Plant Genomics

The combination of climate change, rapidly growing population, and urbanization are creating tremendous stress on the planet’s ability to provide enough food for everyone. A better understanding of how plants grow, develop and reproduce at the basic level will be critical for addressing this challenge. Understanding the genomes of plants will play a critical role in achieving these goals.

Plant genomes, especially those of crop plants, are incredibly complex compared to the genomes of the most animals. For instance the genome of wheat is about six times the size the human genome. The reasons for this are an interesting question but of broader importance is the unique challenge this presents to genome scientists trying to understand the genomes.

We have been active participants in plant genomics since the field began with the sequencing of the first plant genome, Arabidopsis thaliana, which we participated in. We are currently working to develop better tools to sequence these complex genomes and understand their content and implementing these new techniques on the genomes of a variety of plants. Most of our efforts are on the varieties of genomes known as the cereals which include rice, corn and wheat. We also participated in a large number of other plant genome projects. These are depicted in the list below.

Plant genomes we have studied:
• Arabidopsis thaliana
• Theobroma cacao
• Rice
• Corn
• Wheat
• Brassica oleracea
• Medicago truncatula
• Sugarcane
• genus Saccharum
• Tomato
• Pigeonpea (Cajanus cajan)

Selected Publications:

Brenchley, R. and Spannagl, M. and Pfeifer, M. and Barker, G. L. A. and D’Amore, R. and Allen, A. M. and McKenzie, N. and Kramer, M. and Kerhornou, A. and Bolser, D. and Kay, S. and Waite, D. and Trick, M. and Bancroft, I. and Gu, Y. and Huo, N. and Luo, M. C. and Sehgal, S. and Gill, B. and Kianian, S. and Anderson, O. and Kersey, P. and Dvorak, J. and McCombie, W. R. and Hall, A. and Mayer, K. F. X. and Edwards, K. J. and Bevan, M. W. and Hall, N. (2012) Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature, 491(7426) pp. 705-710.

The Tomato Genome Consortium, (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature, 485(7400) pp. 635-41.

Argout, X. and Salse, J. and Aury, J. M. and Guiltinan, M. J. and Droc, G. and Gouzy, J. and Allegre, M. and Chaparro, C. and Legavre, T. and Maximova, S. N. and Abrouk, M. and Murat, F. and Fouet, O. and Poulain, J. and Ruiz, M. and Roguet, Y. and Rodier-Goud, M. and Barbosa-Neto, J. F. and Sabot, F. and Kudrna, D. and Ammiraju, J. S. S. and Schuster, S. C. and Carlson, J. E. and Sallet, E. and Schiex, T. and Dievart, A. and Kramer, M. R. and Gelley, L. and Shi, Z. and Bérard, A. and Viot, C. and Boccara, M. and Risterucci, A. M. and Guignon, V. and Sabau, X. and Axtell, M. J. and Ma, Z. and Zhang, Y and Brown, S. and Bourge, M. and Golser, W. and Song, X. and Clement, D. and Rivallan, R. and Tahi, M. and Akaza, J. M. and Pitollat, B. and Gramacho, K. and D’Hont, A. and Brunel, D. and Infante, D. and Kebe, I. and Costet, P. and Wing, R. and McCombie, W. R. and Guiderdoni, E. and Quetier, F. and Panaud, O. and Wincker, P. and Bocs, S. and Lanaud, C. (2011) The genome of Theobroma cacao. Nature Genetics, 43(2) pp. 101-108.

