Table 3. Comparison of fruit and seed transcriptome with root, leaf and flower transcriptome.

Transcriptome	Unigenes with no significant similarity to other transcriptome	Unigenes with significant similarity to other transcriptome
Fruit and seed	21 961 (39%)	33 988 (61%)
Root, leaf and flower	2177 (4%)	47 433 (96%)

A reciprocal BLAST search was conducted to compare the two C. pepo transcriptomes. Each transcriptome was compared to the other transcriptome using the blastn algorithm with a significance threshold of 1.0×10⁻²⁵.