Department Aquatic Ecology

Sequencing the Daphnia galeata genome

Water fleas (Daphnia) are important in aquatic food webs as link between algae and fish. Further they act as important model organsims for Toxicology: because Daphnia reproduce clonally, many genetic identical individuals can be used for tests. Also, Daphnia was chosen as one of 13 model organisms for biomedical research by the NIH (National Institute of Health).
For two Daphnia subgenera (Daphnia and Ctenodaphnia), a genome has already been sequenced (
D. pulex (Colbourne et al. 2011 and D. magna), however no member of the third subgenera Hyalodaphnia has ben sequenced yet. Daphnia produce resting eggs that can be retreived from lake sediments, these can be "ressurected" or studied genetically. New genetic tools are needed to understand observed changes.

The goal of the project is to sequence a member of the subgenus Hyalodaphnia, since these are the Daphnia that are predominantly found in European lakes, with that we will be able to do "paleogenomics" in the future. 

We chose a Daphnia galeata clone (G100) that was inbred once. Aiming at a high quality assembly, large amounts of DNA were needed, therefore the clone was grown in mass cultures. We extracted DNA of 16033 individuals in 312 extractions. The purity, concentration, and quality of each extract was checked. 445 µg of DNA was obtained.
Sequencing is done using the Illumina platform by the Environmental Genomics, National GeneBank, BGI China using insert libraries of different lengths

People

Dr. Stuart DennisTel. +41 58 765 6450Send Mail
PD Dr. Piet SpaakTel. +41 58 765 5617Send Mail
Prof. Dr. Kristin SchirmerHead of departmentTel. +41 58 765 5266Send Mail
Prof. Dr. Juliane HollenderHead of DepartmentTel. +41 58 765 5493Send Mail