Genome-Wide Characterization and Multi-Omics Integration Identify Candidate UDP-Glycosyltransferase Associated with Flavonoid Diversification During Pineapple Fruit Development

UDP-dependent glycosyltransferases (UGTs) are a large and diverse enzyme family involved in the modification and diversification of plant secondary metabolites, including flavonoids associated with fruit nutritional value and quality traits. However, the evolutionary organization of UGT families and their associations with flavonoid metabolism remain insufficiently characterized in tropical monocot fruit crops. Here, we performed a genome-wide characterization of the UGT family in pineapple (Ananas comosus) and integrated transcriptomic and metabolomic information to prioritize AcUGT candidates associated with flavonoid accumulation. A total of 68 AcUGT genes were identified and classified into 16 phylogenetic clades. Comparative genomic analyses demonstrated conserved syntenic relationships with other monocots, while tandem and segmental duplication contributed to AcUGT family expansion under predominant purifying selection. Structural analyses revealed conservation of the C-terminal plant secondary product glycosyltransferase (PSPG) motif involved in UDP-sugar recognition, whereas N-terminal sequence diversification distinguished AcUGT members. Promoter analysis identified cis-regulatory elements associated with hormone, developmental, environmental, and secondary metabolism responses. Integration of transcriptomic and metabolomic datasets revealed stage- and cultivar-associated AcUGT expression patterns that were statistically associated with flavonoid profiles. Candidate prioritization based on phylogeny, developmental or cultivar specificity and transcript–metabolite associations highlighted AcUGT29, AcUGT02, and AcUGT51 as high-priority candidates for future functional investigation. This study provides a genomic and metabolic framework for investigating UGT-associated flavonoid diversification and for guiding subsequent functional and fruit-quality studies in pineapple.