Riccia_fluitans_annotations.gtf

Abstract
Background
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.

Results
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, enablingRiccia fluitansto fine-tune gene expression in response to its living conditions.

摘要
背景
浮苔（Riccia fluitans）是一种两栖苔类植物，拥有精妙的适应机制以实现陆生与水生环境间的转换。本研究采用纳米孔直接RNA测序（nanopore direct RNA sequencing）技术，旨在捕捉其在水陆转换过程中发生的复杂表观转录组变化。

结果
本研究的核心发现为鉴定得到45个差异表达基因（differentially expressed genes, DEGs），其中陆生型有33个基因表达下调，水生型有12个基因表达上调，表明该植物对环境变化存在强烈的转录响应。对N6-甲基腺嘌呤（N6-methyladenosine, m6A）修饰的分析显示，水生型样本中共检测到173个m6A修饰位点，而陆生型仅检测到27个，表明前者的甲基化水平显著升高，这可能有助于其快速适应环境变化。水生型样本的poly(A)尾呈现全局延长偏好，这与mRNA稳定性提升及翻译效率增强相关，可提高植物应对水分胁迫的抗逆能力。两种生态型的多聚腺苷酸化信号存在显著差异，其中9个转录本的尾长发生显著变化，这表明存在一种适应性机制，可通过调控mRNA稳定性与翻译效率来响应环境条件。这种差异化的甲基化与多聚腺苷酸化模式，揭示了一套精细的转录后调控层级，使得浮苔能够根据生存环境精准调控基因表达。