Differentially expressed (DE) and alternatively spliced (AS) genes are associated with transcriptional plasticity
We start by expanding our scope of transcriptional change to characterize genome-wide patterns of differential gene expression (DE) and differential alternative splicing (AS) significantly associated with transcriptional plasticity in larva and adult stages of D. mojavensis . We observed a wide spectrum of genes associated with both types of plasticities and life stages (Figure 2a). Overall, we found that more than twice as many genes were significantly associated with transcriptional plasticity in larvae compared to adult samples (2719 vs. 1096 genes, respectively, Figure 2a). In addition, we found similar (e.g., adults) or even higher numbers (e.g., larvae) of AS genes, relative to DE genes, associated with acclimation performed in the offspring generation (WGP) (Figure 2a). Interestingly, AS genes are particularly associated with WGP, with no AS genes significantly responding to TGP (Figure 2a).
Figure 2. Overall results of transcriptional within- (WGP) and transgenerational plasticity (TGP) in larvae and adults of D. mojavensis. All comparisons were performed between acclimated samples at 36 °C and control samples at 25 °C using three biological replicates following FDR corrections. a) Barplots show the number of genes detected with significant WGP (only), TGP (only), and their overlap (WGP and TGP). Each bar shows the number of detected genes with significant DE-only, AS-only and their overlap (DE and AS). b) Error bars show the intron retention (IR) change estimated for up- and down-regulated genes following WGP and TGP. IR change was estimated as the Euclidian distance between the IR rates of acclimated samples at 36 °C vs control samples at 25 °C. Significant comparisons (α < 0.05) following GLM analysis are indicated with *. c) Venn diagram shows the number of DE genes detected with significant WGP in larvae (only), adults (only), and their overlap (larvae and adults).d) Venn diagram shows the number of AS genes detected with significant WGP in larvae (only), adults (only), and their overlap (larvae and adults). e) Venn diagram shows the number of DE genes detected in larvae with significant WGP (only), TGP (only), and their overlap (WGP and TGP).