Genome-wide characterization, identification, and expression analysis of the WD40 protein family in cotton.

WD40 repeat proteins are largely distributed across the plant kingdom and play an important role in diverse biological activities. In this work, we performed genome-wide identification, characterization, and expression level analysis of WD40 genes in cotton. A total of 579, 318, and 313 WD40 genes were found in Gossypium hirsutum, G. arboreum, and G. raimondii, respectively. Based on phylogenetic tree analyses, WD40 genes were divided into 11 groups with high similarities in exon/intron features and protein domains within the group. Expression analysis of WD40 genes showed differential expression at different stages of cotton fiber development (0 and 8 DPA) and cotton stem. A number of miRNAs were identified to target WD40 genes that are significantly involved in cotton fiber development during the initiation and elongation stages. These include miR156, miR160, miR162, miR164, miR166, miR167, miR169, miR171, miR172, miR393, miR396, miR398, miR2950, and miR7505. The findings provide a stronger indication of WD40 gene function and their involvement in the regulation of cotton fiber development during the initiation and elongation stages.