INDIANA U. (US) — The animal with the most genes—about 31,000—is the water flea, a near-microscopic freshwater crustacean. By comparison, humans have about 23,000 genes.
The water flea, or Daphnia pulex, is the first crustacean to have its genome sequenced. An international network of researchers report their findings in the journal Science. Among the highlights is identification of genes shared by Daphnia and unrelated aquatic vertebrates—and therefore likely key for living life in water.
Daphnia have the largest inventory of genes ever recorded for a sequenced animal, packaged within a tiny genome of only 200 million bases. The genome is made compact by the reduction in size of spaces (introns) between the gene parts that code for proteins.
“Daphnia’s high gene number is largely because its genes are multiplying, by creating copies at a higher rate than other species,” says project leader John Colbourne, who directs the Center for Genomics and Bioinformatics at Indiana University. “We estimate a rate that is three times greater than those of other invertebrates and 30 percent greater than that of humans.”
Scientists have studied Daphnia for centuries because of its importance in aquatic food webs and for its transformational responses to environmental stress. Predators signal some of the animals to produce exaggerated spines, neck-teeth or helmets in self-defense.
And like the virgin nymph of Greek mythology that shares its name, Daphnia thrives in the absence of males—by clonal reproduction, until harsh environmental conditions favor the benefits of sex.
“We were surprised to find the incredibly high level of complexity of the set of Daphnia vision genes,” says co-author Todd Oakley, an associate professor at the University of California, Santa Barbara. Oakley’s team focused on vision genes in the tiny creature.
“While humans have four light-sensing proteins (opsins), the Daphnia genome has 46 opsins,” says Oakley. “A possible explanation for this complexity is that Daphnia use these genes to understand the complex light regime of their aquatic environment.”
No ordinary genome
“More than one-third of Daphnia’s genes are undocumented in any other organism—in other words, they are completely new to science,” says Don Gilbert, coauthor and biologist at Indiana University.
Sequenced genomes often contain some fraction of genes with unknown functions, even among the most well-studied genetic model species for biomedical research, such as the fruit fly Drosophila.
By using microarrays (containing millions of DNA strands affixed to microscope slides) that are made to measure the conditions under which these new genes are transcribed into precursors for proteins, experiments that subjected Daphnia to environmental stressors point to these unknown genes having ecologically significant functions.
“If such large fractions of genomes evolved to cope with environmental challenges, information from traditional model species used only in laboratory studies may be insufficient to discover the roles for a considerable number of animal genes,” Colbourne says.
Daphnia is emerging as a model organism for a new field of science—environmental genomics—that aims to better understand how the environment and genes interact. This includes a practical need to apply scientific developments from this field toward managing our water resources and protecting human health from chemical pollutants in the environment.
James Klaunig, a professor and chair of the School of Health, Physical Education, and Recreation’s Department of Environmental Health at Indiana, predicts the present work will yield a more realistic and scientifically based risk evaluation.
“Genome research on the responses of animals to stress has important implications for assessing environmental risks to humans,” Klaunig says. “The Daphnia system is an exquisite aquatic sensor, a potential high-tech and modern version of the mineshaft canary. 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.”
The scientists learned that of all sequenced invertebrate genomes so far, Daphnia shares the most genes with humans.
The idea behind environmental genomics for risk assessment is fairly simple. Daphnia’s gene expression patterns change depending on its environment, and the patterns indicate what state its cells are in.
A water flea bobbing in water containing a chemical pollutant will express by tuning-up or tuning-down a suite of genes differently than its clonal sisters accustomed to water without the pollutant. Importantly, the health effects of most industrially produced compounds at relevant concentrations and mixtures in the environment are unknown, because current testing procedures are too slow, too costly, and unable to indicate the causes for their effects on animals, including human.
The new findings suggest that Daphnia’s research tools (like microarrays) and genome information can provide a higher-throughput and information-rich method of measuring the condition of our water supply.
“Until now, Daphnia has primarily been used as sentinel species for monitoring the integrity of aquatic ecosystems,” says Joseph Shaw, coauthor and Indiana University biologist. “But with 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.
“This puts us in a position to begin integrating studies of environmental quality with research of human diseases.”
This work was supported by the Office of Science of the U.S. Department of Energy, the National Science Foundation, Lilly Endowment Inc., Roche NimbleGen Inc., the National Institutes of Health, the U.S. Department of Health and Human Services, and Indiana University.
Over the course of the project, the Daphnia Genomics Consortium has grown from a handful of founding members to more than 450 investigators distributed around the globe. Nearly 200 scientists have contributed published work resulting from the genome study, many in open-source journals published as a thematic series by BioMedCentral.
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