4. Conclusions
The comprehensive study on Riccia fluitans utilizing nanopore direct RNA sequencing has unveiled critical insights into the plant’s transcriptomic adjustments in response to environmental transitions between terrestrial and aquatic habitats. Analysis of native mRNA sequences revealed variations in poly(A) tail lengths, m6A modifications, and differential expression profiling, which collectively underscore the complex regulatory mechanisms Riccia fluitansemploys to adapt to changing environments. The identification of specific transcripts with altered poly(A) tail lengths and m6A modifications suggests a fine-tuned post-transcriptional regulatory layer that responds to environmental cues. The differential poly(A) tail length, particularly in transcripts involved in stress responses and metabolic processes, indicates a strategic modulation of mRNA stability and translational efficiency as an adaptation strategy. Similarly, the variability in m6A modifications, especially in transcripts coding for ribosomal proteins and enzymes, hints at a sophisticated mechanism to adjust mRNA processing, translation, and decay in response to aquatic versus terrestrial conditions. The differential expression analysis further complements these findings by highlighting genes that are upregulated or downregulated depending on the environment. The downregulation of specific genes in terrestrial conditions and upregulation in aquatic conditions reflects a robust transcriptional response to environmental stresses and challenges. This differential expression not only pertains to coding RNAs but also to long non-coding RNAs and other RNA types, suggesting a broad and integrated gene regulatory network that encompasses various RNA molecules.