Our genome assembly pilot project
The aim of our pilot project is to test and prove our community's ability to generate high-quality reference genomes through teamwork and collaboration. Germany has selected 6 species for the country's pilot project and will also work on the generation of two other reference genomes in collaboration with Belgium, France and the Czech Republic.
What are we working on?
Rhogostoma pseudocylindrica
This protist belongs to the supergroup Rhizaria, which is a phylum as species rich as plants, but of which there are only three genomes available yet! R. pseudocylindrica is very small and admittedly not a beauty, but environmental surveys report occasional huge abundances in limnic, terrestrial and even aerial habitats. There it is an important consumer of bacteria and other microbes. This specie's ambassador is Kenneth Dumack. Conducted by worm~lab and West German Genome Center.
Echinocardium cordatum
Also known as the sea potato, it is a specie of sea urchin that lives buried on sandy and muddy seabeds. IT is often found in association with bivalve molluscs (commensalism). This specie's ambassador is Gert Wörheide. Conducted by worm~lab and West German Genome Center.
Camptopoeum frontale
This bee species belongs to the family Andreniadae. They are also know as colourful bees and range in size from 6 to 10 mm. This specie's ambassador is Eckart Stolle. Conducted by XXXXX and West German Genome Center.
Spongilla lacustris
Also known as fresh water sponge, inhabits rivers and lakes preferably where water is clear and shallow, they can reproduce sexually or asexually. This specie's ambassador is Philipp Schiffer. Conducted by worm~lab and West German Genome Center.
Enchytraeus crypticus
These soil invertebrates have a size of 6-9 mm. Members of this genus are often used as models for evaluating environmental risk of human-made compounds.This specie's ambassador is Miklós Bálint. Conducted by LOEWE-TBG/Senckenberg and the University of Cologne.
Acrobeloides nanus
This species can be found in soil and forests. This bacterial feeder nematode has been identified as a dominant nematode specie in areas with disturbed forest vegetation and soil as they are r-strategists. This specie's ambassador is Miklós Bálint. Conducted by LOEWE-TBG/Senckenberg and the University of Cologne.
Acrobeloides buchneri
This specie's ambassador is Miklós Bálint. Conducted by LOEWE-TBG/Senckenberg and the University of Cologne.
Megalothorax minimus
This springtail can be found in moist mosses in mountains up to 1500m. It shares morphological features with the species Megalothorax aquaticus that seem to be related to hygrophilous ecology. This specie's ambassador is Miklós Bálint. Conducted by LOEWE-TBG/Senckenberg and the University of Cologne.
Zygaena transalpina
This mot is known in Germany as "Hufeisenklee-Widderchen". It is frequent at higher altitude than 2000 m in the Alps and occurs in warm dry areas.Their larvae feed on the horseshoe vetch. This specie's ambassador is Marianne Espeland. Conducted by Zoological Research Museum Alexander König.
Alburnus alburnus
This small fresh water coarse fish known as the common bleak has an elongated and flat body. It lives in great schools and feeds on molluscs, insects and their larvae, worms, shellfish and plant detritus
Desoria tigrina
This species can be found in the upper layer of soil and litter, it is commonly found in crop fields in vegetal compost. Sequencing and assembly was performed by teams at the Max Planck Institute for Plant Breeding Research, and the LOEWE-Centre for Translational Biodiversity Genomics and Senckenberg – Leibniz Institution for Biodiversity and Earth System Research. The study was led by Miklós Bálint and Bruno Huettel. The project was partly sponsored by PacBio.
Sminthurides aquaticus
This springtail is a hygrophilous species widely spread in the Holarctic region. They have an elongated claws and a strong furca that allows them to walk and jump on water surfaces. Sequencing and assembly was performed by teams at the Max Planck Institute for Plant Breeding Research, and the LOEWE-Centre for Translational Biodiversity Genomics and Senckenberg – Leibniz Institution for Biodiversity and Earth System Research. The study was led by Miklós Bálint and Bruno Huettel. The project was partly sponsored by PacBio.
Lasius platythorax
Lasius platyhtorax is a small, brownish ant. It is distributed across Central Europe and is typically found in different kinds of woodland, bogs and fens and avoids urban habitats. The species is monogynous and colonies can contain several thousands of workers. It is highly similar to Lasius niger, and has only recently been described as a separate species. This species ambassador is Barbara Feldmeyer.
Who is involved?
1
Sample ambassadors
Species are selected according to relevant characteristics such as ecological importance and category of endangerment. A team of ambassadors for the species is selected to lead the process.
2
Pilot study leaders
The pilot study in Germany is managed by jun. Prof. Ann-Marie Waldvogel and Dr. Philipp Schiffer at the Institute for Zoology at the University of Cologne, and Dr. Astrid Böhne at the ZFMK at Museum König in Bonn.
3
Laboratory team
Most laboratory tasks (e.g. DNA and RNA extraction) are done at the worm~lab (AG Schiffer) at the IfZ at the University of Cologne. Additional support is provided by the Waldvogel group at the IfZ and by the Böhne lab at the ZMFK.
4
Sequencing
Sequencing is done in close collaboration with the DFG Competence Centers, in particular with the WGGC in Cologne and Düsseldorf under the lead of Prof. Peter Nürnberg. We also closely work with Prof. Bruno Hüttel at the MPIPZ, as well as with Prof. Gene Myers MPI-CBG. Carola Greve in collaboration with Miklos Balint's team at the Senckenberg conduct sequencing of additional species.
We are open for contribution!
Do you want to provide information on species found in Germany? Are you currently sequencing a species found in Germany? Download the species list template and send it to derga-biodiversity@tutanota.com
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