Characterization and expression analysis of UBC gene family provide insights into the potential roles in pigment biosynthesis in pepper fruit

<h4>Background</h4>Ubiquitin-conjugating enzymes (UBCs) are a critical part of the ubiquitin-proteasome pathway and play diverse roles in growth, development, and abiotic stress responses in pepper (Capsicum annuum L.). Although UBC genes have been reported in several plant species, genome-wide characterization of this gene family remains unexplored in pepper.<h4>Results</h4>In this study, 56 putative CaUBCs were identified in pepper, which were clustered into 11 groups based on phylogenetic analysis, including ubiquitin E2 enzyme variant (UEV), SOMO (HUS), and COP10. CaUBCs within each subgroup showed relatively conserved domains and motifs. Most CaUBC genes contain plenty of light or stress response elements. qRT-PCR analysis demonstrated distinct expression patterns of CaUBCs in the pericarp and placenta during fruit development, as well as in response to light/dark transitions and low-temperature treatments. In a natural open-pollinated population, strong associations were observed between CaUBC33/43 and the chlorophyll biosynthesis gene CaCPOX, as well as between CaUBC33 and Ca06g24560 (r = 0.7531, p < 0.0001) or Ca00g64500 (r = 0.6287, p < 0.0001). These findings suggest that the protein ubiquitination pathway is involved in fruit pigment metabolism in pepper. This study provides critical insights into the functional roles of CaUBC genes in pigment biosynthesis and lays a solid foundation for further investigations into the molecular mechanisms regulating pigment homeostasis.<h4>Conclusions</h4>The genome-wide analysis of UBC E2 ligases provides essential genomic resources for functional studies on UBC genes and is significant for the molecular breeding of pepper.