Developing cucumber fruit exhibit a transition in response to inoculation by Phytophthora capsici. From initial fruit set through exponential growth phase [until ca. 10-12 days post pollination (dpp)] young fruit are highly susceptible, after which they become resistant. Analysis of fruit peel sections suggests that changes in peel properties be important for the age-related resistance. 454 sequence analysis was performed on two replicate fruit peel samples from 8dpp (susceptible) and 16ddp (resistant) fruit. The resulting approximately 800,000 EST reads (ca. 200,000 per sample) were combined with 1.13 million prior reads from pericarp and placenta samples at 0, 4, 8, 12, and 16dpp, and aligned with the full cucumber genome sequence for transcript assembly. The combined sequences resulted in approximately 53,000 putative transcripts with a mean length of 931 bp, representing approximately 32,500 loci. All assemblies were mapped onto the cucumber genome. BLAST analysis provided putative homologs for 95% of the contigs represented by <u>></u> 30 ESTs and was used to assign putative gene functions. Greater similarity in overall gene expression was observed between peel samples at 8 and 16dpp than between tissue types at a given age. Peel samples were enriched for expression of genes associated with electron transport, response to abiotic and biotic stimuli and stress, and extracellular, cell wall, plastid and ER associated genes. Electron transport and plastid associated genes were most highly enriched in 8dpp peel samples, while 16dpp peel samples were more enriched for abiotic/biotic stimuli, stress, ER, golgi, hydrolase, and transferase related genes.