THE TOMATO SEQUENCING PROJECT, THE FIRST CORNERSTONE OF THE INTERNATIONAL SOLANACEAE PROJECT (SOL)

Authors: MUELLER, LUKAS - CORNELL UNIVERSITY; TANKSLEY, STEVE - CORNELL UNIVERSITY; Giovannoni, James; VAN ECK, JOYCE - BOYCE THOMPSON INSTITUTE

Submitted to: Comparative and Functional Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/18/2005
Publication Date: 10/27/2005
Citation: Mueller, L., Tanksley, S., Giovannoni, J.J., Van Eck, J. 2005. The tomato sequencing project, the first cornerstone of the international solanaceae project (sol). Comparative and Functional Genomics. 6:153-158.

Interpretive Summary: The Solanaceae, also called nightshades, are a large family of more than 3000 species, including the tuber-bearing potato, a number of fruit-bearing vegetables (tomato, eggplant, peppers), ornamental plants (petunias, Nicotiana), plants with edible leaves (Solanum aethiopicum, S. macrocarpan) and medicinal plants (i.e. Daturea, Capsicum). The Solanaceae are the third most important plant taxon economically and the most valuable in terms of vegetable crops, and are the most variable of crops species in terms of agricultural utility. The closely related coffee (Rubiaceae) is the second most valuable commodity in the world behind oil. In addition to their role as important food sources, many solanaceous species have a role as scientific model plants, such as tomato and pepper for the study of fruit development. Approximately three fourths of the tomato genome resides in pericentromeric heterochromatin. The remaining one fourth of the tomato genome is found in the distal, euchromatic segments of the chromosomes. The DNA found in heterochromatin is rich in repetitive sequences and poor in genes, making it difficult to sequence. The euchromatin is thought to contain mostly single copy sequences that include more than 90% of the genes, making it relatively easy to sequence. Therefore the strategy is to sequence only the euchromatic portion of the genome to cover most of the gene space. Sequencing of the tomato genome is therefore a little less than twice the effort of sequencing the Arabidopsis 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 goal of this grassroots initiative, initiated 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 sequence the euchromatic portions of the tomato genome as a reference genome for the Solanaceae using an ordered BAC approach. The starting points for sequencing the genome are BACs anchored to the genetic map by overgo hybridization and AFLP technology. The overgos are derived from approximately 1500 markers of the tomato high density F2-2000 genetic map (http://sgn.cornell.edu/). These “seed BACs” will be used to radiate out into the tiling path using BAC end sequence data. Annotation will be performed to SOL project guidelines.