II. EST clustering: giant cells are non-dividing meristems

As part of a sequencing effort on tomato, 131,988 ESTs (release 7.1 - August 15, 2001) have been generated by TiGR and assembled into the tomato gene index (LeGI). We queried LeGI with each of the 197 giant cell sequences to identify orthologs in the tentative consensus sequence clusters (TCs). Approximately 70% of these sequences matched TiGR tomato TCs containing ESTs (Fig. 2). The remaining ESTs are novel tomato genes, and reiterate the power of subtractive cDNA cloning.

 
Figure 2. Blastn score and probability of the TiGR dataset queried with a giant cell EST. TC87678 clearly defines the same gene as the query.
Figure 2 Figure 2 Figure 2

Figure 3. Cluster analysis of giant cell transcripts in libraries from tomato tissues.

The TiGR LeGI contains ESTs from multiple tomato libraries. To compare gene expression in giant cells with expression in multiple tomato tissues we constructed a matrix of the 197 giant cell genes and scored for presence or absence (as 0 or 1) in 18 of the LeGI libraries. We applied a neighbor-joining technique (widely used for phylogenetic reconstruction), and the pairwise distance estimates were used to cluster the libraries (Fig. 3). This method supports our independent findings (Koltai et al., Overlapping plant signal transduction pathways induced by a parasitic-nematode and a rhizobial endosymbiont. MP-MI, 2001, in press) that at the transcriptional level, giant cells most closely resemble mersistems.

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