Evolutionary Conservation and Regulatory Characteristics of SF3B3 in Plants

Pre-mRNA splicing is essential for eukaryotic gene expression, and alternative splicing contributes substantially to plant development and stress adaptation. Splicing factor 3B subunit 3 (SF3B3), a core component of the U2 snRNP complex, is required for spliceosome assembly, but its evolutionary and functional features in plants remain poorly understood. Here, we performed a comprehensive analysis of plant SF3B3 genes using comparative genomics, phylogenetics, gene structure and motif analysis, alternative splicing profiling, promoter analysis, expression assays, subcellular localization, and protein interaction validation. We identified 105 SF3B3 genes from 71 plant species and found that SF3B3 is highly conserved in plants, especially in land plants, with most genes showing a typical three-exon/two-intron structure and conserved MMS1_N and CPSF_A domains. Intron retention was the major alternative splicing event detected. Moreover, SF3B3 was predominantly localized in the nucleus and interacted with SF3B5 and SF3B14, supporting its conserved role in processes associated with the spliceosome. These results provide a framework for understanding the conservation and functional diversification of SF3B3 in plants.