The role of 6mA methylation in organellar genomes of Riccia fluitans

DNA N6-methyladenine (6mA) has recently emerged as an important epigenetic mark associated with transcriptional regulation and stress adaptation in plants. However, its role in organellar genomes remains poorly understood, especially in early-diverging lineages. The amphibious liverwort Riccia fluitans offers a unique opportunity to investigate environmentally induced epigenetic plasticity, as it can reversibly transition between terrestrial and aquatic morphotypes. Using Oxford Nanopore native DNA sequencing, we profiled 6mA methylation across chloroplast and mitochondrial genomes of Riccia fluitans cultivated under aquatic and terrestrial conditions, and integrated these data with RNA-seq–based gene expression profiles. We identified 6mA methylation sites characteristic of each habitat, with a markedly higher frequency of methylation in the aquatic form. Several differentially expressed genes (e.g., accD, psbA) were co-located with environment-specific methylation sites, suggesting potential spatial association between differential methylation and gene expression. Our results provide the first evidence of environmentally responsive organellar 6mA methylation in a bryophyte, highlighting a previously unrecognized layer of epigenetic control that may contribute to the adaptive plasticity of early land plants.