Skip to main content
PMC home page
Comparative and Functional Genomics logoLink to Comparative and Functional Genomics
. 2005 Apr;6(3):153–158. doi: 10.1002/cfg.468

The Tomato Sequencing Project, the First Cornerstone of the International Solanaceae Project (SOL)

Lukas A Mueller 1,✉, Steven D Tanksley 1, Jim J Giovannoni 2, Joyce van Eck 2, Stephen Stack 3, Doil Choi 4, Byung Dong Kim 5, Mingsheng Chen 6, Zhukuan Cheng 6, Chuanyou Li 6, Hongqing Ling 6, Yongbiao Xue 6, Graham Seymour 7, Gerard Bishop 8, Glenn Bryan 9, Rameshwar Sharma 10, Jiten Khurana 11, Akhilesh Tyagi 11, Debasis Chattopadhyay 12, Nagendra K Singh 13, Willem Stiekema 14, P Lindhout 15, Taco Jesse 16, Rene Klein Lankhorst 17, Mondher Bouzayen 18, Daisuke Shibata 19, Satoshi Tabata 19, Antonio Granell 20, Miguel A Botella 21, Giovanni Giuliano 22, Luigi Frusciante 23, Mathilde Causse 24, Dani Zamir 25
PMCID: PMC2447522  PMID: 18629226

Abstract

The genome of tomato (Solanum lycopersicum) 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 a larger initiative called the ‘International Solanaceae Genome Project (SOL): Systems Approach to Diversity and Adaptation’. The goal of this grassroots initiative, launched in November 2003, is to establish a network of information, resources and scientists to ultimately tackle two of the most significant questions in plant biology and agriculture: (1) How can a common set of genes/proteins give rise to a wide range of morphologically and ecologically distinct organisms that occupy our planet? (2) How can a deeper understanding of the genetic basis of plant diversity be harnessed to better meet the needs of society in an environmentally friendly and sustainable manner? The Solanaceae and closely related species such as coffee, which are included in the scope of the SOL project, are ideally suited to address both of these questions. The first step of the SOL project is to use an ordered BAC approach to generate a high quality sequence for the euchromatic portions of the tomato as a reference for the Solanaceae. Due to the high level of macro and micro-synteny in the Solanaceae the BAC-by-BAC tomato sequence will form the framework for shotgun sequencing of other species. The starting point for sequencing the genome is BACs anchored to the genetic map by overgo hybridization and AFLP technology. The overgos are derived from approximately 1500 markers from the tomato high density F2-2000 genetic map (http://sgn.cornell.edu/). These seed BACs will be used as anchors from which to radiate the tiling path using BAC end sequence data. Annotation will be performed according to SOL project guidelines. All the information generated under the SOL umbrella will be made available in a comprehensive website. The information will be interlinked with the ultimate goal that the comparative biology of the Solanaceae—and beyond—achieves a context that will facilitate a systems biology approach.

