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Comp Funct Genomics. Apr 2005; 6(3): 153–158.
PMCID: PMC2447522

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

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.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Knapp Sandra. Tobacco to tomatoes: a phylogenetic perspective on fruit diversity in the Solanaceae. J Exp Bot. 2002 Oct;53(377):2001–2022. [PubMed]
  • Tanksley Steven D. The genetic, developmental, and molecular bases of fruit size and shape variation in tomato. Plant Cell. 2004;16 (Suppl):S181–S189. [PMC free article] [PubMed]
  • 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. [PubMed]
  • Giovannoni James J. Genetic regulation of fruit development and ripening. Plant Cell. 2004;16 (Suppl):S170–S180. [PMC free article] [PubMed]
  • Adams-Phillips Lori, Barry Cornelius, Giovannoni Jim. Signal transduction systems regulating fruit ripening. Trends Plant Sci. 2004 Jul;9(7):331–338. [PubMed]
  • Brummell DA, Harpster MH. 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]
  • Hamilton AJ, Fray RG, Grierson D. Sense and antisense inactivation of fruit ripening genes in tomato. Curr Top Microbiol Immunol. 1995;197:77–89. [PubMed]
  • 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. [PubMed]
  • Fray RG, Grierson D. Molecular genetics of tomato fruit ripening. Trends Genet. 1993 Dec;9(12):438–443. [PubMed]
  • Fernie AR, Willmitzer L. Molecular and biochemical triggers of potato tuber development. Plant Physiol. 2001 Dec;127(4):1459–1465. [PMC free article] [PubMed]
  • Prat S, Frommer WB, Höfgen R, Keil M, Kossmann J, Köster-Töpfer M, Liu XJ, Müller B, Peña-Cortés H, Rocha-Sosa M, et al. Gene expression during tuber development in potato plants. FEBS Lett. 1990 Aug 1;268(2):334–338. [PubMed]
  • 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. [PubMed]
  • Li L, Li C, Howe GA. 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]
  • Gebhardt C, Valkonen JP. Organization of genes controlling disease resistance in the potato genome. Annu Rev Phytopathol. 2001;39:79–102. [PubMed]
  • Bogdanove AJ, Martin GB. 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. [PMC free article] [PubMed]
  • 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. [PMC free article] [PubMed]
  • 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. [PMC free article] [PubMed]
  • 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. [PubMed]
  • Whitelaw CA, Barbazuk WB, Pertea G, Chan AP, Cheung F, Lee Y, Zheng L, van Heeringen S, Karamycheva S, Bennetzen JL, et al. Enrichment of gene-coding sequences in maize by genome filtration. Science. 2003 Dec 19;302(5653):2118–2120. [PubMed]
  • 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. [PubMed]
  • 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;135(4):2040–2045. [PMC free article] [PubMed]
  • 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. [PMC free article] [PubMed]
  • Yuan Yinan, SanMiguel Phillip J, Bennetzen Jeffrey L. High-Cot sequence analysis of the maize genome. Plant J. 2003 Apr;34(2):249–255. [PubMed]
  • Tanksley SD, Ganal MW, Prince JP, de Vicente MC, Bonierbale MW, Broun P, Fulton TM, Giovannoni JJ, Grandillo S, Martin GB, et al. High density molecular linkage maps of the tomato and potato genomes. Genetics. 1992 Dec;132(4):1141–1160. [PMC free article] [PubMed]
  • 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. [PMC free article] [PubMed]
  • 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. [PMC free article] [PubMed]
  • Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature. 2000 Dec 14;408(6814):796–815. [PubMed]
  • May Gregory D, Dixon Richard A. Medicago truncatula. Curr Biol. 2004 Mar 9;14(5):R180–R181. [PubMed]
  • 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. [PMC free article] [PubMed]
  • Budiman MA, Mao L, Wood TC, Wing RA. 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]
  • Cai WW, Reneker J, Chow CW, 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. [PubMed]
  • Peterson DG, Lapitan NL, Stack SM. 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. [PMC free article] [PubMed]

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