Functional analysis of DE and AS genes in transcriptional WGP
DE genes in larval WGP show significant enrichment for 14 gene ontology categories (GO), while 21 are associated with WGP in adults (Figure S1). Of these, only four categories are common to both stages (Figure S1), although some of them are related to similar biological functions. Most DE genes in larvae are associated with i) proteolysis and ii) several additional pathways with structural/cell/metabolic functions. Moreover, DE genes in adults are associated with i) proteolysis, ii) chaperone activity and heat-shock response, iii) other stresses, iv) Egg development, and v) several additional structural/cell/metabolic functions (Figure S1). The overlapping genes that respond to acclimation in both larvae and adults are associated with ten GO categories, eight of which are already present in the two independent analyses (Figure S1). As expected, most overlapping categories between the two stages are associated with the heat-shock response (Figure S1), including proteolysis and chaperone activity.
The molecular pathways associated with AS genes in WGP differ substantially from those of DE genes and show functional differences between larvae and adults. We detected 19 GO functions associated with WGP in larvae, while 27 are associated with WGP in adults (Figure S2). Of these, only three categories are common to both stages (Figure S2). AS genes in larva and adult samples are associated with multiple types of structural/cell/metabolic functions, and, unlike DE genes, none of them are part of the heat-shock response (Figure S2). Interestingly, larva samples are associated with alternative splicing via spliceosome, and both larva and adult samples are associated with molecular functions of gene regulation, such as chromatin remodeling and the regulation of translation. The overlapping AS genes between larvae and adults are enriched by nine GO categories, eight of which are already present in the two independent analyses (Figure S2). The majority of these overlapping categories between the two life stages are associated with muscle activity, in addition to chromatin remodeling and protein binding (Figure S2).
Figure 3. Transcriptional landscape comparing differential gene expression (DE) with significant within-generation plasticity (WGP) between larvae and adults of D. mojavensis. All comparisons were performed between acclimated samples at 36 °C and control treatments at 36 °C using three biological replicates following FDR corrections. a) Scatterplot shows the transcriptional landscape with relative expression levels (log2-fold-change) for DE genes with significant WGP in larva vs adult samples. b) Boxplots show the level of differential gene expression (log2-fold-change) for genes of the heat-shock response (i.e., proteolysis and Hsps) with significant WGP in larva and adult samples.