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Consortium Sequences Water Flea Genome

By a GenomeWeb staff reporter

NEW YORK (GenomeWeb News) – Members of the Daphnia Genomics Consortium reported online today in Science that they have sequenced and analyzed the draft genome of the water flea, Daphnia pulex.

Researchers from Indiana University at Bloomington and elsewhere used a combination of sequencing and microarray-based gene expression experiments to characterize the tiny crustacean's genome. Their analyses suggest the genome houses nearly 31,000 genes — about 8,000 more than the human genome. More than a third of these seem to be unique to D. pulex, they found, with many new genes apparently springing up as a result of frequent gene duplication.

"Daphnia's high gene number is largely because its genes are multiplying, by creating copies at a higher rate than other species," corresponding author John Colbourne, director of IU Bloomington's Center for Genomics and Bioinformatics, said in a statement.

Water fleas are found in freshwater ponds and lakes, where they feed on algae and are consumed by fish, Colbourne and his co-authors explained. And because their phenotypes, behavior, and mating patterns can shift with changing environmental conditions, they added, water fleas can be used as a model system for scrutinizing the effects of toxins, environmental change, and more.

"The Daphnia system is an exquisite aquatic sensor," IU Bloomington researcher James Klaunig, who was not involved in the current study, said in a statement. "With knowledge of its genome, and using both field sampling and laboratory studies, the possible effects of environmental agents on cellular and molecular processes can be resolved and linked to similar processes in humans."

For the current study, researchers sequenced about 80 percent of the D. pulex nuclear genome. Their subsequent analyses of this draft sequence turned up 50 microRNA genes, 468 ribosomal RNA loci, 3,798 transfer RNA genes, and 30,907 predicted protein-coding genes that are able to be packed into the 200 million base genome, in part, because of their small intron sizes.

Some 36 percent of the protein-coding genes have not been found in any other organism so far, the team reported. Many of these genes seem to have stemmed from gene duplication followed by changes in the way these duplicated genes are expressed, function, and interact with other genes, they explained — a notion supported by the gene expression experiments assessing water fleas grown under different conditions.

"We had all assumed that newly copied genes that code for the same proteins would initially have the same functions, and that new functions evolve slowly with age, by acquiring rare beneficial mutations," co-author Michael Pfrender, a biology researcher at the University of Notre Dame, said in a statement. "Instead, we found that half of the newly copied genes had changed their expression very soon, possibly at the time of their origin."

Even so, the researchers noted, the water flea genome also shares more genes with humans than any other invertebrate characterized to date, hinting that its role as a model organism may extend to studies related to human health and environmental exposures.

"[W]ith many shared genes between Daphnia and humans, we will now also apply Daphnia as a surrogate model to address issues directly related to human health," co-author Joseph Shaw, a biologist with Indiana University's School of Public and Environmental Affairs, said in a statement. "This puts us in a position to begin integrating studies of environmental quality with research of human diseases."

Indeed, in an accompanying perspectives article in Science, University of Basel researcher Dieter Ebert highlighted some of the potential applications of the water flea genome for those using the crustacean as a model for environmental and other studies.

"The Daphnia model is currently being used in such fields as ecotoxicology, population genetics, the evolution of sex, phenotype plasticity, ecophysiology (including global change biology), and Daphnia-parasite interactions," he noted. "The publication of the D. pulex genome will allow this list to expand to embrace the emerging field of environmental genomics."

Along with the Daphnia genome paper in Science today, dozens of related articles are reportedly set to appear in other journals. Information on the genome sequencing study and other research being done by the Daphnia Genomic Consortium is available through the group's website.

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