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.

Tobacco Transcription Factors: Novel Insights into Transcriptional Regulation in the Solanaceae

“…Others are prized for their medicinal, poisonous, or psychotropic effects and are the source of drugs such as atropine, scopolamine, and hyoscyamine (OksmanCaldentey, 2007). As a result, the Solanaceae has been the focus of considerable research, including genome sequencing projects for both tomato and potato (Mueller et al, 2005;Mullins et al, 2006).…”

Enzyme Activity Profiles during Fruit Development in Tomato Cultivars andSolanum pennellii

“…An expanding range of molecular and genomics tools are available for tomato, including facile transformation (Klee et al, 1991), a large EST collection (Van der Hoeven et al, 2002), oligonucleotide-based arrays (Slocombe et al, 2008;Wang et al, 2009), emerging genome sequence information (Mueller et al, 2005a(Mueller et al, , 2005b, and a wide range of phenotyping (Causse et al, 2004) and metabolite profiling (Tikunov et al, 2005;Schauer et al, 2006;Fraser et al, 2007) technologies. Very recently, a prepublication tomato genome sequence was made available by the International Tomato Genome Sequencing Consortium (http:// solgenomics.net/).…”

Genetic Transformation in Tomato: Novel Tools to Improve Fruit Quality and Pharmaceutical Production

“…Since the beginning of 1990s, the contribution of molecular markers and maps to tomato breeding and gene identification has been widely documented (Foolad, 2007;Frary et al, 2005;Gupta et al, 2009), and more than 15.000 different markers are collected in the SGN database, where markers can be searched by name, chromosome position and mapping population. Moreover, cytological and cytogenetic maps are also available, as well as a detailed physical map, which was the foundation for the tomato genome sequencing project (Mueller et al, 2005). Contemporarily, gene expression analyses performed on different tissues and developmental stages, as well as on genotypes that differ in their answer to environmental stimuli, have dramatically raised the number of ESTs available at various websites.…”

“…Since tomato is considered the model species among the Solanaceae, these novel techniques have been also exploited for other economically important crops, such as potato, pepper, and eggplant. Moreover, due to the high sinteny existing among Solanaceae species, tomato was chosen as reference genome to be completely sequenced by the International Tomato Genome Sequencing Consortium at the end of the year 2003 (Mueller et al, 2005). Molecular comparative mapping studies revealed a high level of conserved gene content and order within this family (Wu & Tanksley, 2010), as well as within other families (i.e grasses, crucifers, legumes).…”