International Tomato Genome Sequencing Project

The International Tomato Genome Sequencing Project is a consortium of groups from ten different countries, including the USA, whose goal is to sequence the euchromatic regions of each of the 12 tomato chromosomes. The USA group is sequencing three of the chromosomes (1,10,11) and the remaining nine chromosomes are each being sequenced by a group from a different country. The breakdown on the countries sequencing the remaining nine chromosomes is as follows: Korea - chromosome 2, China - chromosome 3, UK - chromosome 4, India - chromosome 5, The Netherlands - chromosome 6, France - chromosome 7, Japan - chromosome 8, Spain - chromosome 9, and Italy - chromosome 12. Each group has acquired funding from agencies within their respective countries. The repository for all information and data related to the project can be found on SGN ( (see Sect. 1.17).

The tomato genome contains 950 Mb of DNA which is organized into 12 chromosomes (n = x = 12) (Arumuganathan and Earle 1991). Unlike the chromosomes of maize or rice, in which heterochromatin and euchromatin are interspersed, the heterochromatin in tomato is concentrated around the centromeres. This pericentric heterochromatin is largely devoid of genes and heavily populated by retrotransposons, but constitutes approximately 77% of the tomato DNA (Peterson et al. 1996; Van der Hoeven et al. 2002; Wang et al. 2006). In contrast, the distal portions of each tomato chromosome are comprised of largely contiguous stretches of gene-rich euchromatin, which corresponds to approximately 23% of the DNA (Peterson et al. 1996; Wang et al. 2006). Rather than sequencing the entire tomato genome (950 Mb), the international consortium has committed to sequencing the approximately 220 Mb of euchromatin which is estimated to contain approximately 85% of the predicted 35,000 genes that comprise the tomato genome (Van der Hoeven et al. 2002; Wang et al. 2006). The consortium has agreed that there are several advantages to sequencing a tiling path through the euchromatin rather than the entire tomato genome.

Sequencing the tomato genome is the cornerstone of a larger international effort: "The International Solanaceae Genome Initiative" or "SOL Initiative". Thegoalofthiseffortistoestablish anetwork ofinfor-mation, resources and scientists to tackle two universal biological questions that the Solanaceae genomes are particularly suited to address: (i) How can a common set of genes/proteins give rise to a wide range of morphologically and ecologically distinct organisms that occupy our planet? (ii) 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 tomato reference sequence gathered through a BAC minimal tiling path approach will provide gene content and order, which is well documented to be similar to other Solanaceae genomes, thus making the phenotypic and evolutionary diversity in this family accessible for exploration at the sequence level. The tomato genome is connected to the other important members of the family by detailed comparative genetic maps (see Sect. 1.6) and the level of microsynteny is known to be well conserved with respect to gene content and order. In addition, because the Solanaceae represents a distinct and divergent clade of flowering plants, distant from Arabidopsis, Medicago, soybean, maize and rice, the tomato genome sequence will provide a rich resource for investigating the forces of gene and genome evolution over long periods of evolutionary time.

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