Photo: Herman Berkhoudt
In this project, we aim to gain deeper insight into the molecular mechanisms of Wolbachia-induced parthenogenesis, using the parasitoid wasp Asobara japonica as a model system. We employ a range of sequencing techniques, including whole-genome, IsoSeq and small RNA sequencing.
Collaborators:
Front cover PhD thesis Peter van der Gulik
Transfer RNAs (tRNA) are an integral component of translation in the three domains of life (Archaea, Bacteria and Eukaryotes). In this project, we are searching for domain-specific patterns in the set of tRNAs that are used.
We are also investigating whether these patterns can help assess the completeness of newly assembled genome sequences.
Collaborators:
This soil metagenomics project at the Leiden Centre for Applied Bioscience is studying the soil microbiome of Tulip fields as part of an effort to transform this industry towards more sustainable practices.
The “Rhinoceromics” project at the Leiden Centre for Applied Bioscience is studying health issues in captive black rhino’s using various omics techniques, including metagenomics. As a sideline, we wanted to see whether we could assemble a large eukaryotic genome using only nanopore reads. This produced an assembly of comparable size and contiguity to the current reference genome for this species. Our assembly will be used as reference assembly in the metagenomics project.
We sequenced the complete genomes of a sexual and an asexual lineage of this parasitoid wasp. The latter are asexual because they are infected by a parthenogenesis-inducing Wolbachia bacterium. This infection became established roughly 100,000 years ago. The comparison of the two genomes provides insight into the genomic consequences of asexual reproduction. In particular, we are interested in the accumulation of mutations and the associated decay of genes in asexuals.
Ongoing work includes:
Publications