Figure 2. Transcript expression differentiation between land and water form of Riccia fluitans
A. The barplot depicts the GO annotation distribution for genes exhibiting statistically significant expression differences. The 20 most enriched GO terms were presented. The bars represent the number of genes involved in a particular process. The colors correspond to different adjusted p-values.
B. The dotplot illustrates the correlations between statistically significant transcripts from nanopore sequencing and transcripts from Illumina sequencing. The x-axis represents log2FoldChange values for nanopore sequencing, while the y-axis depicts log2FoldChange values for Illumina sequencing. The red line highlights the Pearson correlations. The R value is displayed in the upper left corner.
C. The MA plot visualizes the association between log2FoldChange and log2 from the average of normalized counts. The x-axis displays the log2 of the average of the normalized transcript counts, while the y-axis illustrates the log2FoldChange for the transcript. Squares represent irrelevant transcripts, triangles represent upregulated transcripts, circles represent downregulated transcripts, and the green color indicates DELs, red indicates DETs, blue indicates other RNA, and gray indicates no significant transcripts.
D. A circular chart depicting two circular heatmaps representing the expression levels of significant genes in eight samples encompassing four terrestrial and four aquatic forms of Riccia fluitans . The heatmaps correspond to Illumina-intersected DETs (Intersected DETs) and unique DETs to Nanopore (Nanopore DETs). The green-white-red color scale represents Nanopore DETs, while the blue-white-red color scale signifies intersected DETs. The subsequent track exhibits a heatmap showcasing purple for DETs, gold for other RNA, and light blue for DELs. The third track illustrates the differential expression values (log2FoldChange) between upregulated (red) and downregulated (blue) genes in each comparison group. The inner heatmap depicts the p-value adjusted for each gene.
E. Incongruent results of SBS and direct RNA DEG analysis. Gene evm.model.group2.1430 of unknown function (containing fasciclin-like domain) is downregulated in water form based on SBS RNA-seq analysis and upregulated in nanopore direct RNA sequencing.