Characterization and evolution of the GH3 gene family in Nymphaea colorata

Introduction Gretchen Hagen 3 ( GH3 ) genes play important roles in auxin homeostasis, plant development, and stress responses. However, their characterization and evolutionary history in early-diverging angiosperms remain poorly understood. Methods Here, we performed a genome-wide identification and comparative evolutionary analysis of the GH3 gene family in the early-diverging flowering plant Nymphaea colorata . Phylogenetic classification, conserved motif and gene structure analyses, promoter cis-element prediction, regulatory network inference, expression profiling, and duplication/selection analyses across 22 plant species were conducted. Results A total of 27 GH3 genes were identified in N. colorata and classified into three conserved groups, with 23 NcGH3 genes assigned to Group 2. Promoter analysis revealed abundant hormone-related and light-responsive cis-elements in NcGH3 promoters, and regulatory network prediction suggested that Dof transcription factors may act as candidate regulators of NcGH3 genes. Expression analysis showed that most NcGH3 genes were preferentially expressed in floral organs, including petals, sepals, stamens, juvenile flowers, and carpels. Comparative analysis across 22 plant species indicated that Group 1 represents the most ancestral GH3 lineage, whereas Groups 2 and 3 emerged later during plant evolution. Group-specific expansion was observed in several species and was mainly associated with whole-genome/segmental duplication and tandem duplication events. Conclusion These findings provide a comprehensive overview of the GH3 gene family in N. colorata and offer new insights into the evolutionary diversification and subgroup-specific expansion of GH3 genes in plants.