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Copious Genes of Tiny Water Flea Promise a Leap in Understanding Environmental Toxins

With the Daphnia genome in hand, scientists hope to put this key environmental indicator species to even better work
daphnia water flea genome



AAAS/SCIENCE

Not far from milepost 200 on a stretch of the Pacific Coast Highway near the Oregon Dunes National Recreation Area is a humble water hole known in some biology circles as Slimy Log Pond. It was from this inauspicious pool that a water flea (Daphnia pulex) dubbed The Chosen One was plucked in 2000, and became the first crustacean to have its genome sequenced.

Analysis of The Chosen One's genome shows that this Lilliputian crustacean contains the most genes of any animal sequenced to date. It also has the potential to accelerate scientists' understanding of synthetic chemicals' effects on the environment—and human health.

The world's most common small freshwater feeder—gobbling up algae in lakes and ponds the world over—Daphnia are also a staple in fishes' diets, proving a crucial link in food webs. This miniscule animal—barely visible to the naked eye—has long been an invaluable aquatic indicator species and is used by agencies across the globe to take stock of the health of freshwater systems.

As such a well-studied species, Daphnia are poised to become a key model organism to delve deeper in the study of environmental genomics. Improved understanding of the interactions among genes and the environment could also diminish the deleterious effects of chemicals on human health as well.

The sequence details, published online February 3 in Science, turned up the most shared genes with humans of any arthropod that has been sequenced to date. This genetic overlap means that the sentinel species could also end up being "a surrogate for humans to show the effects of the chemicals on shared pathways," says John Colbourne of Indiana University Bloomington's Center for Genomics and Bioinformatics and the lead author on the new paper. "The majority of the genome is a reflection of how the animal has evolved to cope with environmental stress."

Previous genetic snapshots of Daphnia have hinted at its overall makeup. But whole genome sequences provide "much better information about the function of genes, and allow us to be much more comprehensive in understanding the effects of toxicants," says Chris Vulpe of the Nutritional Science and Toxicology group at University of California, Berkeley, who was not involved in the new study. "It really adds to your ability to understand what's going on" in the environment.

Muddy biology
Named for the Greek mythological nymph Daphne (who shuns the god Apollo's advances and in Ovid's telling was transformed into a tree), aquatic Daphnia, with its gently branching antennae, generally reproduce without males by passing along a diploid genome (a complete set of chromosomes) to offspring. This consistency creates clone lines, making them excellent candidates for laboratory study.

But like the water they often live in, these crustaceans "have a really muddy biology," Colbourne says. That murkiness, however, has turned out to be fertile territory for genetic research, he notes. "The genome is a lot more plastic and a lot more responsive to the environment than we had given it credit for."

Researchers working to sequence Daphnia—as part of the Daphnia Genomics Consortium—were expecting to find one about the size of the fruit fly, with its 14,000 genes. So they were stunned to find that the D. pulex genome contains at least 30,907 genes—nearly 8,000 more than the human genome. Some 36 percent of these genes have not previously been identified in any other organism. And researchers found that rather than being evolutionary deadweight, most of these unfamiliar genetic signatures "tend to be the genes that are most responsive to Daphnia's ecology," Colbourne says.

Not all of the crustacean's genes are active at any given time. Rather, a large portion of them are switched on or off with changes in the flea's environment. They are "more or less environment-specific," Colbourne says. Although they are "coding for the same proteins, they're being expressed differently depending on what environmental stresses you expose the animal to." And finding the genes that allow the animal to tolerate outside stressors—whether they are chemicals or UV radiation—could help researchers search for parallel pathways in humans.

Modeling complexity
One of the reasons the Daphnia genome contains so many genes, the researchers found, is because gene duplication in this species occurs at a much higher rate than in other familiar species—about 30 percent higher rate than in humans and about three times the rate in fruit flies.

"There's obviously a selective advantage to having so many genes," Colbourne says. "We were able to discover for the very first time that newly duplicated genes can acquire new functions very, very rapidly." In other species duplicate genes tend to become harmful or irrelevant and thus get weeded out quickly. Daphnia genes stick around longer, suggesting that they are often put to good use—and quickly—responding to environmental factors.

In the past, diploid Daphnia have been bred in the lab to cut down on extraneous genetic material that, in the wild, is necessary for their mainly mateless reproductive strategy. But this artificial inbreeding is less than desirable for researchers who are looking to study gene-environment interactions. So members of the research project launched a transcontinental search to find a specimen that was naturally inbred. What they found in The Chosen One was just that—a Daphnia in which "nature has gotten rid of all the bad alleles," simplifying the genome without losing its ecologically attuned adaptations, Colbourne says.

This little arthropod and her progeny received such a grand nickname as another Slimy Log Pond candidate line—now known as The Rejected One—was being sidelined. In preliminary analyses The Rejected One was found to have a genome that is quite heterozygous (with more differentiated alleles), Colbourne recalls. Its radical differences, however, did allow for some useful comparison with The Chosen One. "There was actually some great science that was done because of the Rejected One, although it created quite a heart attack in the community," he says.

Although D. pulex is the most common species, others, such as D. magna and Ceriodaphnia dubia are usually called on in standardized water quality tests. The D. magna genome sequence is currently in the pipeline, says Vulpe, who uses that species in his research and is part of the larger consortium. For his research, the D. pulex genome "has been an incredible boon to be able to compare and help us understand what's happening" in the D. magna genetics.

Beyond death
With its substantial genome now decoded, Daphnia might soon play an even more integral role in environmental assessment—beyond simple tests for dissolved oxygen or excessive chlorine.

Only a small fraction of tens of thousands of man-made chemicals have been tested for safety, and then they are usually only tested as isolated compounds—rather than in more realistic amalgamations as they often crop up in the environment. "We have so many damn chemicals," Vulpe says. "We're concerned about their effect on humans and on ecosystems."

But with so much analysis that remains to be done, "there's no way that our current methods of screening for the danger of these chemicals can catch up," Colbourne says. If Daphnia prove to be a solid model organism to study the effects of chemicals and environment on genes, they could enable a more efficient high-throughput process for assessing chemicals.

The relatively new field of "ecotoxicogenomics"—which Vulpe admits "doesn't really roll off the tongue very well"—is working to catch up to more biologically based genetics. But with the genome sequence of Daphnia, he hopes that it will allow the field to catch up. "We have the sequence of the mouse and human—and we can use genomics in a very powerful way—but unfortunately this has lagged behind in these eco-indicator species."

Bringing a genomic approach to studying toxicology promises to create a more "mechanistic understanding" of the field, Colbourne says. Vulpe explains that toxicology has relied on the "kill 'em and count 'em" approach, in which death was the primary endpoint in a chemical's dosage assessment: "We previously asked the question: Did they die?" he says. As researchers are now starting to be able to suss out particular genetic pathways, "it might help us consider endpoints that we hadn't considered," Vulpe adds, such as how chemicals are having more nuanced effects on reproductive or immune systems.

Daphnia are of course not a perfect foil for studying chemicals' potential effects on human biology, and their use as screening organisms will have to be validated by further research. "But it's certainly exciting that there is a similarity," Vulpe says. "Who would have thought that a little crab would have been similar to people?"

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