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 Riccia fluitans grown in both aquatic and terrestrial environments. Our study revealed the presence of Ψ, m5C, and m6A modifications and expression profiling in R. fluitans 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.