Daphnia magna transcriptome by RNA-Seq across 12 environmental stressors (original) (raw)
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Environmental Science & Technology, 2014
The present study investigated the possibilities and limitations of implementing a genome-wide transcription-based approach that takes into account genetic and environmental variation to better understand the response of natural populations to stressors. When exposing two different Daphnia pulex genotypes (a cadmium-sensitive and a cadmium-tolerant one) to cadmium, the toxic cyanobacteria Microcystis aeruginosa, and their mixture, we found that observations at the transcriptomic level do not always explain observations at a higher level (growth, reproduction). For example, although cadmium elicited an adverse effect at the organismal level, almost no genes were differentially expressed after cadmium exposure. In addition, we identified oxidative stress and polyunsaturated fatty acid metabolism-related pathways, as well as trypsin and neurexin IV gene-families as candidates for the underlying causes of genotypic differences in tolerance to Microcystis. Furthermore, the whole-genome transcriptomic data of a stressor mixture allowed a better understanding of mixture responses by evaluating interactions between two stressors at the gene-expression level against the independent action baseline model. This approach has indicated that ubiquinone pathway and the MAPK serine-threonine protein kinase and collagens gene-families were enriched with genes showing an interactive effect in expression response to exposure to the mixture of the stressors, while transcription and translation-related pathways and genefamilies were mostly related with genotypic differences in interactive responses to this mixture. Collectively, our results indicate that the methods we employed may improve further characterization of the possibilities and limitations of transcriptomics approaches in the adverse outcome pathway framework and in predictions of multistressor effects on natural populations.
Single nucleotide polymorphism discovery from expressed sequence tags in the waterflea Daphnia magna
BMC Genomics, 2011
Background Daphnia (Crustacea: Cladocera) plays a central role in standing aquatic ecosystems, has a well known ecology and is widely used in population studies and environmental risk assessments. Daphnia magna is, especially in Europe, intensively used to study stress responses of natural populations to pollutants, climate change, and antagonistic interactions with predators and parasites, which have all been demonstrated to induce micro-evolutionary and adaptive responses. Although its ecology and evolutionary biology is intensively studied, little is known on the functional genomics underpinning of phenotypic responses to environmental stressors. The aim of the present study was to find genes expressed in presence of environmental stressors, and target such genes for single nucleotide polymorphic (SNP) marker development. Results We developed three expressed sequence tag (EST) libraries using clonal lineages of D. magna exposed to ecological stressors, namely fish predation, parasite infection and pesticide exposure. We used these newly developed ESTs and other Daphnia ESTs retrieved from NCBI GeneBank to mine for SNP markers targeting synonymous as well as non synonymous genetic variation. We validate the developed SNPs in six natural populations of D. magna distributed at regional scale. Conclusions A large proportion (47%) of the produced ESTs are Daphnia lineage specific genes, which are potentially involved in responses to environmental stress rather than to general cellular functions and metabolic activities, or reflect the arthropod's aquatic lifestyle. The characterization of genes expressed under stress and the validation of their SNPs for population genetic study is important for identifying ecologically responsive genes in D. magna.
Molecular ecology, 2017
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 differ...
Integrative and Comparative Biology, 2011
The increased overexploitation of freshwater ecosystems and their extended watersheds often generates a cascade of anthropogenic stressors (e.g., acidification, eutrophication, metal contamination, Ca decline, changes in the physical environment, introduction of invasive species, over-harvesting of resources). The combined effect of these stressors is particularly difficult to study, requiring a coordinated multidisciplinary effort and insights from various sub-disciplines of biology, including ecology, evolution, toxicology, and genetics. It also would benefit from a welldeveloped and broadly accepted model systems. The freshwater crustacean Daphnia is an excellent model organism for studying multiple stressors because it has been a chosen focus of study in all four of these fields. Daphnia is a widespread keystone species in most freshwater ecosystems, where it is routinely exposed to a multitude of anthropogenic and natural stressors. It has a fully sequenced genome, a well-understood life history and ecology, and a huge library of responses to toxicity. To make the case for its value as a model species, we consider the joint and separate effects of natural and three anthropogenic stressors-climatic change, calcium decline, and metal contaminants on daphniids. We propose that integrative approaches marrying various subfields of biology can advance our understanding of the combined effects of stressors. Such approaches can involve the measuring of multiple responses at several levels of biological organization from molecules to natural populations. For example, novel interdisciplinary approaches such as transcriptome profiling and mutation accumulation experiments can offer insights into how multiple stressors influence gene transcription and mutation rates across genomes, and, thus, help determine the causal mechanism between environmental stressors and population/community effects as well as long-term evolutionary patterns.
Transcriptional responses of Daphnia magna exposed to Akaki river water
Environmental Monitoring and Assessment
Pollution of the aquatic environment is a global problem, with industrial waste, farming effluents, sewage, and wastewater as the main contributors. Many pollutants are biologically active at low concentrations, resulting in sublethal effects, which makes it a highly complex situation and difficult to assess. In many places, such as the Akaki river in Ethiopia, the pollution situation has resulted in streams with minimal presence of invertebrates or vertebrates. As it is difficult to perform a complete chemical analysis of the waters, the present study focused on using gene expression analysis as a biological end point to determine the effects of Akaki river contaminants. The present study was conducted using the small planktonic crustacean Daphnia magna with toxicogenomic molecular markers. Daphnia magna neonates were exposed to Akaki water samples collected from two different sites on the river and analyzed for mortality and expression of genes involved in different biological pat...
International journal of molecular sciences, 2015
Due to the rapid advent in genomics technologies and attention to ecological risk assessment, the term "ecotoxicogenomics" has recently emerged to describe integration of omics studies (i.e., transcriptomics, proteomics, metabolomics, and epigenomics) into ecotoxicological fields. Ecotoxicogenomics is defined as study of an entire set of genes or proteins expression in ecological organisms to provide insight on environmental toxicity, offering benefit in ecological risk assessment. Indeed, Daphnia is a model species to study aquatic environmental toxicity designated in the Organization for Economic Co-operation and Development's toxicity test guideline and to investigate expression patterns using ecotoxicology-oriented genomics tools. Our main purpose is to demonstrate the potential utility of gene expression profiling in ecotoxicology by identifying novel biomarkers and relevant modes of toxicity in Daphnia magna. These approaches enable us to address adverse phenotyp...
Transcriptome profiling in crustaceans as a tool for ecotoxicogenomics
Cell Biology and Toxicology, 2008
Chemicals released into the environment have the potential to affect various species and it is important to evaluate such chemical effect on ecosystems, including aquatic organisms. Among aquatic organisms, Daphnia magna has been used extensively for acute toxicity or reproductive toxicity tests. Although these types of tests can provide information on hazardous concentrations of chemicals, they provide no information on their mode of action. Recent advances in toxicogenomics, the integration of genomics with toxicology, have the potential to afford a better understanding of the responses of aquatic organisms to pollutants. In a previous study, we developed an oligonucleotide-based DNA microarray with high reproducibility using a Daphnia expressed sequence tag (EST) database. In this study, we increased the number of genes on the array and used it for a careful ecotoxicogenomic assessment of Daphnia magna. The DNA microarray was used to evaluate gene expression profiles of neonate daphnids exposed to beta-naphthoflavone (bNF). Exposure to this chemical resulted in a characteristic gene expression pattern. As the number of the genes on an array was increased, the number of genes that were found to respond to the chemicals was also increased, which made the classification of the toxic chemicals easier and more accurate. This newly developed DNA microarray can be useful for a obtaining a better mechanistic understanding of chemical toxicity effects on a common freshwater organism.