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.
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.
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.