Figure 3
(A) Principal components analysis (PCA). Distribution of differentially expressed genes. Three-dimensional representation according to PCA of the differentially expressed genes among the four treatments used in the RNA-Seq analysis: J2 of M. javanica exposed to protoplasts, 9-HOT, or MES + ethanol (MES + Eth), or freshly hatched J2. Samples with similar expression profiles lie closer to each other than those with dissimilar profiles. Axes 1 and 2 show robust class separation into two major groups: (1) 9-HOT, (2) J2 and MES + ethanol and protoplasts. (B) Venn diagram showing number of overlapping and non-overlapping differentially expressed M. javanica genes following exposure to: protoplasts/control (Cont.) and 9-HOT/control. (B.1) distribution of all differentially expressed genes. (B.2) Distribution of up-regulated genes found in each treatment as well as genes overlapping between both treatments. (B.3) Distribution of down-regulated genes found in each treatment as well as genes overlapping between both treatments. Fold change with an absolute value > 2 and < − 2 and p value ≤ 0.001 was used for the analyses. (C) Gene ontology (GO) annotations of differentially expressed genes of M. javanica J2 exposed to 9-HOT vs. control unigenes at multilevel using BLAST2go software. The GO terms were categorized into (C.1) biological process and (C.2) molecular function. Pie chart slices represent the percentages of genes identified in a particular category among the differentially expressed genes.
