Functional Annotation and Classification of Bitter<br>Melon. We used BLASTX to annotate 51,745 transcripts<br>against the nonredundant (NR) protein database and the nucleotide (NT) database at the National Center for Biotechnology<br>Information (NCBI) Web site; approximately 58.34% of all<br>transcripts were annotated (Table 1). Of the total 88,703<br>transcripts, 43,635 transcripts (49.19%) had BLAST hits to<br>known proteins in the NR database, and 36,768 transcripts<br>(41.45%) had BLAST hits to nucleotides in the NT database.<br>In addition, some transcripts were aligned to other public<br>databases, including 34,214 (38.57%) transcripts in the SWISSPROT protein database, 41,726 (47.04%) transcripts in the<br>Brassica database (BRAD), 41,031 (46.26%) transcripts in the<br>Arabidopsis information resource (TAIR) database, 14,579<br>(16.44%) transcripts in the Clusters of Orthologous Group<br>(COG) database, and 34,214 (38.57%) transcripts in the Gene<br>Ontology (GO) database.<br>The E-value distributions showed that approximately 59.8%<br>of the transcripts had strong similarity (
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