Genome-wide identification, phylogenetic analysis, and functional prediction of histone deacetylase genes in Spinacia oleracea L

Official URL: https://dx.doi.org/10.1007/s40415-024-00995-z

Histone deacetylation process is controlled by histone deacetylases (HDAs), which catalyze removal of an acetyl group from the lysine residues of histone N-terminal tails. Although the HDAs are known to be involved in stress response and development in model plants, little is known about the roles of HDAs in crop species. Up to date, the HDAs in spinach (Spinacia oleracea L.) have not been identified and characterized. Here, we carried out genome-wide identification of HDA gene family in spinach, including physicochemical properties, subcellular localization prediction, phylogenetic analysis, conserved motifs, gene structure, Ka/Ks ratio, synteny analysis, functional prediction through cis-acting elements, and protein–protein interaction. Totally, six HDAs were identified from the spinach genome, and named SoSRT1, SoSRT2, SoHDA1, SoHDA2, SoHDA3, and SoHDA4. The phylogenetic tree showed that spinach HDAs were divided into four clades (Class I, Class II, RPD3-like, SIR2). RPD3/HDA1 family proteins and RPD3-like protein consisted of motif 1, Hist_deacetyl domain (PF00850), while two SIR2 class proteins included SIR2 domain (PF02146). Subcellular localization analysis indicated that the SoSRT and SoHDA proteins might localize in cytoskeleton, peroxisome, nucleus, and cytosol. SoSRT1 and SoSRT2 were located on chromosome 1, and the remaining four genes (HDA1-4) were distributed on chromosome 6. Ka/Ks ratio was lower than 1, suggesting that HDA genes might undergo purifying selection during evolution. Analysis of cis-acting elements revealed that the SoHDA genes participate in hormone regulation, light response, and abiotic stress response. New insights into the potential roles of histone deacetylases will be gained from this study in spinach, which is a cold-tolerant/heat-sensitive vegetable.