Heterodimeric interaction of the C/S1 basic leucine zipper transcription factors in black raspberry: a genome-wide identification and comparative analysis

The basic leucine zippers (bZIPs) transcription factors play crucial roles in various vital biological processes and have been extensively studied across multiple species. However, their presence in the Rubus species has received limited attention. In this study, we identified 49 bZIP transcription factor genes in the genomes of black raspberry (R. occidentalis) and red raspberry (R. idaeus). Phylogenetic analysis successfully classified the bZIPs into 13 subfamilies. Comparative genomic analysis revealed a conservation of bZIP gene numbers among ten Rosaceae species, with gene duplications partially contributing to the expansion of this family in Rubus. Microsynteny analysis further supported the evolutionary conservation of this gene family among Rosaceae genomes. Tissue-specific expression of black raspberry bZIPs was observed, and gene ontology enrichment analyses revealed their involvement in various biological processes. Those members that respond to nitrogen were identified. Dimerization properties of bZIP proteins were predicted based on the amino acid composition of their coiled-coil domains. Protein interaction network analysis and yeast two-hybrid assays unveiled the formation of heterodimers between the S1/C groups in R. occidentalis. This comprehensive characterization of the bZIP transcription factor family provides valuable insights into the evolution and functions of bZIP genes in Rubus.