The genome of tomato (Solanum lycopersicum L.) is being sequenced by an international consortium of 10 countries (Korea, China, the United Kingdom, India, the Netherlands, France, Japan, Spain, Italy, and the United States) as part of the larger “International Solanaceae Genome Project (SOL): Systems Approach to Diversity and Adaptation” initiative. The tomato genome sequencing project uses an ordered bacterial artificial chromosome (BAC) approach to generate a high-quality tomato euchromatic genome sequence for use as a reference genome for the Solanaceae and euasterids. Sequence is deposited at GenBank and at the SOL Genomics Network (SGN). Currently, there are around 1000 BACs finished or in progress, representing more than a third of the projected euchromatic portion of the genome. An annotation effort is also underway by the International Tomato Annotation Group. The expected number of genes in the euchromatin is ∼40,000, based on an estimate from a preliminary annotation of 11% of finished sequence. Here, we present this first snapshot of the emerging tomato genome and its annotation, a short comparison with potato (Solanum tuberosum L.) sequence data, and the tools available for the researchers to exploit this new resource are also presented. In the future, whole-genome shotgun techniques will be combined with the BAC-by-BAC approach to cover the entire tomato genome. The high-quality reference euchromatic tomato sequence is expected to be near completion by 2010.
A snapshot of the emerging tomato genome sequence / L.A. Mueller, R.K. Lankhorst, S.D. Tanksley, J.J. Giovannoni, R. White, J. Vrebalov, Z. Fei, J. van Eck, R. Buels, A.A. Mills, N. Menda, I.Y. Tecle, A. Bombarely, S. Stack, S.M. Royer, S. Chang, L.A. Shearer, B.D. Kim, J. Sung-Hwan, C. Hur, D. Choi, L. Chang-Bao, J. Zhao, H. Jiang, Y. Geng, Y. Dai, H. Fan, J. Chen, L. Fei, J. Shi, S. Sun, J. Chen, X. Yang, L. Chen, M. Chen, Z. Cheng, L. Chuanyou, H. Ling, Y. Xue, Y. Wang, G.B. Seymour, G.J. Bishop, G. Bryan, J. Rogers, S. Sims, S. Butcher, D. Buchan, J. Abbott, H. Beasley, C. Nicholson, C. Riddle, S. Humphray, K. Mclaren, S. Mathur, S. Vyas, A.U. Solanke, R. Kumar, V. Gupta, A.K. Sharma, P. Khurana, J.P. Khurana, A. Tyagi, Sarita, P. Chowdhury, S. Shridhar, D. Chattopadhyay, A. Pandit, P. Singh, A. Kumar, R. Dixit, A. Singh, S. Praveen, V. Dalal, M. Yadav, I.A. Ghazi, K. Gaikwad, T.R. Sharma, T. Mohapatra, N.K. Singh, D. Szinay, H. de Jong, S. Peters, M. van Staveren, E. Datema, M.W.E.J. Fiers, R.C.H.J. van Ham, P. Lindhout, M. Philippot, P. Frasse, F. Regad, M. Zouine, M. Bouzayen, E. Asamizu, S. Sato, H. Fukuoka, S. Tabata, D. Shibata, M.A. Botella, M. Perez-Alonso, V. Fernandez-Pedrosa, S. Osorio, A. Mico, A. Granell, Z. Zhang, H. Jun, S. Huang, D. Yongchen, Q. Dongyu, L. Liu, D. Liu, J. Wang, Y. Zhibiao, W. Yang, G. Wang, A. Vezzi, S. Todesco, G. Valle, G. Falcone, M. Pietrella, G. Giuliano, S. Grandillo, A. Traini, N. D'Agostino, M.L. Chiusano, M. Ercolano, A. Barone, L. Frusciante, H. Schoof, A. Jöcker, R. Bruggmann, M. Spannagl, K.X.F. Mayer, R. Guigó, F. Camara, S. Rombauts, J.A. Fawcett, Y. Van de Peer, S. Knapp, D. Zamir, W. Stiekema. - In: THE PLANT GENOME. - ISSN 1940-3372. - 2:1(2009), pp. 78-92. [10.3835/plantgenome2008.08.0005]
A snapshot of the emerging tomato genome sequence
A. Bombarely;
2009
Abstract
The genome of tomato (Solanum lycopersicum L.) is being sequenced by an international consortium of 10 countries (Korea, China, the United Kingdom, India, the Netherlands, France, Japan, Spain, Italy, and the United States) as part of the larger “International Solanaceae Genome Project (SOL): Systems Approach to Diversity and Adaptation” initiative. The tomato genome sequencing project uses an ordered bacterial artificial chromosome (BAC) approach to generate a high-quality tomato euchromatic genome sequence for use as a reference genome for the Solanaceae and euasterids. Sequence is deposited at GenBank and at the SOL Genomics Network (SGN). Currently, there are around 1000 BACs finished or in progress, representing more than a third of the projected euchromatic portion of the genome. An annotation effort is also underway by the International Tomato Annotation Group. The expected number of genes in the euchromatin is ∼40,000, based on an estimate from a preliminary annotation of 11% of finished sequence. Here, we present this first snapshot of the emerging tomato genome and its annotation, a short comparison with potato (Solanum tuberosum L.) sequence data, and the tools available for the researchers to exploit this new resource are also presented. In the future, whole-genome shotgun techniques will be combined with the BAC-by-BAC approach to cover the entire tomato genome. The high-quality reference euchromatic tomato sequence is expected to be near completion by 2010.
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