Profile – Douglas Cook

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Douglas Cook

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Work Address:

Dept Plant Pathology, One Shields Ave, Davis, CA 95616-8680


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Douglas R. Cook is a Professor in the Department of Plant Pathology at the University of California-Davis. He was formerly the Director of the College of Agriculture and Environmental Sciences Genomics Facility at UC Davis and is currently Director of the Feed the Future Innovation Lab for Climate Resilient Chickpea. He received his doctoral degree from the University of Wisconsin-Madison as a bacterial geneticist in the Department of Plant Pathology, and conducted postdoctoral research at the Carnegie Institution of Washington’s Department of Embryology at The Johns Hopkins University. He served on the faculty of Texas A&M University from 1992-2000, prior to joining UC Davis, and as an adjunct Professor of International Graduate School in Bioinformatics and Genome Research at the Universitat Bielefeld in Germany from 2002-2008. He was among a small group of colleagues who together pioneered the use of Medicago truncatula as a model genetic and genomic system for investigation of legume biology. For the past decade has been a leading advocate for the application of basic legume science towards pressing agricultural needs in the developing world. His current research spans model and crop legume systems, with a dual focus on (1) forward genetics, biochemistry and cell biology to characterize genes governing symbiotic development in M. truncatula, and (2) ecological genomics and association genetics to understand gene function in complex natural and agricultural legume systems. He currently leads an international consortium focused on the collection and characterization of crop wild relatives of cultivated chickpea, including both culture independent and living collections of the wild species’ microbiome.

Research Areas:

  • Plant pathology

Current N-related Projects:


Bisseling T and Cook D (2017) Live on Air: Rizobium and legumes, the nitrogen fixing nodule symbiosis. Microanaon, in press.

R. Varma Penmetsa, Noelia Carrasquilla-Garcia, Emily M Bergmann, Lisa Vance, Brenna Castro, Mulualem T. Kassa, Birinchi K. Sarma, Subhojit Datta, Anuja Dubey, Neha Gujaria, Jong-Min Baek1, Jimmy E Woodward, Andrew D Farmer, Clarice J Coyne, Eric J.B. von Wettberg, Rajeev K Varshney, Douglas R Cook (2016) Multiple post-domestication origins of kabuli chickpea through allelic variation in a diversification-associated transcription factor. New Phytologist 211:1440-1451.

Larrainzar E, Riely BK, Kim SC, Carrasquilla-Garcia, N, Yu HJ, Hwang HJ, Oh M, Kim GB, Surendrarao AK, Chasman D, Siahpirani AF, Penmetsa RV, Lee GS, Kim N, Roy S, Mun JH, Cook DR (2015) Deep sequencing of the Medicago truncatula transcriptome reveals a massive early response to Nod factor and ethylene signals. Plant Physiology 169:233-265.

Warschefsky E, Penmetsa RV, Cook DR, von Wettberg EJ (2014). Back to the wilds: tapping evolutionary adaptations for resilient crops through systematic hybridization with crop wild relatives. Am J. of Botany 101:1791-1800.

Laporte, P., Lepage, A., Fournier, J., Catrice, O., Moreau, S., Jardinaud, M-F., Mun, J-H., Larrainzar, E., Cook, D.R., Gamas, P. and Niebel A. (2014) The CCAAT box-binding transcription factor MtNF-YA1 controls rhizobial infection. Journal of Experimental Botany 65:481-94.

Varshney, R.K. et al., & Cook, D.R. (2013) Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. Nature Biotechnology 31:240-246.

Riely, BK, Larrainzar, E, Mun, JH, Gil-Quintana, E, González, EM, Tricoli, D, Yu, HJ, Cook, DR (2013) Development of tools for the biochemical characterization of the symbiotic receptor-like kinase DMI2. MPMI 26:216-226.

Young, N.D et al. (2011) The Genome Sequence of Medicago truncatula and the Evolution of Nodulation. Nature 480:520-4.

Varshney, R, et al. (2011) Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers. Nature Biotechnology 30(1):83-9.

Cara H. Haney, Brendan K. Riely, David Tricoli, Doug R. Cook, David W. Ehrhardt, Sharon R. Long (2011) Symbiotic Rhizobia Bacteria Trigger a Change in Localization and Dynamics of the Medicago truncatula Receptor Kinase LYK3. Plant Cell 23:2774.

Javot H, Penmetsa RR, Breuillin F, Bhattarai KK, Noar RD, Karen Gomez S, Zhang Q, Cook DR, Harrison MJ (2011). Medicago truncatula mtpt4 mutants reveal a role for nitrogen in the regulation of arbuscule degeneration in arbuscular mycorrhizal symbiosis. Plant J. 68:954-965.

Riely, BK, He H, Venkateshwaran M, Sarma B, Schraider J, Ane JM and Cook DR (2011) Identification of legume RopGEF gene families and characterization of a Medicago truncatula RopGEF mediating polar growth of root hairs. Plant Journal 65:230-243.

Friesen ML, Cordeiro MA, Penmetsa RV, Badri M, Huguet T, Aouani ME, Cook DR, Nuzhdin SV. (2010) Population genomic analysis of Tunisian Medicago truncatula reveals candidates for local adaptation. The Plant Journal 63:623-635.

Varshney, R.K. and Cook, D.R. (2010) From genome studies to agricultural biotechnology: closing the gap between basic plant science and applied agriculture. Current Opinion in Plant Biology 13:115-118.

Varshney, R.K., et al and Cook, D.R. (2009) Pigeonpea genomics initiative: an international effort to improve crop productivity of pigeonpea (Cajanus cajan L.) Mol Breeding, DOI 10.1007/s11032-009-9327-2.

Penmetsa, R.V. Uribe, P., Anderson, J., Lichtenzveig, J., Gish, J-C., Nam, Y-W., Engstrom, E., Xu, K., Siskel, G., Pereira, M., Baek, J-M., Lopez-Meyer, M., Long, SR, Harrison, M.J., Singh, J.B., Kiss, G.B., and Cook, D.R. (2008) The Medicago truncatula ortholog of Arabidopsis EIN2, sickle, is a negative regulator of symbiotic and pathogenic microbial associations. Plant Journal 55:580-595.

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.

Messinese, E., Mun, J.H., Yeun, L.H., Jayaraman, D., Lougnon, G., Rougé, P., Barre, A., Bono, J.J., Cook, D.R., and Ané, J.M. (2007) A novel nuclear protein interacting with the symbiotic DMI3 CCaMK. MPMI 20:912-21.

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, Ané, JM (2007) The Medicago truncatula DMI1 Protein Modulates Cytosolic Calcium Signaling. Plant Physiol 145: 192-203.

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., Ané, 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.

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, Debellé, F, Mudge, J., Denny, R., Endré, G, Dénarié, 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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Ané, J.M., Kiss, G.B., Riely, B.K., Penmetsa, R.V., Ayax, C., Lévy, J., Debellé, F., Baek, J.M., Kalo, P., Roseberg, C., Roe, B.A., Long, S.R., Dénarié, 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., Dénarié, 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.

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.

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

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.

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.

Ané, J-M., Lévy, J., Thoquet, P., Kulikova, O., de Billy, F., Penmetsa, V., Debellé, F., Rosenberg, C., Kim, D.J., Cook, D., Bisseling, T., Huguet, T., and Dénarié, 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.

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.

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.

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.

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., Dénarié, 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.

Cook, D.R., and Dénarié, 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.

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., Vögeli-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 region of pea. In, Nitrogen fixation: from molecules to crop productivity, pp 309-310.

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

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.

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

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.

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.

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., 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.