U.S. Contribution to the International Solanaceae Genome Effort

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PI James Giovannoni (Boyce Thompson Inst. for Plant Research)Co-PIs Lukas Mueller (Cornell Univ.), Stephen Stack (Colorado State Univ.), Steven Tanksley (Cornell Univ.), Joyce Van Eck (Boyce Thompson Inst. for Plant Research)Key Collaborators Chuanyou Li, Ying Wang (Chinese Acad. Sci., China), Mondher Bouzayen, Farid Regad (INRA, France), Akhilesh Tyagi, Arun Sharma (Univ. of Delhi South Campus, India), Daniel Zamir (Hebrew Univ., Israel), Giovanni Giuliano (ENEA, Italy), Satoshi Tabata, Daisuke Shibata (Kazusa DNA Res. Inst., Japan), Doil Choi (KRIBB, Korea), Miguel Botella (Univ. Malaga,Spain), Antonio Granell (IBMCP, Spain), Pim Lindhout, Hans de Jong (Wageningen Univ., The Netherlands), Willem Stiekema (Centre for BioSystems Genomics, The Netherlands), Gerard Bishop (Univ. Wales, U.K.); Graham Seymour (Hort. Res. Inst., U.K.)Scientific objectives and approaches: In the tomato genome, euchromatin occurs in long contiguous stretches at the end of each chromosome. Euchromatin accounts for only 25% of the DNA, yet contains more than 90% of the estimated 38,000 genes. As part of an international consortium to sequence the euchromatin of all twelve tomato chromosomes, we will provide clone and informatic resources towards an international effort to sequence a minimal tiling path of BAC clones through this gene-rich DNA. The project will: 1) Coordinate the international sequencing effort by supplying verified BAC clones for sequencing and performing the necessary genetic and physical mapping required to guide sequencing through the euchromatin. 2) Continue to serve the international project as a central repository and web interface for all sequence and annotation data. 3) Contribute to the structural and functional annotation for the genomic sequence with the international collaborators. 4) Continue to develop integrated bioinformatics for genomic research in the Solanaceae and related taxa through the SOL Genome Network database. This will include computationally mapping ESTs and other gene sequences from related species (e.g. potato, eggplant, pepper, coffee, etc.) onto the tomato reference sequence in order to generate predictive sequence maps for those species.Broader impacts of project: Sequencing the tomato genome is the cornerstone of a larger international effort: "The International Solanaceae Genome Initiative" or "SOL Initiative". The tomato reference sequence 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 and the level of microsynteny is known to be well conserved (gene content and order). Because the Solanaceae represents a distinct and divergent clade of flowering plants, distant from Arabidopsis, Medicago, soybean, maize and rice, the tomato sequence will also provide a rich resource for investigating the forces of gene and genome evolution over long periods of evolutionary time.We will continue our Bioinformatics Summer Intern Program, in addition to offering research/computational biology opportunities to students during the academic year. Assignment of projects to students will serve two purposes by providing training opportunities while simultaneously advancing the goals of our proposed research. We are committed to the recruitment of students from underrepresented groups to both provide novel opportunities and experiences and to foster confidence in pursuit of broader career goals by working in a diverse group. Providing such opportunities could impact the diversity of students who go on to pursue this area of research or scientific careers in general.Access to project outcomesAll data will be accessible via the Solanaceous Genomes Network (SGN: http://www.sgn.cornell.edu/).