Categorie archief: Genomics projects

tRNA evolution

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.


Black Rhinoceros genome

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.

Leptopilina clavipes

image Herman Berkhoudt

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:


  • Geuverink E, Kraaijeveld K, van Leussen M, Chena F, Pijpe J, Linskens MHK, Beukeboom LW, van de Zande L 2018 Evidence for involvement of a transformer paralog in sex determination of the wasp Leptopilina clavipes. Insect Molecular Biology 27: 78-795
  • Kraaijeveld K, Anvar Y, Frank J, Schmitz A, Bast J, Wilbrandt J, Petersen M, Ziesmann T, Niehuis O, de Knijff P, den Dunnen JT, Ellers J 2016 Decay of sexual trait genes in an asexual parasitoid wasp. Genome Biology and Evolution 8:3685-3995.
  • Kraaijeveld K, Zwanenburg B, Hubert B, Vieira C, de Pater S, van Alphen JJM, den Dunnen JT & de Knijff P 2012 Transposon proliferation in an asexual wasp. Molecular Ecology 21: 3898-3906.
  • Kraaijeveld K, Franco P, de Knijff P, Stouthamer R & van Alphen JJM 2011 Clonal genetic variation in a Wolbachia-infected asexual wasp: horizontal transmission or historical sex? Molecular Ecology 20: 3644-3652.
  • Kraaijeveld K., Franco P., Reumer B.M. & van Alphen J.J.M. 2009 Effects of parthenogenesis and geographic isolation on female sexual traits in a parasitoid wasp. Evolution 63: 3085-3096.
  • Reumer B., Kraaijeveld K. & van Alphen J.J.M. 2007 Selection in the absence of males does not affect male-female conflict in the parasitoid wasp Leptopilina clavipes (Hymenoptera: Figitidae). Journal of Insect Physiology 53: 994-999.