The role of DE and AS in transcriptional plasticity
In addition to differential gene expression (DE), we found evidence for differential alternative splicing with substantial consequences for transcriptional plasticity not reflected in DE. Moreover, we detected the functional specialization of alternatively spliced genes (AS) relative to DE genes in response to thermal acclimation. AS genes are only linked to WGP, while DE genes are associated with WGP and TGP.Our results of transcriptional WGP show that the number of AS genes often exceeded that of the DE genes, demonstrating that AS is an important mechanism of transcriptional regulation in response to thermal acclimation in D. mojavensis . These mechanisms appear mutually exclusive, with only 4 % of overlapping genes between DE and AS. The role of AS in transcriptional plasticity following acclimation is well supported in multiple organisms (Anduaga et al., 2019; Dikaya et al., 2021; John et al., 2021; Steward et al., 2022). The great majority of this evidence comes from studies of WGP, while the evidence for TGP is more limited. Our results suggest that differential AS may have little or no role in TGP (Ryu et al., 2018). However, we provide evidence for a more general role of intron retention (IR), which is a particular case of AS, being likely linked to negative gene regulation (Farlow et al., 2010). An increased rate of retained introns, which often contain premature stop codons, has been associated with higher transcript degradation that might result from the nonsense-mediated mRNA decay (NMD) pathway (Jacob and Smith, 2017; Hadar et al., 2022). We found that IR rates are significantly higher for down-regulated genes than for up-regulated genes, suggesting IR is a mechanism for regulating gene expression in response to thermal acclimation within and across generations. This finding is consistet with increased IR rates in response to stress conditions in other species (Jacob and Smith, 2017; Hadar et al., 2022).