Genome-wide DNA Methylation Patterns in Daphnia magna are Not Significantly Associated with Age

Studying DNA methylation in Daphnia magna, a model organism in ecological and evolutionary research, offers valuable insights into pharmaceutical toxicity and behavioral ethology. In this study, we characterized DNA methyltransferases and mapped DNA methylation across the D. magna genome using whole-genome bisulfite sequencing. Our analysis revealed a highly expressed, nonfunctional de novo methyltransferase (DNMT3.1) alongside lowly expressed functional de novo methyltransferase DNMT3.2 and maintenance methyltransferase DNMT1. D. magna displays overall low DNA methylation, targeting primarily CpG dinucleotides. Methylation is sparse at promoters but elevated in the first exons downstream of transcription start sites, with these exons showing hypermethylation relative to adjacent introns. In contrast to prior studies, we observed minimal age-related changes in DNA methylation patterns that were not sufficiently robust to build an accurate epigenetic clock. These findings expand our understanding of the epigenetic landscape in D. magna.