Daphnia pulex Empirical Genome Annotation
PROJECT DESCRIPTION:
The globally distributed zooplankton
Daphnia (commonly called the waterflea) is the first crustacean to have its genome sequenced, helping to create a new model system for ecological genomics. The sequence is produced by the
Joint Genome Institute in collaboration with the
Daphnia Genomics Consortium. Investigations of the data are uncovering how the genome's structure, gene inventory and regulation are products of the many challenges common in aquatic environments. A surprising result is the genome's impressive catalog of genes; only half the predicted loci have sequence similarity to other characterized eukaryotic proteomes. The large number of orphan genes is due to the phylogenetic distances between Crustacea and insect model species, variable rates of evolutionary change, and gene family expansions specific to the
Daphnia lineage. Experimental annotations are required to understand how the genome's organization is coupled to the animal's biology. Our characterization of gene functions is based on genome-wide expression profiling using ESTs and microarrays, generated by challenging
Daphnia to ecologically relevant conditions. We further study transcriptional profiles from more modern conditions that threaten zooplankton populations: environmental pollutants, the depletion of essential elements and nutrients. Overall, these data suggest that many of the novel components of the genome reflect physiological and adaptive responses of
Daphnia to its complex environments.
PROJECT LEADERS: John Colbourne
FUNDING: The National Science Foundation, The National Institutes of Health, The US Department of Energy, The Center for Genomics and Bioinformatics
DATA: Public early access to data on 2007/07/07. JGI Daphnia Genome Portal. Annotation project updates are at the DGC Collaboration Wiki.
