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 (<3%) and the presence of DNMT2, a pattern also reported in Drosophila . Oomycetes, another significant group within the Stramenopiles, appear to lack cytosine methylation. Collectively, available evidence indicates that 5-methylcytosine represents the predominant and functionally validated DNA methylation mark in stramenopiles, whereas 6-methyladenine remains comparatively sparse and lineage-specific. Despite generally lower methylation levels compared to other eukaryotes, DNA methylation in stramenopiles appears to contribute significantly to phenotypic regulation by facilitating environmentally responsive gene expression, thus providing a mechanism for adaptive plasticity. This role of DNA methylation could be harnessed to confer desirable traits for aquaculture, and to mitigate climatic conditions in the natural populations through methods like epibreeding and priming. Highlight: This review summarizes current knowledge on the presence and distribution of methylation within and across life cycle stages in this evolutionarily interesting and economically important group. • This article provides a comprehensive comparison of DNA methylation patterns between stramenopiles (brown algae, diatoms, and oomycetes) and other eukaryotes. • This emphasizes the low methylation levels (<3%) in brown algae and discusses the potential role of DNMT2 in DNA methylation, paralleling findings in Drosophila . • Explores the role of DNA methylation in adaptation, phenotypic plasticity, and its potential applications in aquaculture and climate resilience strategies.