Early transcriptional response pathways in Daphnia magna are coordinated in networks of crustacean‐specific genes

Abstract

Natural habitats are exposed to an increasing number of environmental stressors that cause important ecological consequences. However, the multifarious nature of environmental change, the strength and the relative timing of each stressor largely limit our understanding of biological responses to environmental change. In particular, early response to unpredictable environmental change, critical to survival and fitness in later life stages, is largely uncharacterized. Here, we characterize the early transcriptional response of the keystone species Daphnia magna to twelve environmental perturbations, including biotic and abiotic stressors. We first perform a differential expression analysis aimed at identifying differential regulation of individual genes in response to stress. This preliminary analysis revealed that a few individual genes were responsive to environmental perturbations and they were modulated in a stressor and genotype-specific manner. Given the limited number of differentially regulated genes, we were unable to identify pathways involved in stress response. Hence, to gain a better understanding of the genetic and functional foundation of tolerance to multiple environmental stressors, we leveraged the correlative nature of networks and performed a weighted gene co-expression network analysis. We discovered that approximately one-third of the Daphnia genes, enriched for metabolism, cell signalling and general stress response, drives transcriptional early response to environmental stress and it is shared among genetic backgrounds. This initial response is followed by a genotype- and/or condition-specific transcriptional response with a strong genotype-by-environment interaction. Intriguingly, genotype- and condition-specific transcriptional response is found in genes not conserved beyond crustaceans, suggesting niche-specific adaptation.

Contrasting patterns of divergence at the regulatory and sequence level in EuropeanDaphnia galeatanatural populations

“…These findings suggest that there may be a hierarchical activation of general mechanisms of stress responses at the metabolic and cellular level. This observation is concordant to another study (Orsini et al 2017) on D. magna. In this study, D. magna were subjected to several environmental perturbations and the GO enrichment analysis revealed a general stress response rather than ontologies specific to local adaptation.…”

Contrasting patterns of divergence at the regulatory and sequence level in European Daphnia galeata natural populations

“…These findings suggest that there may be a hierarchical activation of general mechanisms of stress responses at the metabolic and cellular level. This observation is concordant to another study (Orsini et al, ) on D. magna. In this study, D. magna were subjected to several environmental perturbations and the GO enrichment analysis revealed a general stress response rather than ontologies specific to local adaptation.…”

R(NA)‐tistic expression: The art of matching unknown mRNA and proteins to environmental response in ecological genomics

“…Interestingly, there were significant differences in the DNA methylation patterns of two of the Daphnia genotypes used in Orsini et al. () in response to both abiotic and biotic stressors, indicating genotype effect in gene regulation (Asselman et al., ). Future studies combining differences seen in DNA methylation and regulation to the genotype‐specific transcriptome responses may help further uncover how this variation exists.…”

“…Orsini et al. () contribute to linking these pieces by mapping the early transcriptional response to six biotic and six abiotic environmental perturbations over three genotypes of Daphnia magna . The stressors and concentration of stressors were chosen to simulate those found in nature.…”

“…Orsini et al. () discovered modules that were shared between genotypes and comprised of many genes. Alternatively, some modules were only found in one or a pair of the genotypes.…”