Full Text

The Full Text of this article is available as a PDF (176.0 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Adams-Phillips Lori, Barry Cornelius, Giovannoni Jim. Signal transduction systems regulating fruit ripening. Trends Plant Sci. 2004 Jul;9(7):331–338. doi: 10.1016/j.tplants.2004.05.004. [DOI] [PubMed] [Google Scholar]
  2. Alexander Lucille, Grierson Don. Ethylene biosynthesis and action in tomato: a model for climacteric fruit ripening. J Exp Bot. 2002 Oct;53(377):2039–2055. doi: 10.1093/jxb/erf072. [DOI] [PubMed] [Google Scholar]
  3. Arabidopsis Genome Initiative Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature. 2000 Dec 14;408(6814):796–815. doi: 10.1038/35048692. [DOI] [PubMed] [Google Scholar]
  4. Bogdanove A. J., Martin G. B. AvrPto-dependent Pto-interacting proteins and AvrPto-interacting proteins in tomato. Proc Natl Acad Sci U S A. 2000 Aug 1;97(16):8836–8840. doi: 10.1073/pnas.97.16.8836. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Brummell D. A., Harpster M. H. Cell wall metabolism in fruit softening and quality and its manipulation in transgenic plants. Plant Mol Biol. 2001 Sep;47(1-2):311–340. [PubMed] [Google Scholar]
  6. Budiman M. A., Mao L., Wood T. C., Wing R. A. A deep-coverage tomato BAC library and prospects toward development of an STC framework for genome sequencing. Genome Res. 2000 Jan;10(1):129–136. [PMC free article] [PubMed] [Google Scholar]
  7. Cai W. W., Reneker J., Chow C. W., Vaishnav M., Bradley A. An anchored framework BAC map of mouse chromosome 11 assembled using multiplex oligonucleotide hybridization. Genomics. 1998 Dec 15;54(3):387–397. doi: 10.1006/geno.1998.5620. [DOI] [PubMed] [Google Scholar]
  8. Doganlar Sami, Frary Anne, Daunay Marie-Christine, Lester Richard N., Tanksley Steven D. A comparative genetic linkage map of eggplant (Solanum melongena) and its implications for genome evolution in the solanaceae. Genetics. 2002 Aug;161(4):1697–1711. doi: 10.1093/genetics/161.4.1697. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Fernie A. R., Willmitzer L. Molecular and biochemical triggers of potato tuber development. Plant Physiol. 2001 Dec;127(4):1459–1465. [PMC free article] [PubMed] [Google Scholar]
  10. Fray R. G., Grierson D. Molecular genetics of tomato fruit ripening. Trends Genet. 1993 Dec;9(12):438–443. doi: 10.1016/0168-9525(93)90108-t. [DOI] [PubMed] [Google Scholar]
  11. Fu Yan, Hsia An-Ping, Guo Ling, Schnable Patrick S. Types and frequencies of sequencing errors in methyl-filtered and high c0t maize genome survey sequences. Plant Physiol. 2004 Aug 6;135(4):2040–2045. doi: 10.1104/pp.104.041640. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Fulton Theresa M., Van der Hoeven Rutger, Eannetta Nancy T., Tanksley Steven D. Identification, analysis, and utilization of conserved ortholog set markers for comparative genomics in higher plants. Plant Cell. 2002 Jul;14(7):1457–1467. doi: 10.1105/tpc.010479. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Gebhardt C., Valkonen J. P. Organization of genes controlling disease resistance in the potato genome. Annu Rev Phytopathol. 2001;39:79–102. doi: 10.1146/annurev.phyto.39.1.79. [DOI] [PubMed] [Google Scholar]
  14. Giovannoni James J. Genetic regulation of fruit development and ripening. Plant Cell. 2004 Mar 9;16 (Suppl):S170–S180. doi: 10.1105/tpc.019158. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Gray J., Picton S., Shabbeer J., Schuch W., Grierson D. Molecular biology of fruit ripening and its manipulation with antisense genes. Plant Mol Biol. 1992 May;19(1):69–87. doi: 10.1007/BF00015607. [DOI] [PubMed] [Google Scholar]
  16. Hamilton A. J., Fray R. G., Grierson D. Sense and antisense inactivation of fruit ripening genes in tomato. Curr Top Microbiol Immunol. 1995;197:77–89. doi: 10.1007/978-3-642-79145-1_6. [DOI] [PubMed] [Google Scholar]
