Genome-Wide Identification and Characterization of the <i>Salvia miltiorrhiza</i> Histone Deacetylase (HDAC) Family in Response to Multiple Abiotic Stresses

<i>Salvia miltiorrhiza</i> is a plant commonly used in traditional Chinese medicine. Its material bases for treating diseases are tanshinones and phenolic acids, including salvianolic acids. Histone deacetylase proteins (HDACs) are a class of specific functional enzymes that interact with acetylation groups on the N-terminal lysine of histone proteins further regulate gene transcription through structural changes at the chromatin level. HDACs involved in the growth and development of various plants, and induced by plant hormones to regulate the internal environment of plants to resist stress, at the same time affect the accumulation of some secondary metabolites. However, the role of SmHDACs on the accumulation of salvianolic acid in <i>S. miltiorrhiza</i> remains unclear. In this study, 16 SmHDACs genes were identified from the high-quality <i>S. miltiorrhiza</i> genome, their physicochemical properties were predicted. In phylogenetic trees co-constructed with HDACs proteins from other plants, SmHDACs was divided into three subfamilies, each with similar motif and conserved domain composition. The distribution of the three subfamilies is similar to that of dicotyledonous plants. Chromosome localization analysis showed that SmHDACs genes were randomly located. Cis-acting element analysis predicted that SmHDACs gene expression may be related to and induced by various phytohormones, such as MeJA and ABA. By combining the expression pattern and co-expression network induced by phytohormones, we speculate that SmHDACs may further influence the synthesis of salvianolic acid, and identified SmHDA5, a potential functional gene, then speculate its downstream target based on the co-expression network. In summary, we analyzed the SmHDACs gene family of <i>S. miltiorrhiza</i> and screened out the potential functional gene <i>SmHDA5</i>. From the perspective of epigenetics, we proposed the molecular mechanism of plant hormone promoting salvianolic acid synthesis, which filled the gap in the subdivision of histone deacetylase in <i>S. miltiorrhiza</i> research, provided a theoretical basis for the culture and transformation of <i>S. miltiorrhiza</i> germplasm resources.