Schnable, P. S. and Ware, D. and Fulton, R. S. and Stein, J. C. and Wei, F. and Pasternak, S. and Liang, C. and Zhang, J. and Fulton, L. and Graves, T. A. and Minx, P. and Reily, A. D. and Courtney, L. and Kruchowski, S. S. and Tomlinson, C. and Strong, C. and Delehaunty, K. and Fronick, C. and Courtney, B. and Rock, S. M. and Belter, E. and Du, F. and Kim, K. and Abbott, R. M. and Cotton, M. and Levy, A. and Marchetto, P. and Ochoa, K. and Jackson, S. M. and Gillam, B. and Chen, W. and Yan, L. and Higginbotham, J. and Cardenas, M. and Waligorski, J. and Applebaum, E. and Phelps, L. and Falcone, J. and Kanchi, K. and Thane, T. and Scimone, A. and Thane, N. and Henke, J. and Wang, T. and Ruppert, J. and Shah, N. and Rotter, K. and Hodges, J. and Ingenthron, E. and Cordes, M. and Kohlberg, S. and Sgro, J. and Delgado, B. and Mead, K. and Chinwalla, A. and Leonard, S. and Crouse, K. and Collura, K. and Kudrna, D. and Currie, J. and He, R. and Angelova, A. and Rajasekar, S. and Mueller, T. and Lomeli, R. and Scara, G. and Ko, A. and Delaney, K. and Wissotski, M. and Lopez, G. and Campos, D. and Braidotti, M. and Ashley, E. and Golser, W. and Kim, H. and Lee, S. and Lin, J. and Dujmic, Z. and Kim, W. and Talag, J. and Zuccolo, A. and Fan, C. and Sebastian, A. and Kramer, M. and Spiegel, L. and Nascimento, L. and Zutavern, T. and Miller, B. and Ambroise, C. and Muller, S. and Spooner, W. and Narechania, A. and Ren, L. and Wei, S. and Kumari, S. and Faga, B. and Levy, M. J. and McMahan, L. and Van Buren, P. and Vaughn, M. W. (2009) The B73 maize genome: complexity, diversity, and dynamics. Science, 326(5956) pp. 1112-5.

International Rice Genome Sequencing Project, (2005) The map-based sequence of the rice genome. Nature, 436(7052) pp. 793-800.

Palmer, L. E. and O’Shaughnessy, A. L. and Preston, R. R. and Santos, L. and Balija, V. S. and Nascimento, L. U. and Zutavern, T. L. and Henthorn, P. S. and Hannon, G. J. and McCombie, W. R. (2003) A Survey of Canine Expressed Sequence Tags and a Display of Their Annotations Through a Flexible Web-Based Interface. Journal of Heredity, 94(1) pp. 15-22.

Brenner, E. D. and Stevenson, D. W. and McCombie, R. W. and Katari, M. S. and Rudd, S. A. and Mayer, K. F. and Palenchar, P. M. and Runko, S. J. and Twigg, R. W. and Dai, G. and Martienssen, R. A. and Benfey, P. N. and Coruzzi, G. M. (2003) Expressed sequence tag analysis in Cycas, the most primitive living seed plant. Genome Biology, 4(12) pp. R78.

Yu, Y. and Rambo, T. and Currie, J. and Saski, C. and Kim, H. R. and Collura, K. and Thompson, S. and Simmons, J. and Yang, T. J. and Nah, G. and Patel, A. J. and Thurmond, S. and Henry, D. and Oates, R. and Palmer, M. and Pries, G. and Gibson, J. and Anderson, H. and Paradkar, M. and Crane, L. and Dale, J. and Carver, M. B. and Wood, T. and Frisch, D. and Engler, F. and Soderlund, C. and Palmer, L. E. and Tetylman, L. and Nascimento, L. and de la Bastide, M. and Spiegel, L. and Ware, D. and O’Shaughnessy, A. and Dike, S. and Dedhia, N. and Preston, R. and Huang, E. and Ferraro, K. and Kuit, K. and Miller, B. and Zutavern, T. and Katzenberger, F. and Muller, S. and Balija, V. and Martienssen, R. A. and Stein, L. and Minx, P. and Johnson, D. and Cordum, H. and Mardis, E. and Cheng, Z. and Jiang, J. and Wilson, R. and McCombie, W. R. and Wing, R. A. and Yuan, Q. and Ouyang, S. and Liu, J. and Jones, K. M. and Gansberger, K. and Moffat, K. and Hill, J. and Tsitrin, T. and Overton, L. and Bera, J. and Kim, M. and Jin, S. and Tallon, L. and Ciecko, A. and Pai, G. and van Aken, S. and Utterback, T. and Reidmuller, S. and Bormann, J. and Feldblyum, T. and Hsiao, J. and Zismann, V. and Blunt, S. and de Vazeilles, A. and Shaffer, T. and Koo, H. and Suh, B. and Yang, Q. and Haas, B. and Peterson, J. and Pertea, M. and Volfovsky, N. and Wortman, J. and White, O. and Salzberg, S. L. and Fraser, C. M. and Robin Buell, C. and Messing, J. and Song, R. and Fuks, G. and Llaca, V. and Kovchak, S. and Young, S. and Bowers, J. E. and Paterson, A. H. (2003) In-depth view of structure, activity, and evolution of rice chromosome 10. Science, 300(5625) pp. 1566-1569.

