Nanopore direct RNA sequencing provides additional insight into
transcriptome differentiation during transition to the aquatic
environment of amphibious liverwort Riccia fluitans L. (Marchantiales)
Abstract
Riccia fluitans, an amphibious liverwort, exhibits a fascinating
adaptation mechanism to transition between terrestrial and aquatic
environments. Utilizing nanopore direct RNA sequencing, we try to
capture the complex epitranscriptomic changes undergo in response to
land-water transition. A significant finding is the identification of 45
differentially expressed genes (DEGs), with a split of 33 downregulated
in terrestrial forms and 12 upregulated in aquatic forms, indicating a
robust transcriptional response to environmental changes. Analysis of
N6-methyladenosine (m6A) modifications revealed 173 m6A sites in aquatic
and only 27 sites in the terrestrial forms, indicating a significant
increase in methylation in the former, which could facilitate rapid
adaptation to changing environments. The aquatic form showed a global
elongation bias in poly(A) tails, which is associated with increased
mRNA stability and efficient translation, enhancing the plant’s
resilience to water stress. Significant differences in polyadenylation
signals were observed between the two forms, with nine transcripts
showing notable changes in tail length, suggesting an adaptive mechanism
to modulate mRNA stability and translational efficiency in response to
environmental conditions. This differential methylation and
polyadenylation underline a sophisticated layer of post-transcriptional
regulation, enabling Riccia fluitans to fine-tune gene expression
in response to its living conditions. These insights into transcriptome
dynamics offer a deeper understanding of plant adaptation strategies at
the molecular level, contributing to the broader knowledge of plant
biology and evolution.These findings underscore the sophisticated
post-transcriptional regulatory strategies Riccia fluitans
employs to navigate the challenges of aquatic versus terrestrial living,
highlighting the plant’s dynamic adaptation to environmental stresses
and its utility as a model for studying adaptation mechanisms in
amphibious plants.