| Summary: | Pomegranate (<i>Punica granatum</i> L.) is regarded as one of the functional fruits because of its large amounts of secondary metabolites. The glycosylation processes mediated by UDP-glycosyltransferases (UGTs) play a decisive role in regulating secondary metabolite availability. In this study, a genome-wide search identified 145 <i>UGT</i> genes in pomegranate, and further phylogenetic analysis defined 17 distinct groups: A to P and R. <i>PgUGT</i>s were dispersed unevenly across all eight chromosomes. Duplication events analysis revealed that both segmental and tandem duplications were the main mechanisms leading to gene family expansions. The comparison of exon–intron patterns identified 53 intron-less genes. A total of 24 types of cis-acting elements related to hormone, stress, and developmental responses were predicted in the promoter regions. Expression analysis of <i>PgUGT</i> genes using RNA-seq data and quantitative real-time PCR (qRT-PCR) verification suggested that <i>PgUGT</i> genes were expressed at specific stages of fruit development, and different <i>PgUGT</i> members likely played different roles in specific fruit developmental stages. In an attempt to identify the <i>UGT</i>s involved in the glycosylation of flavonoids, 44 <i>PgUGT</i>s were putatively determined, and 5 well-defined orthologous groups (OGs) were characterized by the regioselectivity of these enzymes. These results provide significant insight into the <i>UGT</i> multi-gene family in pomegranate, and will be helpful to further elucidate their roles involved in secondary and specialized metabolism in pomegranate.
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