genomes & transcriptomes

The homoscleromorph sponge Oscarella lobularis is a marine sponge that occurs in the northeastern Atlantic Ocean and the Mediterranean Sea. It is an important model organism for evolutionary biology and - as a representative of one of the earliest forms of multicellular (metazoan) animals, for deciphering early traits of multicellularity.

O. lobularis possesses a true epithelial layer, with adherens junctions and a basement membrane, making it an ideal model organism to study the evolution of epithelia.

We are currently in the process of performing long-read sequencing of O. lobularis.

This project is carried out in close collaboration with Andre le Bivic (IBDM) and Carole Borchiellini (IMBE).

The mexican Axolotl (Ambystoma mexicanum) is able to regenerate entire body ports, such as limb or tail. Consequently, it is an important model organism for research on regeneration. For a long time, the lack of a completely sequenced genome has made genetic work in Axolotl difficult. Over the years, we have in close collaboration with the group of Elly Tanaka worked on the sequencing and assembly of the Axolotl transcriptome; first, based on standard Sanger EST sequencing (Habermann B, et al., Genome Biol. 2004;5(9):R67); with the advent of next-generation sequencing, we have focused on whole-transcriptome RNA-sequencing. We were able to sequence and assemble more than 1 billion NGS-reads from a various tissues of the Axolotl. In the course of this work and together with High-Performance Computing center in Dresden, we have moreover contributed to the parallelization and optimization of assembly algorithms within the BMBF project NGS goes HPC.

Our work has significantly contributed to the de novo sequencing of the Axolotl genome, the largest genome ever sequenced, which was recently published (Nowoshilow S, et al. Nature. 2018;554(7690):50-55. doi:10.1038/nature25458).

Aeromonads are wide-spread, mostly aquatic, gram-negative bacteria, which are pathogenic for animals. A. hydrophila for example is a human pathogen, A. salmonicida is pathogenic to fish. A subspecies of A. salmonicida called pectinolytica, however, shows no pathogenic potential, but is rather adapted to living in a highly polluted, aquatic environment.

Together with the lab of Stephan Gruber from the University of Lausanne, we have sequenced, assembled and annotated a high-quality, complete genome of A. salmonicida pectinolytica and compared this subspecies to fish- and human-pathogenic species (Pfeiffer, et al., BMC Genomics 2018;19(1):20. doi: 10.1186/s12864-017-4301-6.).

We have used PacBio, as well as Illumina sequencing and compared the two approaches, confirming the strength and precision of the rolling circle technology in bacterial genome sequencing. Another advantage of long-read sequencing is the easy generation of a complete, circular genome, making studies on genome plasticity possible.