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Background  Two major biological stressors of freshwater zooplankton of the genus  Daphnia  are predation and fluctuations in food quality. Here we use kairomones released from a planktivorous fish ( Leucaspius delineatus ) and from an invertebrate predator (larvae of  Chaoborus flavicans ) to simulate predation pressure; a microcystin-producing culture of the cyanobacterium  Microcystis aeruginosa  and a microcystin-deficient mutant are used to investigate effects of low food quality. Real-time quantitative polymerase chain reaction (QPCR) allows quantification of the impact of biotic stressors on differential gene activity. The draft genome sequence for  Daphnia pulex  facilitates the use of candidate genes by precisely identifying orthologs to functionally characterized genes in other model species. This information is obtained by constructing phylogenetic trees of candidate genes with the knowledge that the  Daphnia  genome is composed of many expanded gene families.    Results  We evaluated seven candidate reference genes for QPCR in  Daphnia magna  after exposure to kairomones. As a robust approach, a combination normalisation factor (NF) was calculated based on the geometric mean of three of these seven reference genes:  glyceraldehyde-3-phosphate dehydrogenase, TATA-box binding protein  and  succinate dehydrogenase . Using this NF, expression of the target genes  actin  and  alpha-tubulin  were revealed to be unchanged in the presence of the tested kairomones. The presence of fish kairomone up-regulated one gene ( cyclophilin ) involved in the folding of proteins, whereas  Chaoborus  kairomone down-regulated the same gene.  We evaluated the same set of candidate reference genes for QPCR in  Daphnia magna  after exposure to a microcystin-producing and a microcystin-free strain of the cyanobacterium  Microcystis aeruginosa . The NF was calculated based on the reference genes  18S ribosomal RNA ,  alpha-tubulin  and  TATA-box binding protein . We found  glyceraldehyde-3-phosphate dehydrogenase  and  ubiquitin conjugating enzyme  to be up-regulated in the presence of microcystins in the food of  D. magna . These findings demonstrate that certain enzymes of glycolysis and protein catabolism are significantly upgregulated when daphnids ingest microcystins. Each differentially regulated gene is a member of an expanded gene family in the  D. pulex  genome. The  cyclophilin ,  GapDH  and  UBC  genes show moderately large sequence divergence from their closest paralogs. Yet  actin  and  alpha-tubulin  genes targeteted by our study have nearly identical paralogs at the amino acid level.    Conclusion  Gene expression analysis using a normalisation factor based on three reference genes showed that transcription levels of  actin  and  alpha-tubulin  were not substantially changed by predator-borne chemical cues from fishes or invertebrates, although changes in expression on the protein level were shown elsewhere. These changes in protein level could be caused by others than the investigated paralogs, showing the importance of the construction of phylogenetic trees for candidate gene approaches. However, fish kairomones caused an up-regulation, and  Chaoborus  kairomone caused a down-regulation of  cyclophylin , which proved to be a potential target gene for further analysis of kairomone effects on the life history of daphnids. Changes in food quality required a different set of reference genes compared to the kairomone experiment. The presence of dietary microcystins led to an up-regulation of two genes involved in the basic metabolism of  D. magna , i.e.  glyceraldehyde-3-phosphate dehydrogenase  and  ubiquitin conjugating enzyme , which suggests that microcystins in cyanobacteria have more general effects on the metabolism of  D. magna  than previously thought. Phylogenetic trees resolving relationships among paralogs that share the same gene name are shown to be important for determining the identity of the candidate genes under investigation.

bmc genomics

Target gene approaches: Gene expression in Daphnia magna exposed to predator-borne kairomones or to microcystin-producing and microcystin-free Microcystis aeruginosa