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

Luisa Orsini, James B Brown, Omid Shams Solari, Dong Li, Shan He, Ram Podicheti, Marcus H Stoiber, Katina I Spanier, Donald Gilbert, Mieke Jansen, et al.
(2018) MOLECULAR ECOLOGY. 27(4). p.886-897
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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.
Keywords
abiotic stressors, biotic stressors, differential co-expression networks differential gene expression, ecological gene annotation, ecoresponsive genes, waterflea, OXIDATIVE STRESS RESPONSES, WATER FLEA DAPHNIA, CLIMATE-CHANGE, FUNCTIONAL GENOMICS, ACUTE TOXICITY, EXPRESSION, CYANOBACTERIA, EVOLUTION, EXPOSURE, PULEX

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Citation

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MLA
Orsini, Luisa, et al. “Early Transcriptional Response Pathways in Daphnia Magna Are Coordinated in Networks of Crustacean-Specific Genes.” MOLECULAR ECOLOGY, vol. 27, no. 4, 2018, pp. 886–97, doi:10.1111/mec.14261.
APA
Orsini, L., Brown, J. B., Shams Solari, O., Li, D., He, S., Podicheti, R., … De Meester, L. (2018). Early transcriptional response pathways in Daphnia magna are coordinated in networks of crustacean-specific genes. MOLECULAR ECOLOGY, 27(4), 886–897. https://doi.org/10.1111/mec.14261
Chicago author-date
Orsini, Luisa, James B Brown, Omid Shams Solari, Dong Li, Shan He, Ram Podicheti, Marcus H Stoiber, et al. 2018. “Early Transcriptional Response Pathways in Daphnia Magna Are Coordinated in Networks of Crustacean-Specific Genes.” MOLECULAR ECOLOGY 27 (4): 886–97. https://doi.org/10.1111/mec.14261.
Chicago author-date (all authors)
Orsini, Luisa, James B Brown, Omid Shams Solari, Dong Li, Shan He, Ram Podicheti, Marcus H Stoiber, Katina I Spanier, Donald Gilbert, Mieke Jansen, Douglas B Rusch, Michael E Pfrender, John K Colbourne, Mikko J Frilander, Jouni Kvist, Ellen Decaestecker, Karel De Schamphelaere, and Luc De Meester. 2018. “Early Transcriptional Response Pathways in Daphnia Magna Are Coordinated in Networks of Crustacean-Specific Genes.” MOLECULAR ECOLOGY 27 (4): 886–897. doi:10.1111/mec.14261.
Vancouver
1.
Orsini L, Brown JB, Shams Solari O, Li D, He S, Podicheti R, et al. Early transcriptional response pathways in Daphnia magna are coordinated in networks of crustacean-specific genes. MOLECULAR ECOLOGY. 2018;27(4):886–97.
IEEE
[1]
L. Orsini et al., “Early transcriptional response pathways in Daphnia magna are coordinated in networks of crustacean-specific genes,” MOLECULAR ECOLOGY, vol. 27, no. 4, pp. 886–897, 2018.
@article{8605204,
  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.}},
  author       = {{Orsini, Luisa and Brown, James B and Shams Solari, Omid and Li, Dong and He, Shan and Podicheti, Ram and Stoiber, Marcus H and Spanier, Katina I and Gilbert, Donald and Jansen, Mieke and Rusch, Douglas B and Pfrender, Michael E and Colbourne, John K and Frilander, Mikko J and Kvist, Jouni and Decaestecker, Ellen and De Schamphelaere, Karel and De Meester, Luc}},
  issn         = {{0962-1083}},
  journal      = {{MOLECULAR ECOLOGY}},
  keywords     = {{abiotic stressors,biotic stressors,differential co-expression networks differential gene expression,ecological gene annotation,ecoresponsive genes,waterflea,OXIDATIVE STRESS RESPONSES,WATER FLEA DAPHNIA,CLIMATE-CHANGE,FUNCTIONAL GENOMICS,ACUTE TOXICITY,EXPRESSION,CYANOBACTERIA,EVOLUTION,EXPOSURE,PULEX}},
  language     = {{eng}},
  number       = {{4}},
  pages        = {{886--897}},
  title        = {{Early transcriptional response pathways in Daphnia magna are coordinated in networks of crustacean-specific genes}},
  url          = {{http://dx.doi.org/10.1111/mec.14261}},
  volume       = {{27}},
  year         = {{2018}},
}
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