A conserved structural framework accompanies evolutionary divergence and expression specialization in the grapevine...

S-phase kinase-associated protein 1 (SKP1) proteins are conserved adaptor components of SCF E3 ubiquitin ligase complexes that connect F-box proteins with the CULLIN1 scaffold. Although SKP1-mediated regulation is essential for diverse plant processes, the evolutionary diversification and regulatory specialization of SKP1 family members in grapevine remain poorly understood.

In this study, genome-wide identification, structural characterization, phylogenetic analysis, promoter analysis, transcriptome profiling, and subcellular localization assays were integrated to investigate the diversification of the grapevine SKP1 family.

Eleven VvSKP1 genes were identified in Vitis vinifera and characterized at structural, evolutionary, regulatory, and expression levels. Although individual VvSKP1 members displayed differences in protein architecture and evolutionary relationships, most retained conserved SKP1-like motifs and structural features, indicating preservation of a common molecular framework. Phylogenetic analysis across eight representative angiosperms revealed three major SKP1 lineages and suggested lineage-specific diversification among retained family members. Promoter analyses revealed distinct transcription factor-binding landscapes among VvSKP1 genes, and grapevine TF DAP-seq datasets identified potential MYB-associated regulation of specific members. Transcriptome analyses across diverse grapevine tissues and floral organs revealed expression specialization among VvSKP1 genes, with VvSKP1-9 and VvSKP1-11 showing preferential expression in anther-associated tissues. Despite evolutionary and regulatory divergence, all tested VvSKP1 proteins predominantly localized to the nucleus.

These findings reveal a conserved structural framework underlying the grapevine SKP1 family while highlighting diversification in evolutionary relationships, promoter regulatory potential, and tissue-associated expression patterns. This study provides a comprehensive resource for understanding SKP1 family diversification and establishes candidate VvSKP1 members for future functional studies of SCF ubiquitin ligase complexes in grapevine.