66: 13-14.

Cook, D. and Sequeira, L. (1991). Genetic and biochemical characterization of a gene cluster from Pseudomonas solanacearum required for extracellular polysaccharide production and for virulence. J. Bacteriol. 173(5):1654-1662.

Cook, D. and Sequeira, L. (1991). Use of subtractive hybridization to identify a DNA probe for Pseudomonas solanacearum race 3. Molecular and General Genetics 227:401-410.

Cook, D., Barlow, E., and Sequeira, L. (1991). DNA probes for the study of host-pathogen evolution: the example of Pseudomonas solanacearum.  Pages 103-108, in: Advances in Molecular Genetics of Plant-Microbe Interactions, v1. H. Henneke and D.P. Verma, ed.  Kulwer Academic Publishers.

Coplin, D.L. and Cook, D. (1990). Molecular genetics of extracellular polysaccharide biosynthesis in phytopathogenic bacteria.  Mol. Plant-Microbe Interact. 3:271-279.

Cook, D., Barlow, E., and Sequeira, L. (1989). Genetic diversity of Pseudomonas solanacearum: detection of restriction fragment length polymorphisms with DNA probes that specify virulence and the hypersensitive response. Mol. Plant-Microbe Interact. 2:113-121.

Cook, D.R. and Robeson, D.J. (1986). Active resistance of cabbage (Brassica oleracea) to Xanthomonas campestris pv. carotae and protection against the causal agent of black rot, X. campestris pv. campestris, by co-inoculation.  Physiological and Molecular Plant Pathology 28:41-52.

Robeson, D.J. and Cook, D.R. (1985). Production of low molecular weight carboxylic acids by Xanthomonas capestris pv. carotae in relation to the amino acid composition of the medium and their possible involvement in pathogenesis.  Physiological Plant Pathology 26:219-230.

Robeson, D.J. and Cook, D.R. (1985). Biotransformation of tryptophan to indole-3-acetic acid by Xanthomonas campestris pv. campestris. Z. Naturforsch 40c:741-742.

Cook, D., Rasche, M., and Eisinger, W. (1985). Regulation of ethylene biosynthesis and action in cut carnation flower senescence by cytokinins. J. Amer. Soc. Hort. Sci. 110:241-227.