Genome-Wide Identification and Phylogenetic Analysis of the ERF Gene Family in Melon

Members of the ERF transcription factor family have significant functions in regulating gene expression in response to biotic and abiotic stresses. In melon (Cucumis melo L.), however, few ERF genes have been studied. In this study, we performed a comprehensive computational analysis of 119 ERF family genes and identified 136 ERF superfamily genes in melon. We present a complete overview of ERF family gene in melon, including the phylogeny, gene structures, and putative conserved motifs of melon ERF family proteins, as well as a comparative analysis between ERF subfamily genes in cucumber. The AP2/ERF gene superfamily in melon can be classified into three families, ERF (ethylene-responsive factor), RAV (related to ABI3/VP1), and AP2 (APETALA2), which comprise 119, 4, and 13 members, respectively. The ERF family in melon was divided into 11 groups, designated I to XI, as in tomato. Our motif analysis indicated that most conserved motifs outside of the AP2/ERF domain are distributed between different clades in the phylogenetic tree. Most ERF family genes have no introns. Based on the observation that 11 of these groups existed in melon, we concluded that the chief functional diversification in the ERF family predated the divergence between monocots and dicots. In our analysis of expression patterns, ERF subfamily genes were distributed widely throughout melon plant tissues and most of the ERF subfamily genes were detected in all seven types of tissues. Some ERF subfamily genes show expression patterns characteristic of tissue-specific expression, implying their probability of performing various roles in growth and development in melon.