N6-methyladenosine (m6A) is a dynamic and reversible RNA modification governed by the tripartite machinery of writers, erasers, and readers, which plays crucial roles in plant adaptation to environmental stresses. However, the repertoire and function of m6A machinery in pepper (Capsicum chinense) remain uncharacterized. Here, we performed a genome-wide identification of m6A regulators in pepper (Ccm6As), revealing 20 high-confidence genes, comprising 6 writers, 7 erasers, and 7 readers. Comprehensive analysis of their phylogeny, conserved domains, and promoter cis-elements revealed structural conservation and a transcriptional architecture highly enriched in stress-responsive elements. Notably, in silico analysis revealed that the core catalytic writer CcMTA, the essential adaptor CcFIP37A, and the paralog CcMTB1 exhibited strong interactions, suggesting the formation of a functional methyltransferase complex. Using a comparative approach with cadmium-tolerant (CdRes-1) and cadmium-sensitive (CdSen-1) genotypes, we found that Cd stress induced a genotype-specific transcriptional reprogramming of the m6A machinery. In the tolerant genotype CdRes-1, eight regulators were significantly upregulated, whereas only CcMTA showed a modest induction in the sensitive CdSen-1. Subcellular localization experiments confirmed dual nuclear and cytoplasmic localization of CcMTA. Our findings provide a foundational epitranscriptomic resource for future functional investigations into the molecular mechanisms underlying cadmium stress responses in pepper.
Keywords: RNA methylation; cadmium stress; epitranscriptomics; gene expression; genotype-dependent response.