The SOL Genomics Network: a comparative resource for Solanaceae biology and beyond

Abstract

The SOL Genomics Network (SGN; http://sgn.cornell.edu) is a rapidly evolving comparative resource for the plants of the Solanaceae family, which includes important crop and model plants such as potato (Solanum tuberosum), eggplant (Solanum melongena), pepper (Capsicum annuum), and tomato (Solanum lycopersicum). The aim of SGN is to relate these species to one another using a comparative genomics approach and to tie them to the other dicots through the fully sequenced genome of Arabidopsis (Arabidopsis thaliana). SGN currently houses map and marker data for Solanaceae species, a large expressed sequence tag collection with computationally derived unigene sets, an extensive database of phenotypic information for a mutagenized tomato population, and associated tools such as real-time quantitative trait loci. Recently, the International Solanaceae Project (SOL) was formed as an umbrella organization for Solanaceae research in over 30 countries to address important questions in plant biology. The first cornerstone of the SOL project is the sequencing of the entire euchromatic portion of the tomato genome. SGN is collaborating with other bioinformatics centers in building the bioinformatics infrastructure for the tomato sequencing project and implementing the bioinformatics strategy of the larger SOL project. The overarching goal of SGN is to make information available in an intuitive comparative format, thereby facilitating a systems approach to investigations into the basis of adaptation and phenotypic diversity in the Solanaceae family, other species in the Asterid clade such as coffee (Coffea arabica), Rubiaciae, and beyond.

Figure 1.

The SGN Comparative Viewer. The viewer shows the relationships between different genetic maps stored in the SGN database and allows users to visualize other information associated with the maps, such as rulers, inbred lines, and the tomato physical map. A zooming function lets the user examine the maps in detail. A second map can be displayed on the right-hand side of the screen; the relationships between markers on the two maps are shown with lines. The interactive Comparative Viewer is controlled with the toolbar visible at the bottom of the screen.

Figure 2.

The overview page for the tomato sequencing project. The chromosomes are shown as small bar graphs, the size corresponding to the chromosome size in centiMorgans, which will fill in as sequencing progresses. The page is available at http://sgn.cornell.edu/help/about/tomato_sequencing.html.