Genome-Wide Identification and Characterization of the CBL Gene Family in Ziziphus jujuba var. spinosa

Background: Calcineurin B-like (CBL) protein-mediated calcium signaling represents a core regulatory pathway underlying plant abiotic stress adaptation. Ziziphus jujuba var. spinosa (sour jujube) is a perennial woody species with remarkable saline–alkali and drought tolerance, yet the CBL gene family in this species has not been systematically characterized. Methods: We performed genome-wide identification and characterization of the CBL gene family in sour jujube through integrated bioinformatic analyses, transcriptomic profiling, qRT-PCR, and yeast two-hybrid (Y2H) assays, with the annotation of one gene manually corrected based on molecular cloning and transcriptome validation. Results: Ten non-redundant ZjCBL genes were identified and grouped into three phylogenetic clades. Synteny and selection pressure analyses identified two collinear gene pairs that have undergone strong purifying selection. All ZjCBL proteins contain canonical EF-hand motifs and are predicted to be mainly localized to the plasma membrane, with ZjCBL4 and ZjCBL9 harboring additional N-terminal transmembrane helices. The promoter regions of ZjCBL genes are enriched in hormone- and stress-responsive cis-acting elements. ZjCBL1, ZjCBL2, ZjCBL3, and ZjCBL5 were highly expressed across multiple tissues, and ZjCBL1 exhibited sustained upregulation under long-term saline–alkali stress, concurrent with the accumulation of osmoprotectants. Y2H assays confirmed that ZjCBL1 interacts with two ZjCIPK proteins, exhibiting a stronger interaction signal with ZjCIPK13. Conclusions: This study provides the first systematic characterization of the CBL gene family in sour jujube and revises the annotation of ZjCBL1, establishing ZjCBL1 as an important component of the ZjCBL–ZjCIPK signaling network and offering candidate gene resources for molecular breeding to enhance stress tolerance in fruit crops.