Kaul, S. and Koo, H. L. and Jenkins, J. and Rizzo, M. and Rooney, T. and Tallon, L. J. and Feldblyum, T. and Nierman, W. and Benito, M. I. and Lin, X. and Town, C. D. and Venter, J. C. and Fraser, C. M. and Tabata, S. and Nakamura, Y. and Kaneko, T. and Sato, S. and Asamizu, E. and Kato, T. and Kotani, H. and Sasamoto, S. and Ecker, J. R. and Theologis, A. and Federspiel, N. A. and Palm, C. J. and Osborne, B. I. and Shinn, P. and Dewar, K. and Kim, C. J. and Buehler, E. and Dunn, P. and Chao, Q. and Chen, H. and Vysotskaia, V. S. and Lenz, C. A. and Hansen, N. F. and Liu, S. X. and Alta, H. and Sakano, H. and Lam, B. and Pham, P. K. and Nguyen, M. and Yu, G. and Southwick, A. and Lee, J. M. and Miranda, M. and Toriumi, M. J. and Davis, R. W. and Conway, A. B. and Conn, L. and Hootan, A. and Wambutt, R. and Murphy, G. and Düsterhöft, A. and Stiekema, W. and Pohl, T. and Entian, K. D. and Terryn, N. and Volckaert, G. and Salanoubat, M. and Choisne, N. and Artiguenave, F. and Weissenbach, J. and Quetier, F. and Rieger, M. and Ansorge, W. and Unseld, M. and Fartmann, B. and Valle, G. and Wilson, R. K. and Sekhon, M. and Pepin, K. and Murray, J. and Johnson, D. and Hillier, L. and de la Bastide, M. and Huang, E. and Spiegel, L. and Gnoj, L. and Habermann, K. and Dedhia, N. and Parnell, L. and Preston, R. and Marra, M. and McCombie, W. R. and Chen, E. and Martienssen, R. and Mayer, K. and Lemcke, K. and Haas, B. and Haase, D. and Rudd, S. and Schoof, H. and Frishman, D. and Morgenstern, B. and Zaccaria, P. and Mewes, H. W. and White, O. and Creasy, T. H. and Bielke, C. (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature, 408(6814) pp. 796-815.

McCombie, W. R. and De la Bastide, M. and Habermann, K. and Parnell, L. and Dedhia, N. and Gnoj, L. and Schutz, K. and Huang, E. and Spiegel, L. and Yordan, C. and Sehkon, M. and Murray, J. and Sheet, P. and Cordes, M. and Threideh, J. and Stoneking, T. and Kalicki, J. and Graves, T. and Harmon, G. and Edwards, J. and Latreille, P. and Courtney, L. and Cloud, J. and Abbott, A. and Scott, K. and Johnson, D. and Minx, P. and Bentley, D. and Fulton, B. and Miller, N. and Greco, T. and Kemp, K. and Kramer, J. and Fulton, L. and Mardis, E. and Dante, M. and Pepin, K. and Hillier, L. and Nelson, J. and Spieth, J. and Simorowski, J. and May, B. and Ma, P. and Preston, R. and Vil, D. and Lei, H. S. and Shekher, M. and Matero, A. and Shah, R. and Swaby, I. and O’Shaughnessy, A. and Rodriguez, M. and Hoffman, J. and Till, S. and Granat, S. and Shohdy, N. and Hasegawa, A. and Hameed, A. and Lodhi, M. and Johnson, A. and Chen, E. and Marra, M. and Wilson, R. K. and Martienssen, R. (2000) The complete sequence of a heterochromatic island from a higher eukaryote. Cell, 100(3) pp. 377-386.

