Comprehensive genomic identification and expression analysis of the U-box gene family and its association with pigment biosynthesis in pepper (Capsicum annuum L.)

Plant U-box E3 ubiquitin ligases play important roles in plant growth and development, and have been extensively studied among various plants, but limited research has been conducted in pepper (Capsicum annuum L.). Here, we identified and characterized 55 U-box genes in the pepper genome, which were classified into 10 groups according to phylogenetic analysis, which was also supported by the conserved motifs and gene structural features. Each group contained different numbers of CaU-box genes. Cis-acting element analysis showed that various numbers of cis elements were predicted in the promoter regions of these genes. The expression levels of most of the CaU-box genes in the pericarp or placenta varied significantly during fruit development. In response to continuous dark and low-temperature (20 °C) treatments, most of the CaU-box genes exhibited significant changes in expression in the pericarp and placenta, respectively. Expression correlation analyses using the nonparametric Spearman correlation method revealed a significant association between CaU-box29/38/54 genes and Ca10g18500, as well as chlorophyll and flavonoid synthesis-related genes CaCPOX/CaF3H, which indicated that the protein ubiquitination pathway is involved in pigment biosynthesis. This study provides valuable insights into the functional roles of CaU-box genes and lays a foundation for future research on their involvement in pigment homeostasis.