Jeffrey Fawcett

PhD Student
(Group member from 2006 until 2010)


+ 32 (0) 9 33 13 821

VIB / Ghent University
Bioinformatics & Systems Biology
Technologiepark 927
B-9052 Gent
BELGIUM

CV

2006- PhD, Bioinformatics and Evolutionary Genomics, University of Gent/VIB, Belgium

2004-2006, MSc, Laboratory of Crop Evolution, Graduate School of Agriculture, Kyoto University, Japan

1999-2004, BSc, Faculty of Agriculture, Kyoto University, Japan

Research

Genome duplication

Several ancient polyploidization, or whole genome duplication events (WGDs) have been documented in various angiosperm lineages, and one of my aims are to identify and determine the number and timing of WGD events in plants to better understand their impact on the evolution of plants. Another rather untested question is why each particular polyploid was able to survive and subsequently give rise to an evolutionarily successful lineage. Although polyploid plants do rather frequently form under natural conditions, it seems that very few actually do become successful lineages in terms of evolution (most plants have experienced no more than 1 or 2 WGDs in the last 100 my, not like 5 or 10). Then why did these particular ancient polyploids (those that we can detect now) make it? Were there any particular conditions that lead to their success? We find that several independent WGDs actually seem to be clustered in time, around 60-70 mya, which coincides with the Cretaceous-Tertiary (KT) extinction event. This suggests that factors associated with the KT extinction event might have lead to the increase of successful polyploids around this period.

Gene and genome evolution

I am interested in a very broad sense, "how plant genes and genomes evolve". The sequencing of the genome of Arabidopsis lyrata (and also Capsella rubella and other A. thaliana ecotypes) allows us to track the evolutionary changes in the genomes of Arabidopsis species in a much finer scale then what has previously been possible in plants. I am looking into what has changed, and what has not changed in the genomes of Arabidopsis thaliana and lyrata since their divergence, and trying to understand their causes and consequences. For example, how many genes/exons have been deleted, duplicated, or perhaps created? And how do these behave? To what extent and how are the genomes conserved and/or constrained?

Genome annotation

A good quality genome annotation and a good understanding of it are crucial for many evolutionary analyses, and an accurate and fast automatic annotation is becoming ever more important as an increasing number of genomes are getting sequenced. I have been involved in the annotation of the genomes of species such as tomato (Solanum lycopersicum) and Arabidopsis lyrata, particularly doing gene prediction using a software called EuGene. My aim is to provide an accurate annotation of these species, and also to improve the existing methods and procedures.

Papers

(13) Fawcett, J., Van de Peer, Y., Maere, S. (2013) Significance and biological consequences of polyploidization in land plant evolution. . Plant Genome Diversity Volume 2: Physical Structure, Behaviour and Evolution of Plant Genomes, Greilhuber, J., Dole┼żel, J., and Wendel, J. F. (Eds). Vienna, Springer-Verlag 277-294 .

(12) Tomato Genome Consortium (TGC): ..., ..., Rombauts, S., Fawcett, J., Van de Peer, Y., ..., ... (2012) The tomato genome sequence provides insights intofleshy fruit evolution. Nature 485(7400):635-41.

(11) Fawcett, J., Rouzé, P., Van de Peer, Y. (2012) Higher intron loss rate in Arabidopsis thaliana than A. lyrata is consistent with stronger selection for a smaller genome. Mol. Biol. Evol. 29(2):849-59.

(10) Grbic, M., Van Leeuwen, T., Clark, T. G., Rombauts, S., Rouzé, P., Grbic, V., Osborne, E., Dermauw, W., Thi Ngoc Cao, P., Ortego, F., Hernandez-Crespo, P., Diaz, I., Martinez, N.J., Navajas, M., Sucena, E., Magalhaes, S., Nagy, L., Pace, N.R., Djuranovic, S., Smagghe, G., Iga, M., Christiaens, M., Veenstra, J., Ewer, J., Mancilla Villalobos, R., Hutter, J., Hudson, A., Velez, M., Yi, S., Zeng, Q., Pires-daSilva, A., Roch, F., Cazaux, M., Navarro, M., Zhurov, V., Acevedo, G., Bjelica, A., Fawcett, J., Bonnet, E., Martens, C., Baele, G., Wissler, L., Sanchez-Rodriguez, A., Tirry, L., Blais, C., Demeestere, K., Henz, SR., Gregory, R., Mathieu, J., Verdon, L., Farinelli, L., Schmutz, J., Lindquist, E., Feyereisen, R., Van de Peer, Y. (2011) The genome of Tetranychus urticae reveals herbivorous pest adaptations. Nature 479,487-492.

