Comparative (pan)genomics

My research aims to contribute to our understanding of the genotype-phenotype relationship through comparative genomics. We use high-throughput measurements at various omics levels (genome, transcriptome, proteome, metabolome) to understand the causal chain leading to the observed variation in phenotype.

Since we are dealing with big data, we need computational tools for the analysis. In my work, both the application and development of computational tools for comparative omics are important aspects. I am particularly interested in early incorporation of biological knowledge in computational analyses.

The focus of my work has been on the evolution of complex eukaryotic genomes. To perform comparative analyses high-quality ingredients are essential. Therefore I am involved in several genome projects, aiming to deliver high-quality reference genomes. Often these are connected to interesting phenotypes, where one species can do a particular trick, while a close relative cannot. Typical questions are: which genetic loci influence the phenotype, how did this trait evolve?

Research projects

Comparative genomics of Parasponia and Trema
PhD student Rens Holmer, collaboration with René Geurs (Molecular Biology, WUR)
Here we aim to understand the evolutionary origin of rhizobium symbiosis in Parasponia by comparing the genomes and transcriptomes of Parasponia and its sister genus Trema. This involves the creation of two high-quality reference genomes and an extensive comparison of the genome, gene expression, and proteome.

Pan-genomics for crops
PhD student Siavash, collaboration with Eric Schranz (Biosystematics, WUR)
In this project we aim to develop algorithms to compress multiple annotated genomes into a pan-genome representation. With growing numbers of genomes becoming available for (groups of) species, data integration at an early stage is very efficient. Ideally, scalable pan-genome representations will take over the role of linear reference genomes in genomic analyses.

Role of copy number variation (CNV) in plant adaptation
PhD student Raúl Wijfjes, collaboration with Mark Aarts (Genetics, WUR)
In this project we aim to develop methods for the accurate detection of copy number variations in plant genomes, and apply them to study the role of CNVs in plant adaptation. Arabidopsis will be evolved under several stress conditions, and DNA samples from several generations will be sequenced and analyzed for CNVs.

Pangenomic applications for plants and pathogens
PhD student Eef Jonkheer, collaboration with Theo van der Lee (Biointeractions, WR) and Genetwister
We will develop novel applications of pangenomic technology, relevant for the analysis of crops and plant pathogens. One research line will focus on the characterization of a pangenome (e.g. core/accessory genes), the other on the analysis of sequence and structural variation.

Madurella mycetomatis
MSc student Barbara Terlouw, collaboration with Wendy van de Sande (ErasmusMC)
We want to understand how Madurella mycetomatis causes mycetoma (a tropical infectious disease) and how we can best treat or prevent it. We have first produced an annotated reference genome for Madurella, and are now comparing this genome to the genomes of various other species that are either related, but don’t cause the disease, or unrelated, but also cause the disease.

Winter moth genome
Collaboration with Marcel Visser (NIOO-KNAW)
In this project we produced a reference genome for winter moth, and performed several genomic analyses aimed to learn more about seasonal timing and phenology in winter moths. The paper has recently been published ( Follow up experiments to study differential gene expression as an effect of photoperiod exposure are underway.