Epitranscriptomic and expression profiling in Riccia fluitans across diverse environmental conditions

Post-transcriptional RNA modifications, such as N6-methyladenosine (m6A), 5-methylcytosine (m5C), and pseudouridine (Ψ), are critical regulators of plant development, stress responses, and environmental adaptation. The roles of m6A, m5C, and Ψ in plant stress responses have been insufficiently explored. To investigate the epitranscriptomic landscape of these modifications, we employed direct RNA sequencing (DRS) to analyze native RNA landscape from the amphibious plant <i>Riccia fluitans</i> grown in both aquatic and terrestrial environments. Our study revealed the presence of Ψ, m5C, and m6A modifications and expression profiling in <i>R. fluitans</i> transcriptomes from diverse environments. Metabolomic profiling further demonstrated environment-dependent shifts in soluble sugars, aligning with transcriptional and epitranscriptomic changes in starch metabolism genes. Collectively, our findings highlight the dynamic regulation of RNA modifications as a crucial and previously underappreciated component of environmental adaptation in early land plants, providing new insights into the molecular basis of phenotypic plasticity and the evolutionary transition to terrestrial life.