Genome-Wide Identification and Expression Analysis of the HDAC Gene Family in Stevia rebaudiana

Histone deacetylases (HDACs) are crucial epigenetic regulators that modulate chromatin structure and gene expression through histone deacetylation. Stevia rebaudiana, a natural source of high-intensity sweeteners, faces significant cultivation challenges due to environmental stresses such as osmotic stress and salinity. However, the HDAC gene family in S. rebaudiana remains largely uncharacterized. Here, we present the first genome-wide analysis of the HDAC family in S. rebaudiana, identifying 22 SrHDAC transcripts derived from 18 gene loci, which were classified into three subfamilies (RPD3/HDA1, SIR2, and HD2). Systematic characterization of gene structure, conserved domains, and promoter cis elements indicated their potential involvement in hormone signaling and abiotic stress regulation. Expression profiling revealed tissue-specific expression patterns and differential responses to methyl jasmonate (MeJA) treatment and PEG-induced osmotic stress. Subcellular localization of representative proteins in Nicotiana benthamiana leaf cells supported nucleolar-associated functions. These findings provide a foundation for understanding HDAC-mediated epigenetic regulation in S. rebaudiana growth, development, and stress adaptation, and identify candidate genes for future functional studies toward stress-tolerant cultivar improvement.