Modular transcriptional responses to environmental changes

Knowledge about the molecular underpinnings of phenotypic plasticity is still scarce and quantifying gene expression in response to abiotic and biotic factors enables to investigate transcriptional plasticity. RNAseq data on clones of the alpine plant Biscutella laevigata (Brassicaceae) subjected to control, cold, heat, drought and herbivory treatments assessed differentially expressed genes (DEGs) and transposable elements (DE-TEs) in comparison to similar experiments in Arabidopsis thaliana. Synergistic and trade-off DEGs presenting parallel and antagonistic regulation among treatments were further identified and used with networks of co-expressed DEGs to characterize transcriptional plasticity in response to environmental changes. Compared to A. thaliana, B. laevigata presented fewer DEGs that were mostly up-regulated by stronger expression shifts in response to environmental treatments. Biscutella laevigata showed constitutive expression of half of the A. thaliana DEGs. It further presented a higher proportion of synergistic DEGs, a lower number of trade-off DEGs and a transcriptome organized in environment-specific subnetworks. Several DE-TEs were identified as activated by heat and herbivory. The stress-tolerant perennial B. laevigata presents a highly modular transcriptional plasticity in response to environmental changes, contrasting with the more integrated transcriptome of A. thaliana. Significance statementLittle is known about the molecular underpinnings of phenotypic plasticity. Here, focusing on expression shifts during changes in abiotic and biotic conditions, we highlight environment-responsive genes acting synergistically or antagonistically among treatments and underlying modular transcriptional plasticity in two Brassicacea species.