Solanum lycopersicum

Taxonomy: Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; Solanum; Lycopersicon

Introduction

The family Solanaceae comprises more than 3000 species, including many widely consumed crops such as tomato, potato, tobacco, eggplant, and chili pepper. The Solanaceae is the third most economically important plant taxa (after grasses and legumes), and the most important in terms of vegetable crops. Many of these species, including tomato, evolved in the Andean/Amazonian basin in South America, and have since adapted to a large variety of habitats from rainforests to deserts.

The International Solanaceae Genome Initiative (SOL) was initiated with the aim of exploring the basis of phenotypic diversity and adaptation to natural and agricultural environments. The sequencing of the euchromatic region of the tomato genome is one of the cornerstones of the SOL project, and will serve as a reference genome for Solanaceae and other closely related taxa. The common tomato Solanum lycopersicum has 12 chromosomes with a modest diploid genome size of 950Mb. Tomato has simple diploid genetics, short generation time, and has been one of the most studied Solanaceae plant, and is thus suitable for its genome being sequenced as a model reference for Solanaceae. Solanaceae belongs to the Asterid clade of eudicots, distant from other available eudicot genomes such as Arabidopsis or Poplar, and will therefore contribute to the effort of reconstructing the evolution of plant genomes.

Our involvement

We are currently part of the International Tomato Annotation Group (ITAG) - a collaborative effort in efficiently and accurately annotating the tomato genome, and are largely responsible for the gene prediction. This is done using the EuGene software, which is able to integrate various probabilistic models, splice-site models, EST/cDNA alignment, and protein alignment. We also hope to utilize the tomato genome for comparative genomic studies to better understand the evolution of plant genomes.

In collaboration with:

Publications

2012

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.

Andolfo, G., Sanseverino, W., Rombauts, S., Van de Peer, Y., Bradeen, J. M., Carputo, D., Frusciante, L., Ercolano, M. (2012) Overview of tomato (Solanum lycopersicum) candidate pathogen recognition genes reveals important Solanum R locus dynamics. New Phytol. 197(1):223-37.

2009

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.

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VIB / UGent
Bioinformatics & Evolutionary Genomics
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