A team of researchers from the University of Oklahoma and Oklahoma State University published a genome sequence and chromosome map for the micro-crustacean Daphnia pulicaria. Researchers in the laboratory of OU biology professor Lawrence Weider, in collaboration with the laboratory of Punidan Jeyasingh in OSU’s Department of Integrative Biology, led the efforts. The results of their work were published in the journal Molecular Ecology, as part of a special issue highlighting the latest advances in DNA sequencing technology.
Daphnia, also known as waterfleas, play critical roles in environmental monitoring. For example, they have served as an important test organism in laboratories around the world for over a century because of their sensitivity to many environmental stressors such as chemicals. In nature, Daphnia act as a keystone species in freshwater food webs globally, as they feed on algae to help keep lake, pond and reservoir water clear and are important food sources for recreational fish species.
The researchers used HiFi DNA sequencing technology, which produces highly accurate and very long stretches of DNA “letters” known as sequencing reads. “Many people describe assembling a genome as a bit like putting together a huge jigsaw puzzle, fitting together many smaller pieces to form a whole image,” said Matthew Wersebe, a doctoral candidate at OU and lead author of the study. “When the pieces are large and the picture crisp, the whole process is a lot easier.”
The use of this type of DNA sequencing technology allowed the researchers to piece together the genome into huge and continuous stretches of DNA and also discern the two copies of the genome, one belonging to each of the two parents of the Daphnia individual they sequenced. To map and orient the long DNA chunks into chromosomes, the researchers also used genome sequencing of 100 “recombinant” individuals that they bred in the lab as part of the project. Finally, the researchers compared their new genome of Daphnia pulicaria to other closely related species. They determined that because Daphnia pulicaria has recently colonized lakes, it has experienced significant natural selection in its recent history as it has adapted to its new lake habitat. The new high-quality genome presented in the study allowed the researchers to examine the genomic basis of speciation in Daphnia.
The genome sequence and chromosome map will form the basis of future collaborations between the Weider and Jeyasingh labs where researchers are studying how waterfleas respond to changes in their environment from stressors like nutrients and road salt pollution, to invasive species and climate change.
The work was funded in part by the National Science Foundation and the OU Board of Regents.
Photo Credit: Dagmar Frisch.
An ancient Daphnia pulicaria individual resurrected from South Center Lake (MN, USA). This individual was hatched from an egg recovered from sediments that date back to circa 1418-1301 (A.D.) OU and OSU scientists have recently sequenced and mapped the genome of this species, enabling them to understand how the species has adapted to changes in its lake habitat.
