All RNA samples were submitted to one extra clean ing step on RNeasy columns and purified on a poly track system. For cDNA library con struction, fruit and flower RNAs 17-AAG msds were pooled, respec tively, by mixing equal amount of RNA from each developmental stage. Full length enriched cDNA libraries were constructed with the RNA Captor proto col, as described previously, and the four standard callus cDNA libraries were constructed using the pBlue script II XR cDNA Library Construction Kit according to the manufacturers instructions. A subset of clones was randomly selected from each cDNA library. Clones from full length enriched cDNA libraries were sequenced at Genoscope and those from standard cDNA libraries at Arizona Genome Institute. EST sequence processing, assembly, and annotation The raw chromatogram files were base called with phred.

Vector, adaptor and low quality bases were trimmed from the raw EST sequences using LUCY. The resulting sequences were then screened against the NCBI UniVec database, E. coli genome, and melon ribo somal RNA sequences using SeqClean, to remove possible contaminations of these sequences. Sequences shorter than 100 bp were discarded. The resulting high quality melon ESTs have been deposited in GenBank dbEST database under accession numbers JG463773 JG557528 and are also available at the Cucurbit Geno mics Database. Melon ESTs were assembled into unigenes using iAs sembler with minimum overlap of 40 bp and mini mum percent identity of 97. Melon unigene sequences were compared against GenBank non redundant and UniProt protein databases using the NCBI BLAST program with a cutoff e value of 1e 5.

The uni gene sequences were translated into proteins using ESTScan and the translated proteins were then compared to pfam domain database using HMMER3. Gene Ontology terms and plant specific GO slim ontology were assigned to each unigene based on terms annotated to its corresponding homologues in the UniProt database and domains in pfam database. Melon biochemical pathways were pre dicted Brefeldin_A from the unigenes using the Pathway Tools pro gram and a melon biochemical pathway database was constructed and is available at the Cucurbit Geno mics Database. Full length transcript identification and analysis Unigenes containing both 5 and 3 sequences of at least one clone from the full length enriched cDNA libraries were identified as full length transcripts. The complete CDS were identified using the getorf application in the EMBOSS package. CDS were also identified based on the ESTScan translations and CDS identified from the two approaches were integrated. 5 and 3 UTRs were then extracted from each candidate full length transcript. Codon usages were calculated with the cusp program in the EMBOSS package.