Multi-Omics Analysis Reveals the Dynamic Changes of RNA N(6)-Methyladenosine in Pear (Pyrus bretschneideri) Defense Responses to Erwinia amylovora Pathogen Infection

N6-methylated adenine (m(6)A) is the most prevalent modification of mRNA methylation and can regulate many biological processes in plants, such as mRNA processing, development, and stress response. Some studies have increased our understanding of its various roles in model plants in recent years. Nevertheless, the distribution of m(6)A and the impact of m(6)A on the regulation of plant defense responses against pathogen inoculation are virtually unknown in pear. In this study, MeRIP-seq and RNA-seq data from healthy and inoculated plants were analyzed to assess the changes in the transcript levels and posttranscriptional modification of pear in response to the fire blight pathogen Erwinia amylovora. Following the analysis of 97,261 m(6)A peaks, we found that m(6)A preferred to modify duplicate genes rather than singleton genes and that m(6)A-methylated genes underwent stronger purifying selection. A total of 2,935 specific m(6)A sites were detected at the transcriptome level after inoculation, which may increase defense-related transcript abundance to enhance pear resistance. In addition, 1,850 transcripts were detected only in the mock-inoculated groups. The hypomethylated transcripts were mainly related to transcriptional regulation and various biological processes, such as chloroplast organization and sucrose biosynthetic processes. In addition, we found that the extent of m(6)A methylation was significantly positively correlated with the transcript level, suggesting a regulatory role for m(6)A in the plant response.