Subgenome-Resolved Analysis and Regulatory Divergence of UDP-Glycosyltransferases in Allotetraploid Panax ginseng

Abstract

Background: Polyploidization generates extensive gene redundancy, but how duplicated metabolic genes are retained and subsequently diversified remains poorly understood. UDP-glycosyltransferases (UGTs) provide a suitable system for examining this process because they participate in specialized metabolism, plant development, and environmental responses. This study aimed to characterize the retention, expansion, and regulatory divergence of the UGT family in allotetraploid Panax ginseng at subgenome resolution. Methods: We integrated telomere-to-telomere (T2T) genome annotation, phylogenetic and chromosomal analyses, duplication classification, collinearity and Ka/Ks analyses, promoter cis-acting element prediction, developmental co-expression networks, and transcriptomic responses to biotic and abiotic treatments. Results: A total of 212 PgUGT genes were identified, including 104 and 108 members in the A and B subgenomes, respectively. The family exhibited an overall near-mirrored retention pattern between the two subgenomes, accompanied by local copy-number asymmetry. Whole-genome and segmental duplication accounted for 64.2% of the family, and 99.5% of the gene pairs with valid Ka/Ks estimates had values below 1, suggesting pervasive purifying selection. PgUGT-containing co-expression modules were associated with bud, stem, leaf, and fruit developmental conditions, while promoter cis-acting element compositions exhibited member-specific variation. Transcriptional responses to fungal pathogens and abiotic, hormone, and chemical treatments were concentrated in particular members and local gene arrays rather than being coordinated across entire clades or subgenomes. Conclusions: The PgUGT family is characterized by extensive ancestral copy retention accompanied by local copy-number changes and copy-specific regulatory divergence. These findings provide a subgenome-resolved framework for understanding UGT family evolution in allotetraploid ginseng and prioritize candidate PgUGT genes for subsequent functional validation.