Conserved transcriptional responses to cyanobacterial stressors are mediated by alternate regulation of paralogous genes in Daphnia

Over the last decade, scientific technologies have improved significantly. While it took more than ten years and about 3 billion dollars to sequence the first human genome, prices for genome sequencing are currently plummeting. Now, you can even send your own DNA sample to commercial compagnies for about 100 dollars and learn about your genetic ancestry. Yet, despite this massive amount of data generated, we still cannot understand what the majority of that DNA is doing. Which genes are causing diseases? Which genes are responding to toxicants?


In our recent paper, we used the water flea, a crucial freshwater organism, to understand how genes respond to toxic blue green algae or cyanobacteria. It has been estimated that the water flea has about 30000 genes, which is more than the 23000 genes currently discovered in the human genome. Furthermore, the water flea has many copies of the same gene or in other words duplicated genes. In our study, we have observed that when we exposed the water flea to different cyanobacteria, the same functions are always responding to these exposures in the animal. However, these functions are triggered by different duplicated genes and each gene copy is responding to a specific cyanobacteria. This suggests that even though duplicated genes in the water flea have a similar function, they each have a specific role in responding to environmental challenges.

Scientific abstract

Despite a significant increase in genomic data, our knowledge of gene functions and their transcriptional responses to environmental stimuli remains limited. Here, we use the model keystone species Daphnia pulex to study environmental responses of genes in the context of their gene family history to better understand the relationship between genome structure and gene function in response to environmental stimuli. Daphnia were exposed to five different treatments, each consisting of a diet supplemented with one of five cyanobacterial species, and a control treatment consisting of a diet of only green algae. Differential gene expression profiles of Daphnia exposed to each of these five cyanobacterial species showed that genes with known functions are more likely to be shared by different expression profiles, whereas genes specific to the lineage of Daphnia are more likely to be unique to a given expression profile. Furthermore, while only a small number of nonlineage-specific genes were conserved across treatment type, there was a high degree of overlap in expression profiles at the functional level. The conservation of functional responses across the different cyanobacterial treatments can be attributed to the treatment-specific expression of different paralogous genes within the same gene family. Comparison with available gene expression data in the literature suggests differences in nutritional composition in diets with cyanobacterial species compared to diets of green algae as a primary driver for cyanobacterial effects on Daphnia. We conclude that conserved functional responses in Daphnia across different cyanobacterial treatments are mediated through alternate regulation of paralogous gene families.

Full reference (link)

Asselman, J., Pfrender, M. E., Lopez, J. A., De Coninck, D. I. M., Janssen, C. R., Shaw, J. R. and De Schamphelaere, K. A. C. 2015. Conserved transcriptional responses to cyanobacterial stressors are mediated by alternate regulation of paralogous genes in Daphnia. Molecular Ecology 24: 1844–1855.