The fourth Daphnia Genomics Consortium Meeting was held from July 7th through July 9th, 2007 at Indiana University (Bloomington, IN, USA). This year’s meeting was entitled The Genome Biology of the Model Crustacean Daphnia and was highlighted by the initial public release of the draft version of the Daphnia pulex genome. In collaboration with the US Department of Energy Joint Genome Institute (JGI; CA, USA), the Daphnia Genomics Consortium (DGC) successfully sequenced the D. pulex genome, representing the first crustacean genome to be analyzed.

Daphnia are freshwater crustaceans found in most lakes and ponds throughout the globe, and have been ecologically investigated since the 1600s. They are arguably one of the best understood organisms. Daphnia are internationally recognized as an indicator of environmental health and, consequently, as a bioassay of aquatic toxicity, to define regulatory limits and to monitor effluents released into fresh water. Daphnia are primary grazers of algae and primary forage for fish; as such, they are considered keystone species in aquatic ecosystems.

The DGC is an international network of investigators committed to establishing Daphnia as a premiere model system, surpassing traditional model systems in investigations of environmental interactions, by incorporating Daphnia’s well-established ecological knowledge base. In a community-wide effort, the DGC is:

As an example of Daphnia’s utility across a variety of disciplines, this year’s DGC meeting featured presentations covering topics in Genome Structure and Evolution; Ecological Genomics; Predicting Gene Function using Comparative Phylogenetics; Gene Diversity and Function in Biological Processes; and Toxicological Genomics.

The first day of the meeting was highlighted by a keynote address by Igor Grigoriev of the JGI, providing an overview of the quality of the genome sequence, assembly and computed annotation. Over 1.8 billion bases were sequenced and assembled, with half of the approximately 200 million base-pair genome represented in 103 scaffolds. Additionally, over 150,000 expressed sequence tags (ESTs) were characterized as part of this project, while functional genomic experiments that give condition-dependent expression information on a gene set comprising 50% unknowns are in full swing. Keynotes were also delivered by Don Gilbert of Indiana University, providing an overview of the genome annotation project; Hugh Robertson of the University of Illinois at Urbana-Campaign (IL, USA), discussing an expansion of the opsin genes in Daphnia; and by Francis Poulin of the University of California at Berkeley (CA, USA), discussing the evolution of developmental pathways in crustaceans and insects, specifically the Daphnia Wnt genes. A common revelation from a variety of researchers is that the number of genes (25,000–35,000) in Daphnia may be much greater than previously believed for a genome size comparable to that of flies (200 million bases) and that several gene families, revealing of the animal’s unique biology and ecological settings, are expanded in Daphnia compared with other invertebrate genomes.

With the completion of the genome sequence, the next challenge for Daphnia researchers is to better connect genes to function. As such, this year’s DGC meeting featured some of the first presentations on the Daphnia transcriptome, using genome tiling path microarrays designed and produced by NimbleGen Systems (WI, USA), and on the Daphnia proteome. Ralph Pirow of the University of Münster (Germany), presented the response of the D. pulex proteome to changes in oxygen concentration and temperature. Using 2D gel electrophoreses, he observed noticeable changes in protein shifts between Daphnia acclimated to different temperatures, as well as differential expression of hemoglobin subunits between Daphnia acclimated to varying oxygen concentrations.

A presentation by Gary Smejkal of Pressure BioSciences, Inc., (MA USA) kicked-off the poster session. Smejkal’s presentation highlighted advances in sample preparation for genomics and proteomics using pressure cycling technology (PCT). Smejkal also presented a poster demonstrating the ability of pressure cycling technology to extract proteins from a single Daphnia. Following PCT, 2D gel electrophoresis was able to resolve differences from single D. magna exhibiting the asexual and sexual phenotypes. In addition, approximately 1000 spots can be resolved from a single D. pulex.

This year’s DGC meeting was highly successful and the public release of the Daphnia genome represented the accomplishment of a major goal of the DGC in its endeavor to establish Daphnia as a premiere model system.

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