We retrieved 4,068 SSR motifs in 3,279 melon unigenes. The major types of melon SSR motifs were tri nucleo tide, followed by di nucleotide, tetra nucleotide, penta nucleotide and hexa nucleotide. The most fre quent SSR motif was AAG CTT, followed by AG CT, AT AT and AAT ATT. CG CG was the least frequent SSR motif identified in melon unigenes, possibly due to the fact that CpG sequences are normally highly methylated, which may further inhibit transcription. These sta tistics are in agreement with previous reports of other plant species. Primer pairs were designed for SSR motifs that had sufficient flanking sequences. The complete list of SSR motifs and their corresponding pri mer pair information is provided in Additional file 6. ESTs generated in this and other studies were from a diversity of melon cultivars.

We expected that SNPs would be enriched in the melon EST dataset. Using very stringent criteria, we identified a total of 3,073 high quality SNPs in 1,331 unigenes, among which 1,972 were transi tions, 976 were transversions, and 125 were single base insertions or deletions. The most frequent Inhibitors,Modulators,Libraries SNPs were C to T transitions, followed Inhibitors,Modulators,Libraries by A to G transitions. The com plete list of SNPs identified from melon ESTs is provided in Additional file 7. Detailed information including alignments of sequences containing each indi vidual SNP is also available Brefeldin_A at the Cucurbit Genomics Database. Both SSRs and SNPs identified in the present study represent an important resource for genetic linkage mapping and marker assisted breeding in melon and closely related crops.

As stated above, they have already been used for these purposes. Conclusion Inhibitors,Modulators,Libraries We present the analysis of more than 71,000 and 22,000 melon ESTs from eleven full length enriched and four standard cDNA libraries, respectively. These Inhibitors,Modulators,Libraries libraries were constructed from a range of tissues and melon genotypes. Analysis of approximately 1,400 melon full length transcripts identified from this EST collection indicated that melon transcripts had 5 and 3 UTRs of similar size as those of tomato, while longer than those of other dicot plants that we investigated. Comparative analysis between melon ESTs and other plant genomes allowed us to identify a number of highly conserved gene families across the plant kingdom, as well as gene families specific to fleshy fruit bearing plants, to the Cucurbitaceae family, and to melon. Digital expression analysis identified genes showing significant tissue speci fic expression and this resource remains to be further exploited from the perspective of mining expression data. Furthermore, SSR and SNP markers were also identified in this melon EST collection and recent research activities have begun to utilize these resources to construct high density genetic maps.