  17. Hui Dequan, Iqbal Javeed, Lehmann Katja, Gase Klaus, Saluz Hans Peter, Baldwin Ian T. Molecular interactions between the specialist herbivore Manduca sexta (lepidoptera, sphingidae) and its natural host Nicotiana attenuata: V. microarray analysis and further characterization of large-scale changes in herbivore-induced mRNAs. Plant Physiol. 2003 Apr;131(4):1877–1893. doi: 10.1104/pp.102.018176. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Johnston J. Spencer, Pepper Alan E., Hall Anne E., Chen Z. Jeffrey, Hodnett George, Drabek Janice, Lopez Rebecca, Price H. James. Evolution of genome size in Brassicaceae. Ann Bot. 2005 Jan;95(1):229–235. doi: 10.1093/aob/mci016. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Knapp Sandra, Bohs Lynn, Nee Michael, Spooner David M. Solanaceae--a model for linking genomics with biodiversity. Comp Funct Genomics. 2004;5(3):285–291. doi: 10.1002/cfg.393. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Knapp Sandra. Tobacco to tomatoes: a phylogenetic perspective on fruit diversity in the Solanaceae. J Exp Bot. 2002 Oct;53(377):2001–2022. doi: 10.1093/jxb/erf068. [DOI] [PubMed] [Google Scholar]
  21. Li L., Li C., Howe G. A. Genetic analysis of wound signaling in tomato. Evidence for a dual role of jasmonic acid in defense and female fertility. Plant Physiol. 2001 Dec;127(4):1414–1417. [PMC free article] [PubMed] [Google Scholar]
  22. May Gregory D., Dixon Richard A. Medicago truncatula. Curr Biol. 2004 Mar 9;14(5):R180–R181. doi: 10.1016/j.cub.2004.02.013. [DOI] [PubMed] [Google Scholar]
  23. Menda Naama, Semel Yaniv, Peled Dror, Eshed Yuval, Zamir Dani. In silico screening of a saturated mutation library of tomato. Plant J. 2004 Jun;38(5):861–872. doi: 10.1111/j.1365-313X.2004.02088.x. [DOI] [PubMed] [Google Scholar]
  24. Palmer Lance E., Rabinowicz Pablo D., O'Shaughnessy Andrew L., Balija Vivekanand S., Nascimento Lidia U., Dike Sujit, de la Bastide Melissa, Martienssen Robert A., McCombie W. Richard. Maize genome sequencing by methylation filtration. Science. 2003 Dec 19;302(5653):2115–2117. doi: 10.1126/science.1091265. [DOI] [PubMed] [Google Scholar]
  25. Pedley Kerry F., Martin Gregory B. Molecular basis of Pto-mediated resistance to bacterial speck disease in tomato. Annu Rev Phytopathol. 2003;41:215–243. doi: 10.1146/annurev.phyto.41.121602.143032. [DOI] [PubMed] [Google Scholar]
  26. Peterson D. G., Lapitan N. L., Stack S. M. Localization of single- and low-copy sequences on tomato synaptonemal complex spreads using fluorescence in situ hybridization (FISH). Genetics. 1999 May;152(1):427–439. doi: 10.1093/genetics/152.1.427. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Peterson Daniel G., Schulze Stefan R., Sciara Erica B., Lee Scott A., Bowers John E., Nagel Alexander, Jiang Ning, Tibbitts Deanne C., Wessler Susan R., Paterson Andrew H. Integration of Cot analysis, DNA cloning, and high-throughput sequencing facilitates genome characterization and gene discovery. Genome Res. 2002 May;12(5):795–807. doi: 10.1101/gr.226102. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Prat S., Frommer W. B., Höfgen R., Keil M., Kossmann J., Köster-Töpfer M., Liu X. J., Müller B., Peña-Cortés H., Rocha-Sosa M. Gene expression during tuber development in potato plants. FEBS Lett. 1990 Aug 1;268(2):334–338. doi: 10.1016/0014-5793(90)81281-r. [DOI] [PubMed] [Google Scholar]
  29. Tanksley S. D., Ganal M. W., Prince J. P., de Vicente M. C., Bonierbale M. W., Broun P., Fulton T. M., Giovannoni J. J., Grandillo S., Martin G. B. High density molecular linkage maps of the tomato and potato genomes. Genetics. 1992 Dec;132(4):1141–1160. doi: 10.1093/genetics/132.4.1141. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Tanksley Steven D. The genetic, developmental, and molecular bases of fruit size and shape variation in tomato. Plant Cell. 2004 May 6;16 (Suppl):S181–S189. doi: 10.1105/tpc.018119. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Whitelaw C. A., Barbazuk W. B., Pertea G., Chan A. P., Cheung F., Lee Y., Zheng L., van Heeringen S., Karamycheva S., Bennetzen J. L. Enrichment of gene-coding sequences in maize by genome filtration. Science. 2003 Dec 19;302(5653):2118–2120. doi: 10.1126/science.1090047. [DOI] [PubMed] [Google Scholar]
  32. Yuan Yinan, SanMiguel Phillip J., Bennetzen Jeffrey L. High-Cot sequence analysis of the maize genome. Plant J. 2003 Apr;34(2):249–255. doi: 10.1046/j.1365-313x.2003.01716.x. [DOI] [PubMed] [Google Scholar]

Articles from Comparative and Functional Genomics are provided here courtesy of Wiley

RESOURCES