Fig. 1

Identification and characterization of lncRNAs in Arabidopsis. (A) Pie chart showing the numbers and proportions of annotated transcripts from Araport11 (orange) and novel transcripts from nanopore DRS transcriptome assembly (green). (B) Bar chart exhibiting the proportions of lncRNA categories in novel lncRNAs (from nanopore DRS assembly) and annotated lncRNAs (from Araport11) according to their genomic positions relative to their neighbouring protein-coding RNAs. (C) Box plot comparing the coding probabilities among novel lncRNAs (blue), annotated lncRNAs (green) and annotated protein-coding RNAs (red). The coding probabilities of lncRNAs were close to 0 and were significantly inferior to those of protein-coding RNAs, which were close to 1 (Mann-Whitney U test; ***, p < 0.001). (D) Density plot presenting the distributions of transcript lengths of novel lncRNAs (blue), annotated lncRNAs (green) and annotated protein-coding RNAs (red). LncRNAs tended to be shorter than protein-coding RNAs. (E) Histogram comparing the exon numbers among novel lncRNAs (blue), annotated lncRNAs (green) and annotated protein-coding RNAs (red). The majority of lncRNAs had fewer than two exons, while protein-coding RNAs had a broader range of exon numbers. (F) Violin plot comparing the GC contents among novel lncRNAs (blue), annotated lncRNAs (green) and annotated protein-coding RNAs (red). The GC contents of lncRNAs were significantly lower than those of protein-coding RNAs (Mann-Whitney U test; ***, p < 0.001)