(9) Velasco, R., Zharkikh, A., Affourtit, J., Dhingra, A., Cestaro, A., Kalyanaraman, A., Fontana, P., Bhatnagar, S.K., Troggio, M., Pruss, D., Salvi, S., Pindo, M., Baldi, P., Castelletti, S., Cavaiuolo, M., Coppola, G., Costa, F., Cova, V., Dal Ri, A., Goremykin, V., Komjanc, M., Longhi, S., Magnago, P., Malacarne, G., Malnoy, M., Micheletti, D., Moretto, M., Perazzolli, M., Si-Ammour, A., Vezzulli, S., Zini, E., Eldredge, G., FitzGerald, L.M., Gutin, N., Lanchbury, J., Macalma, T., Mitchell, J.T., Reid, J., Wardell, B., Kodira, C., Chen, Z., Desany, B., Niazi, F., Palmer, L., Koepke, T., Jiwan, D., Schaeffer, S., Krishnan, V., Wu, C., Chu, V.T., King, S.T., Vick, J., Tao, Q., Mraz, A., Stormo, K., Stormo, K., Bogden, R., Ederle, D., Stella, A., Vecchietti, A., Kater, M.M., Masiero, S., Lasserre, P., Lespinasse, Y., Allan, A.C., Bus, V., Chagné, D., Crowhurst, R.N., Gleave, A.P., Lavezzo, E., Fawcett, J., Proost, S., Rouzé, P., Sterck, L., Toppo, S., Lazzari, B., Hellens, R.P., Durel, C., Gutin, A., Bumgarner, R.E., Gardiner, S.E., Skolnick, M., Egholm, M., Van de Peer, Y., Salamini, F., Viola, R. (2010) The genome of the domesticated apple (Malus x domestica Borkh.). Nat. Genet. 42(10):833-9.

(8) Fawcett, J., Van de Peer, Y. (2010) Angiosperm polyploids and their road to evolutionary success. Trends in Evolutionary Biology 2(e3):16-21.

(7) Van de Peer, Y., Fawcett, J., Proost, S., Sterck, L., Vandepoele, K. (2009) The flowering world: a tale of duplications. Trends Plant Science 14(12):680-8.

(6) Mueller, L., Lankhorst, R., Tanksley, S., Giovannoni, J., White, O., Vrebalov, J., Fei, Z., van Eck, J., Buels, R., Mills, A., Menda, N., Tecle, I., Bombarely, A., Stack, S., Royer, S., Chang, Y., Shearer, L., Kim, J.R., Jo, S., Hur, C., Choi, D., Li, C., Zhao, Q., Jiang, H., Geng, Y., Dai, Y., Fan, M.-J., Chen, J., Lu, F., Shi, J., Sun, S., Chen, J., Yang, X., Lu, C., Chen, M., Cheng, Y.-Y., Li, C., Ling, H., Xue, Y., Wang, X., Seymour, G., Bishop, G., Bryan, G., Rogers, J., Sims, S., Butcher, S., Buchan, D., Abbott, J., Beasley, H., Nicholson, C., Riddle, C., Humphray, S., McLaren, K., Mathur, S., Vyas, S., Solanke, A., Kumar, R., Gupta, A., Sharma, A., Khurana, J., Khurana, J., Tyagi, A., Sarita, ., Chowdhury, P., Shridhar, S., Chattopadhyay, D., Pandit, A., Singh, N., Kumar, A., Dixit, R., Singh, N., Praveen, S., Dalal, V., Yadav, M., Ghazi, I., Gaikwad, K., Raj Sharma, T., Mohapatra, T., Singh, N., Szinay, D., de Jong, P.J., Peters, S., van Staveren, M., Datema, E., Fiers, M., van Ham, R., Lindhout, P., Philippot, M., Frasse, P., Regad, F., Zouine, M., Bouzayen, M., Asamizu, E., Sato, S., Fukuoka, H., Tabata, S., Shibata, M., Botella, M., Perez-Alonso, M., Fernandez-Pedrosa, V., Osorio, S., Mico, A., Granell, A., Zhang, J., He, Y., Huang, S., Du, Y., Qu, D., Liu, L., Liu, D., Wang, X., Ye, Z., Yang, W., Wang, X., Vezzi, A., Todesco, S., Valle, G., Falcone, G., Pietrella, M., Giuliano, G., Grandillo, S., Traini, A., D?Agostino, N., Chiusano, M., Ercolano, M., Barone, A., Frusciante, L., Schoof, H., Jöcker, A., Bruggmann, R., Spannagl, M., Mayer, K., Guigó, R., Camara, F., Rombauts, S., Fawcett, J., Van de Peer, Y., Knapp, S., Zamir, D., Stiekema, W. (2009) A Snapshot of the Emerging Tomato Genome Sequence: The Tomato Genome Sequencing Consortium. The Plant Genome 2:78-92.

