Researchers map flea genome

The genome of a water flea may be the key to understanding how organisms adapt to immediate and long-term environmental changes. \nThe Daphnia Genomics Consortium, a group of international researchers, mapped the genome of the Daphnia pulex, more commonly known as the water flea, making it the first crustacean to have its genome mapped. \nJohn Colbourne, Daphnia project director at the IU Center for Genomics and Bioinformatics, said this sequencing, though time consuming and painstaking, may have far-reaching effects on the study of how organisms adapt to environmental changes. \n“The Daphnia Project has, since its conception, (aimed) to bring the same type of technology... to an organism... more in terms of telling us something about environmental concerns,” Colbourne said. \nColbourne said the Daphnia is a good case study in this kind of research because it is an organism common to several different types of freshwater ecosystems. It is also a “keystone species,” Colbourne said, meaning the water flea occupies a critical spot on the food chain of such ecosystems.\nStudying the DNA of water fleas and how they adapt to environmental stresses, both natural and man-made, can help scientists – biologists and ecologists – understand how such stresses will affect other organisms, including humans. Colbourne said one major purpose behind the research was to share results with several different fields of scientific study, so the months of work required to map the genome could be used across many disciplines. \nThe process of genome sequencing involves taking large pieces of DNA and breaking them into smaller, more manageable pieces, then isolating individual molecules. Then, those broken pieces are attached to artificial materials called “plasmids,” which complete the broken pieces. \nThose millions of completed, circular pieces are then put into a machine called a sequencer, which takes the DNA and attempts to find overlap in the artificial molecules – overlaps that are then used to determine chromosomes – and eventually, a genome map. Colbourne said the process took a long time, and lots of collaboration within the consortium to complete.\nColbourne said another advantage of mapping the Daphnia genome is that it can now be compared to other mapped genomes, such as that of the fruit fly, to see where similar organisms may have diverged from the Daphnia on the evolutionary tree.\n“Given that it’s the first crustacean (ever mapped), its closest kin is the insects,” Colbourne said. “That places Daphnia in an interesting situation. … Evolutionarily speaking … the Daphnia genome roots all the insect genomes.”\nColbourne emphasized that the focus of his research is in trying to find out how organisms adapt to “environmental stresses” at the DNA level, topics he said were fundamental issues of adaptation.\n“We can now ask the question: Given that this organism has to prosper in these natural environments, what are the genes doing in order for it to prosper? And more importantly,” Colbourne said, “how are the genes changing?”\nColbourne said one important aspect of analyzing such changes is examining how human-induced environmental stresses affect genomes. He said because only 7 percent of the 80,000 launched into the environment in America alone are tested before release, this new information can help scientists understand how untested chemicals can affect organisms in those environments, including humans. \nColbourne also said he was happy with the success of the consortium, which coordinated efforts across several states and countries to complete the mapping of the Daphnia genome.\nColbourne said the genome is available through two Web portals, one at IU and one at the Department of Energy’s Joint Genome Institute in Walnut Creek, Calif. \nColbourne said study of the water flea is just beginning, and said this genome mapping is “tool-building” for future research projects that will use the map. He said researchers hope these kinds of projects can lead to a greater understanding of how organisms adapt, or go extinct, in the face of environmental changes.\n“It’s time,” Colbourne said, “to ask the question: How different are populations, really, from each other? Can we predict if a population will survive or go extinct?”