Ontogenetic Sequence of Differential Gene Expression in Predator-Induced Daphnia pulex

In response to predators, many Daphnia species develop inducible morphological defenses. These traits are phenotypically plastic, meaning their production is suppressed in the absence of the predator. While previous studies have identified several neurohumoral factors and candidate genes involved in the development of the defenses, the involvement of specific genes and factors remains uncertain, and minimal information is available about the timing of gene expression changes during development. In the current study, we thus performed a candidate-independent gene expression analysis of defense development over juvenile developmental stages in D. pulex. We analyzed transcriptome responses of the microcrustaceans to the natural mix of predator-emitted compounds and also to the recently identified pure kairomone synthesized in the lab. With the data obtained, we show that the main factor correlating with the global gene expression patterns in Daphnia is molt cycle. Influence of kairomone treatment on the global gene expression is evident only in certain stages. The different stages generally show unique patterns of kairomone-induced gene expression. However, expression profiles are similar for the naturally released and the chemically synthesized kairomone in each one of the stages. A number of genes with regulatory, structural and detoxification roles are differentially expressed as a reaction to the kairomone treatment. The most consistent response was found in the expression levels of ilp-3 coding for an insulin-like peptide. Gene knockdown experiments suggest that this hormone plays a role in the production of the defense. Many of the genes responding to the kairomone treatment have no predicted function, stressing the need to investigate gene functions in Daphnia.