(5) Fawcett, J., Maere, S., Van de Peer, Y. (2009) Plants with double genomes might have had a better chance to survive the Cretaceous-Tertiary extinction event. Proc Natl Acad Sci 106(14):5737-42.

(4) Rensing, S.A., Lang, D., Zimmer, A., Terry, A., Salamov, A., H,Shapiro, , Nishiyama, T., P.-Perroud, F., Lindquist, E., Kamisugi, Y., Tanahashi, T., Sakakibara, K., Fujita, T., Oishi, K., Shin-I, T., Kuroki, Y., Toyoda, A., Suzuki, Y., S.-Hashimoto, I., Yamaguchi, K., Sugano, S., Kohara, Y., Fujiyama, A., Ashton, N., Anterola, A., Aoki, S., Barbazuk, W.B., Barker, E., Bennetzen, J., Blankenship, R., Cho, S.H., Dutcher, S., Estelle, M., Fawcett, J., Gundlach, H., Hanada, K., Heyl, A., Hicks, K. A., Hughes, J., Lohr, M., Mayer, K., Melkozernov, A., Murata, T., Nelson, D.R., Pils, B., Prigge, M., Reiss, B., Renner, T., Rombauts, S., Rushton, P., Sanderfoot, A., Schween, G., S.-Shiu, H., Stueber, K., Theodoulou, F.L., Tu, H., Van de Peer, Y., Verrier, P.J., Waters, E., Wood, A., Yang, G., Cove, D., Cuming, A.C., Hasebe, M., Lucas, S., Mishler, B.D., Reski, R., Grigoriev, I., Quatrano, R.S., Boore, J.L. (2008) The Physcomitrella Genome Reveals Evolutionary Insights into the Conquest of Land by Plants. Science 319(5859):64-9.

(3) Velasco, R., Zharkikh, A., Troggio, M., Cartwright, D.A., Cestaro, A., Pruss, D., Pindo, M., FitzGerald, L.M., Vezzulli, S., Reid, J., Malacarne, G., Iliev, D., Coppola, G., Wardell, B., Micheletti, D., Macalma, T., Facci, M., Mitchell, J.T., Perazzolli, M., Eldredge, G., Gatto, P., Oyzerski, R., Moretto, M., Gutin, N., Stefanini, M., Chen, Y., Segala, C., Davenport, C., Demattè, L., Mraz, A., Battilana, J., Stormo, K., Costa, F., Tao, Q., Si-Ammour, A., Harkins, T., Lackey, A., Perbost, C., Taillon, B., Stella, A., Solovyev, V., Fawcett, J., Sterck, L., Vandepoele, K., Grando, M.S., Toppo, S., Moser, C., Lanchbury, J., Bogden, R., Skolnick, M., Sgaramella, V., Bhatnagar, S.K., Fontana, P., Gutin, A., Van de Peer, Y., Salamini, F., Viola, R. (2007) A High Quality Draft Consensus Sequence of the Genome of a Heterozygous Grapevine Variety. PLoS One 2(12):e1326.

(2) Rensing, S.A., Ick, J., Fawcett, J., Lang, D., Zimmer, A., Van de Peer, Y., Reski, R. (2007) An ancient genome duplication contributed to the abundance of metabolic genes in the moss Physcomitrella patens. BMC Evol. Biol. 7:130.

(1) Fawcett, J., Watanabe, H., Kawahara, T., Yasui, Y. (2006) A SINE family widely distributed in the plant kingdom and its evolutionary history. Plant Mol. Biol. 61(3):505-14.











Contact:
VIB / UGent
Bioinformatics & Evolutionary Genomics
Technologiepark 927
B-9052 Gent
BELGIUM
+32 (0) 9 33 13807 (phone)
+32 (0) 9 33 13809 (fax)

Don't hesitate to contact the in case of problems with the website!