Genome-wide identification and expression profiling of the histone deacetylase gene family in Fusarium oxysporum

Histone deacetylases (HDACs) are key epigenetic regulators governing chromatin structure and gene expression, playing critical roles in growth, development, virulence, and multi-stress resistance of plant-pathogenic fungi. Despite their importance, the HDAC gene family (FoHDACs) in <i>Fusarium oxysporum</i> remains poorly characterized. Through genome-wide analysis, we identified 11 <i>FoHDAC</i> genes, phylogenetically classified into three subfamilies: Class I (2 genes), Class II (2 genes), and SIR2 (7 genes). Subcellular localization predicted 6 in the nucleus, 3 in the cytoplasm, and 2 in mitochondria, indicating functional diversity across organelles. Structural analyses revealed conserved domains/motifs specific to each subfamily. Genes showed asymmetric distribution across 6 chromosomes with no recent duplication events. Promoter analysis identified 22 putative <i>cis</i>-elements, including antioxidant (ARE, as-1) and stress response elements (STRE), linking FoHDACs to development and environmental responses. Functional annotation highlighted putative roles in transcriptional regulation, macromolecular catabolism, and heterochromatin assembly beyond core HDAC activity. Molecular docking showed binding affinities < -5 kcal/mol with significant differences across subfamilies. RT-qPCR revealed stage-specific expression: 8 genes peaked in dormant conidia, were suppressed during germination, and recovered during growth/sporulation; 2 showed continuous activation, and 1 was sporulation-specific. Abiotic stresses induced stimulus-dependent regulation, e.g., 33.67-fold repression of <i>FoHST3</i> under salt stress and > 100-fold induction of <i>FoHOS3</i> under cold stress. Collectively, our findings reveal that FoHDACs exhibit substantial functional diversity, forming a sophisticated regulatory network mediating fungal development and environmental adaptation.