The NSF sequencing effort on tomato has generated 131,988 ESTs from multiple libraries (TiGR release 7.1), and these have been assembled into the tomato gene index (LeGI). We queried LeGI with each of 197 genes specifically expressed in giant cell (GC), identified by subtractive cDNA. Approximately 70% of the GC sequences matched a TiGR tentative consensus sequence cluster (TC). The remaining GC ESTs are novel tomato genes.

S +  R -
S -  R +
	0.001%	>0.3%

To compare gene expression in GCs with expression in multiple tomato tissues, we constructed a matrix of the 197 GC genes and scored for presence or absence (as 0 or 1) in 18 of the LeGI libraries. We applied a neighbor-joining technique and the pairwise distance estimates were used to cluster the libraries. This method supports our histological findings that at the transcriptional level, giant cells most closely resemble mersistems.

Although subject to sampling bias, the abundance of an EST in a TC is an approximate surrogate of that gene’s transcript level in the tissue used to make the library. To better visualize differences between libraries, we extracted and color-coded that abundance information into a spread sheet, which was sorted library-by-library. Here, CG transcripts are compared to transcript profiles from pathogen-resistant and susceptible tomato lines.