Available tomato microarray platforms Tom1: cDNA spotted array; 12K spots; 8K unigenes; Developed at Cornell University. Publicly available. Tom2: Long oligo spotted array; 12K spots; 11K unigenes; International collaboration. Includes all Tom1 unigenes. Publicly available. Affy public microarray: 10K probe sets; 9K unigenes; Company-developed; Publicly available. <30% overlap with Tom2. Affy-Syngenta microarray: 23K unigenes; Company-developed; Proprietary. Custom platforms: Nimblegen, Agilent, Combimatrix. There is a need for a comprehensive, widely used, reasonably priced tomato transcriptional profiling platform

The tomato transcriptome Databases: TIGR/Dana Farber, MicroBASE, SGN, TomatEST 250K ESTs, 18K TCs + 28K singletons = 46K Unigenes Projected number of tomato genes = 35-38K Covered non-redundant transcriptome: 28 Mb Projected transcriptome length = Mb Efforts under way: Developmental stage-specific 454 cDNA sequencing  More extensive coverage, assembly of singletons Full-length cDNA sequencing  More complete 5’ coverage, assembly of singletons IL-specific 454 cDNA sequencing  More complete 3’ coverage, SNPs and their mapping to S. lycopersicum x S. pennelli bins SAGE, Solexa  miRNA sequences

Affy chip Affy’s proposal: 1 M probes (and mismatch probes) Full transcript, custom design A minimum of 540 microarrays ordered Our desires: Publicly available array Coverage of all available unigenes Upgradability at no cost as genome sequence progresses Possible bonus features: miRNA probes, antisense probes, probes for validation of gene models, SNP mapping

How to do it Expression database ESTs 454 sequencingSolexa sequencing Gene models Chip design Full-length cDNAs Chip fabrication and validation Chip distribution By September 2007 Allow grace period for data submitted to the database before they go public