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United States Department of Agriculture

Agricultural Research Service

Research Project: GENOMICS APPROACHES FOR IMPROVING NUTRITIONAL QUALITY OF FOOD CROP SPECIES

Location: Plant, Soil and Nutrition Research

Title: A snapshot of the emerging tomato genome sequence

Authors
item Mueller, Lukas - BOYCE THOMPSON INST.
item Tanksley, Steven - CORNELL
item Giovannoni, James
item Vaneck, Joyce - BOYCE THOMPSON INST.
item Stack, Stephen - COLORADO STATE
item Buels, Robert - BOYCE THOMPSON INST.

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: January 30, 2009
Publication Date: March 16, 2009
Citation: Mueller, L., Tanksley, S., Giovannoni, J.J., Vaneck, J., Stack, S., Buels, R. 2009. A snapshot of the emerging tomato genome sequence. The Plant Genome. 2:78-92.

Interpretive Summary: The Solanaceae, also called nightshades, are a large family of more than 3000 species, including economically important species such as tomato, potato, pepper, eggplant, tobacco, and petunia. In addition to including important food crops, the Solanaceae also have roles as scientific model plants, for the study of fruit development, tuber development, biosynthesis of anthocyanin pigments and for plant defense. The nightshades have also attracted interest because they produce a number of secondary metabolites that have medicinal properties. The Solanaceae are remarkable in that the gene content of the different species is similar despite the markedly different phenotypic outcomes, making the Solanaceae an excellent model for the study of adaptation to natural and agricultural environments. Key to understanding genome evolution and genetic diversity in the Solanaceae will be access to a reference genome species. Tomato has been selected as the target reference and its genome will be sequenced by an international scientific consortium. Here we report the strategy, initiation and progress to date in sequencing the tomato genome.

Technical 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 first step of the SOL project is to use an ordered BAC approach to generate a high quality tomato euchromatic genome sequence as a reference for the Solanaceae and Euasterids. Sequence is deposited at Genbank and at the SOL Genomics Network (SGN). Currently, there are about one thousand BACs finished or in progress, more than a third of the projected euchromatic portion of the genome, and an annotation effort is underway by the International Tomato Annotation Group (ITAG). The expected number of genes in the euchromatin is in the order of 40,000, as estimated from a preliminary annotation of 11% of finished sequence. Here we look at this first snapshot of the emerging genome, its annotation, and present a short comparison with the potato sequence, and present some of the tools available for the researchers to exploit this new resource. The tomato sequence is expected to be near completion by 2010.

Last Modified: 4/15/2014
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