Late blight, caused by the oomycete Phytophthora infestans, is one of the most destructive diseases affecting potato production globally. However, the function of DNA methylation (DNAm) and its association with simultaneous alteration in gene expression in potato’s response to P. infestans infection remain largely unknown. Here, we conducted whole-genome bisulfite sequencing and RNA sequencing on potato cultivar Qingshu No.9 inoculated with P. infestans. Significantly, we identified 18 119 differentially expressed genes (DEGs) across at least one of the four post-inoculation time points. A few pathogenesis-related (PR) genes involved in salicylic acid, ethylene signaling, and DNAm regulation exhibited activation at early infection stages, although they were predominantly downregulated after the onset of necrosis in plants. Hypomethylation changes at 12 h post-inoculation (hpi) were followed by hypermethylation at 24 hpi, with CHH methylation being the primary factor influencing the DNAm pattern. Differentially methylated regions (DMRs) showed significant enrichment at DEGs. Specially, DNAm variations could be associated with subsequent transcriptional changes. This is exemplified by 24 h-hyper-CHG methylation at the gene body that correlates with expression downregulation at 48 hpi, including genes involved in chromatin remodeling pathways. Furthermore, we observed a significant enrichment of hypomethylation changes at the exon of NB-LRR genes, which ultimately resulted in their downregulation. In summary, we have elucidated the DNAm pattern of potato in response to infection by P. infestans, and identified the involvement of epigenetic mechanisms in the reprogramming of the transcriptome, which ultimately contributed to the suppression of immunity and the development of potato late blight.

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