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).