Oklahoma State University: OSU, OU Scientists Collaborate To Sequence, Map New Genome

Press release from Oklahoma State University:

2022-02-10

A team of researchers from Oklahoma State University and the University of Oklahoma published a genome sequence and chromosome map for
the micro-crustacean Daphnia pulicaria.

Researchers in the laboratory of Punidan Jeyasingh in OSU’s Department of Integrative Biology — in collaboration with the laboratory of OU biology professor Lawrence Weider —
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.”

Jeyasingh added, “These technological advances are answering longstanding questions
in ecology and evolutionary biology, and I’m glad the next generation, like Matt,
are mastering these methods and advancing our science.”

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 Jeyasingh and Weider 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.  

For more information, contact Matthew Wersebe at matthew.wersebe@ou.edu.

This press release was produced by Oklahoma State University. The views expressed here are the author’s own.