Genome-Wide Analysis of Transcription Factor Gene Superfamily in Chili Pepper (Capsicum annuum)

Transcription factors (TFs) are proteins that bind to specific DNA sequences and control gene expression in the entire biological processes of life. In plants, over 80 families containing 2,000~5,000 TFs or transcriptional regulators have been identified. Here, we identified 2,232 TFs or transcriptional regulators representing 84 families in Capsicum annuum ‘CM334’ draft genome sequence. They comprise 6.3 percent of the total predicted proteins, and the ratio is the similar level as that of other flowering plants. Among them, WRKY TFs have been implicated in regulating diverse plant development and defense system such as germination, senescence, and response to biotic and abiotic stresses. We identified 77 WRKY TFs in pepper genome, compared to 81, 85, 59, 72 and 94 in the genome of tomato, potato, grapevine, arabidopsis and rice, respectively. A phylogenetic analysis was performed using all predicted WRKY domains from the 6 species above, and most of them were grouped into I, IIa-e, III as it is known. However, 2, 9, and 8 WRKY TFs in pepper, tomato, and potato were branched out into specific group. In addition, some WRKY TFs in pepper and tomato showed specific expression pattern in digital expression analysis suggesting functions of development or ripening. In-depth studies in other TFs relevant to plant biological processes are in progress. These data could provide valuable information for diversity and function of TFs in pepper and other Solanaceous species.