Genome-Wide Identification and Characterization of the Bromodomain Gene Family in Olive (Olea europaea) and Its Association with Salt Stress Responses

Bromodomain (BRD) proteins are evolutionarily conserved epigenetic readers that bind acetylated lysine residues on histone tails, linking chromatin remodeling to transcriptional regulation and abiotic stress adaptation. Although salinity is among the most economically damaging abiotic stresses worldwide, the bromodomain-level epigenetic mechanisms underlying salt tolerance in the perennial crop olive (Olea europaea L.) remain unstudied. This study aimed to identify and characterize the complete Olea europaea bromodomain (OeBRD) gene family in olive, resolve its evolutionary relationships with Arabidopsis thaliana, and identify candidate genes potentially associated with salt-stress responses. Genome-wide identification, physicochemical characterization, promoter cis-regulatory element analysis, phylogenetic reconstruction, orthogroup clustering, conserved-motif and gene-structure analysis, AlphaFold3 structural modeling, RNA sequencing (RNA-seq) data (BioProject PRJNA841838) from control, primed (75 → 150 mM NaCl) and non-primed (150 mM NaCl) plants, and Search Tool for the Retrieval of Interacting Genes/Proteins (STRING)-based protein–protein interaction (PPI) and Gene Ontology (GO) enrichment analyses were performed. Twenty-one non-redundant OeBRD genes were identified in the O. europaea genome (GCF_002742605.1), with molecular weights of 43,076–242,620 Da, isoelectric points of 5.05–9.67, and universally negative grand average of hydropathicity (GRAVY) values. Phylogenetic analysis resolved four clades, including olive-specific paralog groups, and orthogroup clustering against A. thaliana identified 16 orthogroups, eight of which are strict 1:1 orthologs, five show copy-number differences between the two species (more copies in olive in three groups, including OeBRD6a/6b/6c, and more copies in Arabidopsis in two), one is a balanced 2:2 group and two contain only Arabidopsis genes. Multiple Em for Motif Elicitation (MEME) analysis identified 10 conserved motifs. Promoter analysis revealed abundant abscisic acid (ABA)-, myeloblastosis (MYB)/myelocytomatosis (MYC)- and jasmonate-responsive cis-elements. DESeq2 differential expression analysis of primed (75→150 mM NaCl) and non-primed (150 mM NaCl) plants relative to untreated controls identified four of the 21 OeBRD genes as significantly differentially expressed (adjusted p < 0.05): OeBRD6b, OeBRD6c, OeBRD10 and OeBRD26 were up-regulated in primed roots, OeBRD26 was also up-regulated in non-primed roots and non-primed leaves, and no gene was significant in primed leaves; STRING PPI analysis identified OeBRD24 and OeBRD13 as the most connected nodes in a network inferred from Arabidopsis orthologues, with chromatin, chromatin remodeling and histone acetyltransferase activity among the most significantly enriched GO terms. Ten proteins—OeBRD26, OeBRD6c, OeBRD6b, OeBRD10, OeBRD13, OeBRD24, OeBRD11, OeBRD16, OeBRD28 and OeBRD29—were prioritized as candidates for future experimental validation of a possible role in salt-stress responses in olive.