Water flea genome sequence completed

Research into genetics-versus-environment and genomic studies has been revolutionized with the completion of the genome for Daphnia pulex, commonly known as the water flea.\nScientists at IU and the Joint Genome Institute recently announced they have completed a "shotgun" sequence of the Daphnia genome. Daphnia is an important organism for genetic-versus-environment studies and serves as a model organism in evolutionary and ecological research projects.\n"Daphnia are long studied as a model system for ecotoxicology studies and for understanding the evolution of sex and its role in genetic recombination," said Jeffrey Boore, head of the evolutionary genomics program at the Joint Genome Institute. \nBoore said in order to understand how organisms respond to environmental challenges at the cellular level and adapt at the population level, there is a clear need for model species that are "globally distributed, ecologically relevant and experimentally tractable."\nHe explained the many natural characteristics that make Daphnia an ideal model species in facilitating the study of evolutionary and ecological genomics: It has a short and quick reproductive cycle (five-10 days); it is a resident in freshwater lakes and ponds, an is considered a "keystone" ecological species; it is a transparent organism, which allows for the study of tissue-specific gene expression.\n"Shotgun" sequencing is the quickest and most cost-effective way to sequence a genome, Boore said. \nBoore said the genome sequencing was accomplished over an eight-month period, and the sequence technique will still need to be refined years from now.\nBiology graduate student Sarah Schaack said the Daphnia Genome Sequencing Project is a critical factor in the completion of her Ph.D.\n"My dissertation is focused on understanding how transposable elements (or 'jumping' genes) behave in sexually-versus-asexually reproducing organisms," she said.\nTo quantify how the "jumping" genes are accumulating in Daphnia, Schaack said she first needs to identify them. This can be done by using "jumping" genes found in other organisms and searching for similar sequences in the Daphnia genome.\nFor scientists, the "shotgun" sequence of the Daphnia genome is very important because it "is the first genome sequence of any crustacean, and will be useful for interpreting the evolution of genomes of many insects," Boore said.\nThis is what makes Daphnia a very important organism to the environmental sciences and ecology. In ecology and environmental sciences, the goal is to understand the role genetic variation plays in organisms adapting to their changing environments and how they survive at a population level, said Professor Vicky Meretsky of the Department of Public and Environmental Affairs.\n"In a changing world, a population with more genetic variation will have individuals with more different tendencies and abilities," Meretsky said. "Some of these will be the right tendencies and abilities for the changing world that comes along. They will be successful, and so the species will continue to prosper."\nUltimately for the environmental sciences, a "shotgun" sequence of the Daphnia genome will allow conservation scientists to efficiently target species and ecosystems that are at a higher risk for becoming extinct or rare. Scientists can provide earlier protection for their habitats, Meretsky said.\nFor evolutionary genomics, a completed sequence of the Daphnia genome "allows for comparative genomic analysis and thereby sheds light on issues of genome architecture and genomic complexity," Schaack said.\nIn understanding the constraints on the evolutionary process, she said, there are two major benefits to having the full sequence of the Daphnia genome. First, Daphnia is one of the most important species in ecotoxicology and environmental sciences, and its ecology and natural history are well-studied.\nAlso, the unique reproductive system in Daphnia allows for examination of several biologically relevant questions related to the evolution of sex and consequences of genetic recombination, which are considered outstanding questions in biology, she said.\n"The (Daphnia) genome sequence will provide materials and information to fuel comparisons of the genomes and gene expression patterns of (organisms) in their natural conditions," Boore said.