The anthracnose caused by Colletotrichum gloeosporioides poses a significant threat to the global mango (Mangifera indica L.) fruit industry. Although histone deacetylases (HDACs) are well recognized to be involved in plant immunity, the role of HDAC-mediated nonhistone deacetylation in the fruit immune response remains elusive. In the present study, MiHDA3, an HDAC from the RPD3/HDA1 subfamily, was identified as a candidate for regulating mango resistance based on the greatest induction of MiHDA3 in response to infection of C. gloeosporioides among the 19 tested HDAC genes. Transient overexpression of MiHDA3 in mango fruit strengthened the disease resistance by enhancing the activities of defense-related enzymes (phenylalanine ammonia-lyase (PAL) and β-1,3-glucanase (GLU)) and upregulating the expression levels of MiPAL and MiGLU. These increases occurred concomitantly with increased accumulation of local H₂O₂, a critical signaling molecule. The opposite effects on resistance and H₂O₂ production were observed in MiHDA3-silenced mango fruit. Physiological assays revealed that exogenous H₂O₂ treatment suppressed anthracnose development in mango fruit after inoculation with C. gloeosporioides, whereas treatment with diphenylene iodonium, an inhibitor of endogenous H₂O₂ generation, exacerbated disease symptoms. Furthermore, the mango catalase 1 (MiCAT1), a redox homeostasis-related protein, was confirmed to negatively regulate the resistance of mango fruit to C. gloeosporioides by catalyzing the decomposition of H₂O₂. Mechanistic investigations revealed that MiHDA3-mediated deacetylation of MiCAT1 at lysine residues K227 and K233 reduced the enzymatic activity and protein stability of MiCAT1, contributing to enhanced resistance in mango fruit. Collectively, these findings highlight that the functional interplay between HDACs and catalases can modulate the immune response in post-harvest fruits, and reveal a novel mechanism by which HDACs enhance mango disease resistance through the deacetylation of nonhistone proteins and the regulation of their biochemical functions.

The domains rearranged methyltransferases (DRMs) play a critical role in the RNA-directed DNA methylation (RdDM) pathway in plants. However, the effects of inactivating the RdDM pathway on gene expression, transposable element (TE) activity, and phenotype in soybean remain unexplored. Here, we employed clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 gene editing to generate a quintuple mutant line in soybean (Gmdrm2a^-/-2b^-/-2c^-/-3a^-/-3b^-/-, designated Gmdrm). Gmdrm exhibited severe developmental abnormalities, including dwarfism and delayed growth, albeit remaining viable and fertile; however, the fully homozygous mutant could be maintained for a limited number of generations (T0-T3). Whole genome bisulfite sequencing revealed a significant reduction in DNA methylation across all cytosine sequence contexts, with an average loss of 10%. The loss of ^mC was biased toward euchromatic regions, which is in contrast to the chromomethylase mutant. Transcriptome profiling identified 1,685 up-regulated genes, including photosynthesis-related genes, accompanied with altered chloroplast ultrastructure. Additionally, a cluster of resistance (R) genes on chromosome 16 was significantly up-regulated, coinciding with their reduced non-CG methylation. We also observed 3,164 differentially expressed TEs (DETs), of which, 2,655 were up-regulated and hypomethylated along their entire length. A substantial reduction in the abundance of 24-nt small interfering RNAs (siRNAs) in the Gmdrm mutant was detected by small RNA sequencing. Of note, the DRM-targeted TEs typically display higher levels of 24-nt siRNA abundance, shorter lengths, and are more AT-rich compared to chromomethylase-targeted TEs, highlighting 24-nt siRNAs as key determinants of DRM-dependent TE regulation. Together, this study documents a critical role of DRM-mediated DNA methylation in regulating gene expression, TE silencing, and normal development in soybean.