EXPRESSION-BASED APPROACH TOWARD FUNCTIONAL CHARACTERIZATION OF TOMATO GENES THAT HAVE NO OR WEAK SIMILARITY TO ARABIDOPSIS GENES

Few tomato genes that have no or weak similarity to Arabidopsis genes, namely non-Arabidopsis genes, have been annotated with functional terms. To speculate functions of non-Arabidopsis genes, we compared expression profiles of these genes with those of functionally annotated genes. We used DNA array with 10,905 tomato cDNA probes for analysis of gene expression during fruit maturation. First, we classified gene expression patterns with a self-organizing map (SOM) and compared the distribution of the non-Arabidopsis genes on the SOM matrices. The non-Arabidopsis genes showed as varied expression patterns as all other annotated genes represented on the DNA array. Secondly, we attempted to find sets of functionally annotated genes that coordinately expressed with the non-Arabidopsis genes by illustrating gene-to-gene expression correlation using a network representation. The non-Arabidopsis genes coordinately expressed with sets of annotated genes in diverse functional categories, not with those in specific categories. Taken together, these results suggested that the tomato non-Arabidopsis genes analyzed in this study appeared to evolve to participate in diverse functions and processes.