A keystone species in freshwater ecosystems, the water flea Daphnia pulex, is roughly the size of the equal sign on a keyboard.
In the February 4 issue of Science, the nearly decade-long collaboration between the Daphnia Genomics Consortium and the DOE JGI culminated with a report on this first crustacean genome.
“Daphnia is one of the most widely used model systems for environmental protection agencies around the world,” said project leader and Indiana University Center for Genomics and Bioinformatics genomics director John Colbourne. “The costly challenge of evaluating conditions in the environment and of our water supplies may be overcome by Daphnia’s potential use as a high-tech and modern version of the mineshaft canary.”
The DOE JGI sequenced the 200-million base water flea genome using the Sanger method and also annotated the sequence. Igor Grigoriev, head of the DOE JGI Eukaryotic Genomics group, noted that Daphnia’s compact genome holds more than 31,000 genes more than are found in any other animal, and a third of these genes are of unknown function. The finding, he said, takes the significance of the work beyond having the first crustacean genome.
“By combining functional genomics assays we can see that the genes of unknown function – the new genes resulting from adaptations, not the ones conserved because they’re key for housekeeping – are the most responsive to environmental changes,” Grigoriev said. “In that sense, the organism’s environment can direct us to areas of interest; if you pick a genome and would like to annotate all the genes, go to the environment.”