February 3, 2011

Scientists Map Genome Of The Waterflea

Scientists have mapped the genome of the waterflea, revealing the most gene-packed animal characterized to date.

The information deciphered of the tiny crustacean could help researchers develop and conduct real-time monitoring systems of the effects of environmental remediation efforts.

The waterflea, or the Daphnia pulex, is considered a keystone species in freshwater ecosystems and is roughly the size of an equal sign on a keyboard. 

The Daphnia pulex is the first crustacean to have its complete genome sequenced. 

Joshua Hamilton, senior scientist and chief academic and scientific officer at the Marine Biological Laboratory (MBL), is co-author of an important companion paper to the Daphnia genome sequence. 

That paper was the first study of the genetic basis for Daphnia's adaptive response to sub-lethal levels of a major environmental contaminant.  Cadmium is one of the most common contaminants found in the U.S. EPA Superfund sites.

The paper said that the technologies used were the first genomic tools developed for Daphnia and they are applicable to testing Daphnia's genetic response to a wide range of environmental contaminants.  Many other environmental stressors have been tested using the waterflea.

"Daphnia can serve as an important 'canary in a coal mine' for freshwater ecosystems and their response to environmental contamination," says Hamilton. "When the Daphnia population is impacted, it is likely that the entire ecosystem is being adversely affected and may be on the verge of collapse."

Hamilton and colleagues demonstrated that Daphnia can adapt to increasing levels of cadmium by up-regulating a unique version of a key protective molecule known as metallothionein. 

The waterflea is emerging as a model organism for a new field of science that aims to better understand how the environment and genes interact.

"Until now, Daphnia has primarily been used as sentinel species for monitoring the integrity of aquatic ecosystems," Joseph Shaw, co-author of the cadmium study and a biologist at Indiana University-Bloomington's School of Public and Environmental Affairs, said in a statement

"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."

The scientists reported their research, which was a collaboration between the Daphnia Genomics Consortium and the U.S. Department of Energy (DOE) Joint Genome Institute (JGI), in the February 4th issue of Science. 

Daphnia's genome is 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," Don Gilbert, coauthor and Department of Biology scientist at IU Bloomington, said in a press release.

By using microarrays that are made to measure the conditions under which sequenced genomes 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 said.

The study found that the DNA evidence presented by examining the patterns of gene duplication in the study's first chapters was combined with clues of the genes' functions in later chapters to propose a new model for how genes accumulate in genomes.

"The smoking gun in this investigation was clear," Kelley Thomas, coauthor and Hubbard Professor in Genomics at the University of New Hampshire, said in a statement. "A high rate of gene duplication, which produces a steady pool of new genes that have different expressions can facilitate the preservation of some gene-copies by natural selection."


Image 1: Daphnia pulex (water flea), a near-microscopic crustacean that lives in ponds and lakes, has a translucent body and a compound eye. Credit: Jan Michels, Christian-Albrechts-Universitaet zu Kiel

Image 2: Daphnia pulex (water flea) with a brood of genetically identical future offspring. Credit: Paul D.N. Hebert, University of Guelph


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