2.7. Functional annotations of DEGs, DETs, methylation, polyadenylation and non-adenine profiles
All DEGs, DETs, transcript with significant polyA tail difference and methylation profile changes were annotated by blastp v.2.12.0 .Due to a lot of Marchantia polymorpha gene symbol annotations are incomplete and uncharacterized in databases, the identification process of Riccia fluitans translated genes/transcripts was based onArabidopsis thaliana protein sequences. For blastp homology searching an e-value < 10e-5 was set as the cut-off threshold. This comparison facilitated the acquisition of descriptions and symbols for newly annotated Riccia proteins. The resulting gene signatures, DEG, DET and other epitranscriptome candidates were subsequently scanned for enrichment in Gene Ontology (GO) function annotations using g:Profiler v.0.2.2 R library . Biological processes (BP), cellular components (CC), and molecular functions (MF) were annotated as ontological terms for the essential genes. Enrichment analysis with a false discovery rate (FDR) cut-off <0.05 was employed to identify GO and pathway annotations regulated by differentially genes. The funkctional connection between DEG, DET and other epitranscriptome modifications of Riccia fluitans were visualized by highlighting those events using the ggplot2 R package.