Evolutionary dynamics and functional divergence of the UGT gene family revealed by a pangenome-wide analysis in tomato

Abstract

UDP-dependent glycosyltransferases (UGTs) play a critical role in producing glycosylated metabolites that mediate plant-environment interactions. Recent studies have examined the role of UGT genes across various plant genomes. However, the evolutionary history and functional divergence of the UGT pan-gene family in the genus Solanum have not yet been explored. This study integrated data from 61 tomatoes and 9 representative genomes, ranging from algae to angiosperms, to identify 12,073 genes. Phylogenetic analysis trajectory the UGT gene family from unicellular algae through ferns, mosses, gymnosperms, and ultimately to angiosperms. The study identified a significant number of tomato-specific UGT genes and explored the expansions of UGT73 and UGT85 subfamilies. The entire UGT genes (10,769) in tomato were classified into 118 orthologous gene groups, including 58 core, 31 softcore, 10 dispensable, 19 private orthologous gene groups, and core groups contained 7,811 genes, representing 72.53% of total UGT genes. Analysis of gene family expansion revealed that whole-genome triplication and tandem duplication events play significant roles in the expansion of the UGT gene family. Selection pressure analysis revealed that the UGT genes experienced purifying selection in the genus Solanum. Additionally, expression profiles of some UGT genes in different tissues demonstrated expression divergence of multicopy genes across different UGT subfamilies due to the increase of gene dosage. Subcellular localization prediction revealed that most genes are localized in the chloroplast. These findings provide critical insights into the evolution and function of the UGT genes in tomato, laying a foundation for further exploration in adaptive evolution.