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

Research output: Contribution to journalArticlepeer-review


  • Omid Shams Solari
  • Dong Li
  • Ram Podicheti
  • Markus Stoiber
  • Katina I Spanier
  • Donald Gilbert
  • Mieke Jansen
  • Douglas Rusch
  • Michael E Pfrender
  • Mikko J Frilander
  • Ellen Decaestecker
  • Karel A. C. De Schamphelaere
  • Luc De Meester

Colleges, School and Institutes

External organisations

  • Statistics Department, University of California, Berkeley, Berkeley, CA, 94720 USA, Preminon LLC, Rodeo, CA, 94572 USA
  • School of Informatics and Computing, Indiana University, 919 E. Tenth Street, Bloomington, IN 47408, USA
  • Department of Molecular Ecosystems Biology, Lawrence Berkeley National Laboratory, Berkeley, California, 94720 USA
  • KU Leuven Univ
  • Biology Department, Indiana University, 1001 E. Third Street, Bloomington, IN 47405, USA
  • KULeuven
  • Center for Genomics and Bioinformatics, Indiana University, School of Informatics and Computing, Indiana University, 1001 E. Third Street, 919 E. Tenth Street, Bloomington, Indiana 47408, USA
  • Laboratory of Environmental Toxicology and Aquatic Ecology, GhEnToxLab, Ghent University, Belgium
  • Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, Ch. Deberiotstraat 32, 3000 Leuven, Belgium
  • Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
  • Laboratory of Aquatic Biology, KU Leuven–Kulak, Kortrijk, Belgium


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.


Original languageEnglish
Pages (from-to)886-897
Number of pages12
JournalMolecular Ecology
Issue number4
Early online date26 Jul 2017
Publication statusPublished - 1 Feb 2018


  • abiotic stressors, biotic stressors, differential co-expression networks, differential gene expression, ecological gene annotation, ecoresponsive genes, waterflea