Water flea genome: a sentinel for the environment

March 16, 2011—The journal Science has published the recently completed 200-million base-pair genome sequence of the water flea, Daphnia pulex. The DNA code is the largest number of genes ever recorded for a multicellular animal (more than in the human genome!), and one-third are of unknown function.

Chris Detter of the Laboratory's Genome Science and leader of the Joint Genome Institute/LANL Center is a member of the scientific team that chose to study Daphnia because it is a keystone species in freshwater ecosystems and a sensitive environmental indicator.

"Canary in the coal mine" for environmental monitoring

Daphnia is a small, algae-grazing crustacean found worldwide, where it is an important food source for fish. This water flea's short life cycle, large brood size, sensitivity to environmental conditions, and ease of laboratory and field manipulation have assured its importance for setting regulatory standards in the environment, testing chemical safety, and monitoring water quality, as well as being a model for ecological and evolutionary research. Environmental protection agencies have used Daphnia for over 50 years to set regulatory limits on pollution.

Daphnia is a crustacean arthropod, the group most closely allied with insects. Genes within the Daphnia lineage appear to have duplicated three times faster than genes within insect lineages and are also three times more likely to be preserved. This explains the large gene number for Daphnia.

Application of genomics to environmental monitoring

Because Daphnia's ecology is superbly understood, access to its genome sequence enables studying environmental influences on gene functions in ways that are difficult in even the best-developed genomic model species. Its genes of unknown function appear to be directly affected by changes in environment. Therefore, scientists plan to use its genome to develop gene-expression tools to assess environmental changes and pinpoint toxins.

The DOE Office of Science funded the Joint Genome Institute research, which supports the Lab's Global Security mission area and the Science of Signatures capability.