Comparative view of DNA methylation in stramenopiles and other eukaryotes: Focus on 5-methylcytosine

This review provides a comparative analysis of DNA methylation patterns, enzymes, and functions in stramenopiles (diatoms, brown algae, oomycetes) and other eukaryotes. Given the ecological and evolutionary importance of stramenopiles, and the relatively limited and fragmented literature on their epigenetic regulation, a comparative synthesis of DNA methylation patterns and mechanisms in this group is both timely and necessary. By integrating current knowledge on DNA methylation in stramenopiles, this review provides a conceptual foundation for exploiting epigenetic mechanisms to enhance stress resilience, growth performance, and environmental adaptability in aquaculture species. Therefore, we synthesize genomic and epigenetic studies to examine the distribution of DNA methyltransferases (DNMTs) and the roles of DNA methylation in adaptation, phenotypic regulation, and life cycle transitions. All DNA methyltransferases (DNMT1, 2, 3, 4, 5, and 6), along with related enzymes such as the repeat-induced protein-deficient family, exhibit homology and therefore appear to share a common ancestor. Stramenopiles are reported to possess DNMT2, DNMT3, DNMT5, and DNMT1-like DNA methyltransferases. Phylogenetic analyses show that DNMT1-like enzymes in stramenopiles constitute a lineage distinct from canonical DNMT1 and DNMT4. Genomic analyses of brown algae reveal absent or very low DNA methylation levels (