Genome-wide identification of CaWD40 proteins reveal a novel complex (CaAN1-CaDYT1-CaWD40-91) involved in anthocyanin biosynthesis and genic male sterility in pepper (Capsicum annuum)

Abstract Background The WD40 domain, as one of the most abundant domains in eukaryotic genomes, is involved in diverse aspects of plant growth and development, secondary metabolic biosynthesis, and responses to biotic and abiotic stresses. To date, WD40 repeat (WD40) protein has been systematically studied in several model plants, but has not been reported in the pepper genome. Results In this paper, 269, 237, and 257 CaWD40 genes were identified in the Zunla, CM334 and Zhangshugang genome, respectively. Then, the CaWD40 sequences from the Zunla genome were selected for subsequent analysis, including chromosomal localization, phylogenetic relationships, sequence characteristics, motif compositions, and expression profile. Moreover, the CaWD40 proteins were unevenly distributed on 12 chromosomes, contained 19 tandem duplicate gene pairs. The 269 CaWD40s could be distinguished into six branches ( A to F), and they have 17 different types of domain distribution. The CaWD40 gene family exhibited diverse expression patterns, and several genes were specifically expressed in flowers and seeds. Finally, yeast two-hybrid (Y2H) and dual-luciferase assay indicated that CaWD40-91 could interact with CaAN1 and CaDYT1, which may be involved in anthocyanin biosynthesis and male sterility in pepper. Conclusions Overall, we have systematacially characterized phylogeny, classification, structure, expression of the CaWD40 gene family in pepper. Our findings provide a valuable foundation for further investigation on the function of WD40 genes in pepper.