Sequencing the tomato genome: a reference genome for the Solanaceae

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We propose to sequence and annotate the estimated 19 Mb of euchromatin on tomato chromosome 4. The starting point for sequencing chromosome 4 will be 100 seed BACs provided from our US collaborators and individually anchored to the tomato high density genetic map (F2.2000; http://www.sgn.cornell.edu). Sequencing for the UK will proceed on a BAC by BAC basis at the Sanger Institute. Each sequenced anchor BAC will serve as a seed from which to radiate out in a minimum tiling path in either direction. Identification of the correct next BACs in the euchromatin minimum tiling path (e-MTP) will be based on the use of a BAC-end sequence database created in the US and a fingerprint contig physical map that is currently being jointly constructed by US and Dutch scientists. The bioinformatics portion of the UK project will be embedded in a well-established infrastructure in collaboration with the Solanaceae Genome Network (SGN) Bioinformatics group and the Munich Information Centre for Protein Sequences (MIPS). Automated annotation will be carried out by the bioinformatician in association with the bioinformatics unit at Imperial. All the annotated sequences will be integrated into worldwide resource at SGN. To disseminate up-to-date information to UK researchers and the public we will establish a Solanaceae Research Community (SRC-UK) web based interface.