Three point five millimeters, or .138 inches, is approximately one-third the size of a pencil eraser. Now image packing 31,000 genes – 200 million base pairs – into that size. The water flea, Daphnia pulex, has managed just that, with a genome larger than any animal ever sequenced, including humans, which have only 23,000 genes.
Dietmar Kueltz, professor of animal science at UC Davis, and his colleagues recently sequenced the genome of Daphnia. Daphnia is the first crustacean, a group that includes crabs and lobsters, to have its genome sequenced.
After genome sequencing and years of research, Daphnia have been one of the most extensively studied organisms.
“We could argue that there is more known about the ecology of Daphnia than any other organism,” said John Colbourne, associate scientist at the Center for Genomics and Bioinformatics at Indiana University.
According to the Daphnia Genome Consortium, in addition to having the largest number of genes, Daphnia create copies of its genes at a rate three times faster than insects and 30 times faster than humans.
Why, researchers asked, does this tiny organism need so many genes? The answer is phenotypic plasticity.
Phenotypic plasticity is a term coined by German scientist Richard Woltereck in regard to Daphnia. Phenotypic plasticity is the ability of an organism’s genes to quickly adapt to changing environmental conditions, thus increasing survival of that organism.
“In Daphnia, all these genes happen to be very specific in response,” said Colbourne. “There are sets of genes that respond to predator threats, a set of genes that respond to not having enough oxygen in water, bacterial infection, PH of water, dissolved carbon, phosphorous carbon ratios in their diet…”
In Daphnia, a huge amount of the genome has evolved in order for the organisms to cope with environmental stress.
Such an example is hemoglobin. Hemoglobin is a molecule that transports oxygen to the blood. There are eleven copies of hemoglobin in Daphnia. When stressed with a low supply of oxygen, these genes turn on. Increased levels of hemoglobin improve Daphnia’s ability to uptake oxygen, allowing it to tolerate low oxygen conditions.
The genome is made up of many of these duplicates, which is the primary reason Daphnia have so many genes comprising its genome. Natural selection is preserving duplicated genes.
“These duplications have generated extra gene copies that could evolve faster in response to environmental challenges because the degree of evolutionary constraint on those genes was relaxed,” said Kueltz. “Thus, these extra gene copies provide Daphnia with the ability to rapidly adjust to environmental change.”
Daphnia have an enormous range of environmental responses. They can change migration in the water column depending on whether predators are in the environment. When food is scarce, they produce a finer mesh in their filtering appendages to collect finer particles of food.
Most impressively, Daphnia can control sex in response to their environment. When environmental conditions are hard, with factors such as crowding and limited food, Daphnia stop producing genetically identical daughters and start producing genetically identical sons, all due to the genes’ response to differing environmental conditions.
More amazing yet, in lake sediments, the water flea can enter a resting stage in which they can live for more than 100 years.
“The female, in stressed environmental conditions, can produce an embryo that can lay dormant for up to a century, and just sit there in the bottom of the lake and wait for an environmental cue to tell them its okay to hatch,” said Colbourne.
Kueltz believes more discovery awaits through the comparison of the genomes of those Daphnia alive in the water and those dormant in the bottom of the lake.
“Another intriguing opportunity that is emerging is directly comparing the genomes of organisms that have remained in an inactive resting state in lake sediment for 100 years or longer with those that are currently present in the lake,” said Kueltz.
Due to its incredibly phenotypic plasticity, Daphnia provides a unique opportunity to study organism’s genetic responses to changing environmental conditions.
As Colbourne pointed out, “I think we are going to have a lot more important discoveries to come.”
CAMMIE ROLLE can be reached at science@theaggie.org.
