Open Access Research article

Single nucleotide polymorphism discovery from expressed sequence tags in the waterflea Daphnia magna

Luisa Orsini1*, Mieke Jansen1*, Erika L Souche23, Sarah Geldof12 and Luc De Meester1

Author Affiliations

1 Laboratory of Aquatic Ecology and Evolutionary Biology, K.U. Leuven, Ch. Deberiotstraat 32, 3000 Leuven, Belgium

2 Laboratory of Animal Diversity and Systematics, K.U. Leuven, Ch. Deberiotstraat 32, 3000 Leuven, Belgium

3 Institut Pasteur, Plate-Forme Intégration et Analyse Génomiques, 28 Rue du Docteur Roux, 75724 Paris Cedex 15, France

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BMC Genomics 2011, 12:309  doi:10.1186/1471-2164-12-309

Published: 13 June 2011



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.


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.


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.