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.