Mayer, K. and Schuller, C. and Wambutt, R. and Murphy, G. and Volckaert, G. and Pohl, T. and Dusterhoft, A. and Stiekema, W. and Entian, K. D. and Terryn, N. and Harris, B. and Ansorge, W. and Brandt, P. and Grivell, L. and Rieger, M. and Weichselgartner, M. and de Simone, V. and Obermaier, B. and Mache, R. and Muller, M. and Kreis, M. and Delseny, M. and Puigdomenech, P. and Watson, M. and Schmidtheini, T. and Reichert, B. and Portatelle, D. and Perez-Alonso, M. and Boutry, M. and Bancroft, I. and Vos, P. and Hoheisel, J. and Zimmermann, W. and Wedler, H. and Ridley, P. and Langham, S. A. and McCullagh, B. and Bilham, L. and Robben, J. and Van der Schueren, J. and Grymonprez, B. and Chuang, Y. J. and Vandenbussche, F. and Braeken, M. and Weltjens, I. and Voet, M. and Bastiaens, I. and Aert, R. and Defoor, E. and Weitzenegger, T. and Bothe, G. and Ramsperger, U. and Hilbert, H. and Braun, M. and Holzer, E. and Brandt, A. and Peters, S. and van Staveren, M. and Dirske, W. and Mooijman, P. and Klein Lankhorst, R. and Rose, M. and Hauf, J. and Kotter, P. and Berneiser, S. and Hempel, S. and Feldpausch, M. and Lamberth, S. and Van den Daele, H. and De Keyser, A. and Buysshaert, C. and Gielen, J. and Villarroel, R. and De Clercq, R. and Van Montagu, M. and Rogers, J. and Cronin, A. and Quail, M. and Bray-Allen, S. and Clark, L. and Doggett, J. and Hall, S. and Kay, M. and Lennard, N. and McLay, K. and Mayes, R. and Pettett, A. and Rajandream, M. A. and Lyne, M. and Benes, V. and Rechmann, S. and Borkova, D. and Blocker, H. and Scharfe, M. and Grimm, M. and Lohnert, T. H. and Dose, S. and de Haan, M. and Maarse, A. and Schafer, M. and Müller-Auer, S. and Gabel, C. and Fuchs, M. and Fartmann, B. and Granderath, K. and Dauner, D. and Herzl, A. and Neumann, S. and Argiriou, A. and Vitale, D. and Liguori, R. and Piravandi, E. and Massenet, O. and Quigley, F. and Clabauld, G. and Mundlein, A. and Felber, R. and Schnabl, S. and Hiller, R. and Schmidt, W. and Lecharny, A. and Aubourg, S. and Chefdor, F. and Berger, C. and Montfort, A. and Casacuberta, E. and Gibbons, T. and Weber, N. and Vandenbol, M. and Bargues, M. and Terol, J. and Perez-Perez, A. and Purnelle, B. and Bent, E. and Johnson, S. and Tacon, D. and Jesse, T. and Heijnen, L. and Schwarz, S. and Scholler, P. and Heber, S. and Francs, P. and Bielke, C. and Frishman, D. and Haase, D. and Lemcke, K. and Mewes, H. W. and Stocker, S. and Zaccaria, P. and Bevan, M. and Wilson, R. K. and de la Bastide, M. and Habermann, K. and Parnell, L. and Dedhia, N. and Gnoj, L. and Schutz, K. and Huang, E. and Spiegel, L. and Sehkon, M. and Murray, J. and Sheet, P. and Cordes, M. and Abu-Threideh, J. and Stoneking, T. and Kalicki, J. and Graves, T. and Harmon, G. and Edwards, J. and Latreille, P. and Courtney, L. and Cloud, J. and Abbott, A. and Scott, K. and Johnson, D. and Minx, P. and Bentley, D. and Fulton, B. and Miller, N. and Greco, T. and Kemp, K. and Kramer, J. and Fulton, L. and Mardis, E. and Pepin, K. and Hillier, L. and Nelson, J. and Spieth, J. and Ryan, E. and Andrews, S. and Geisel, C. and Layman, D. and Du, H. and Ali, J. and Berghoff, A. and Jones, K. and Drone, K. and Cotton, M. and Joshu, C. and Antonoiu, B. and Zidanic, M. and Strong, C. and Sun, H. and Lamar, B. and Yordan, C. and Ma, P. and Zhong, J. and Preston, R. and Vil, D. and Shekher, M. and Matero, A. and Shah, R. and Swaby, I.K. and O’Shaughnessy, A. and Rodriguez, M. and Hoffmann, J. and Till, S. and Granat, S. and Shohdy, N. and Hasegawa, A. and Hameed, A. and Lodhi, M. and Johnson, A. and Chen, E. and Marra, M. and Martienssen, R. and McCombie, W. R. (1999) Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana. Nature, 402(6763) pp. 769-77.

Copenhaver, G. P. and Nickel, K. and Kuromori, T. and Benito, M. I. and Kaul, S. and Lin, X. and Bevan, M. and Murphy, G. and Harris, B. and Parnell, L. D. and McCombie, W. R. and Martienssen, R. A. and Marra, M. and Preuss, D. (1999) Genetic definition and sequence analysis of Arabidopsis centromeres. Science, 286(5449) pp. 2468-2474.

Rabinowicz, P. D. and Schutz, K. and Dedhia, N. and Yordan, C. and Parnell, L. D. and Stein, L. and McCombie, W. R. and Martienssen, R. A. (1999) Differential methylation of genes and retrotransposons facilitates shotgun sequencing of the maize genome. Nature Genetics, 23(3) pp. 305-308.