Verhoeven Group

Research in the Verhoeven group focuses on plant microevolution and adaptation. We combine tools from genetics, genomics and ecology to explore the capacity of plants to adapt to rapidly changing environments. We work on the following topics:

Causes and consequences of epigenetic variation in natural plant populations. What role does epigenetic variation play in the adaptive capacity of plants?

• Plant gene expression plasticity and adaptation to climate change. We use transcriptomic analysis and experimental evolution assays in duckweed to test if thermal gene expression plasticity is adaptive under variable and unpredictable temperature environments. (postdoc project Mario Blanco-Sanchez)
• Epigenetic contribution to phenotypic plasticity in the Lombardy poplar. What is the effect of environmental stress on DNA methylation in the genome of poplar, and is there evidence that such induced DNA methylation changes regulate a gene expression response to stress? (PhD project Cristian Pena-Ponton)
• Environmental and transgenerational dynamics of DNA methylation in plants with different life histories. How stable are environment-induced DNA methylation changes, and is stability different between plant species? We compare the stability of DNA methylation in plants that reproduce either sexually or asexually, to test if reproduction without germline passage results in higher transgenerational stability of epigenomes. (PhD project Morgane van Antro)
• Epidiverse: linking ecology, molecular biology and bioinformatics in plant epigenetic research. We coordinated the Marie Skłodowska-Curie Action EPIDIVERSE (2017-2023), which linked European research groups from different disciplines to study causes and consequences of epigenetic variation in different wild plant species.

Plant urban evolution. How do plant species adapt to city environments?

• Linking space to time in ecology: Urban Evolution in Dandelions. Using dandelion as a model system, we study if and how plants adapt to different aspects of urbanization, including increased temperature and habitat fragmentation in cities. We combine evolutionary ecology and (herbarium) genomics to track adaptive differences in traits and genes, both in contemporary populations and through time via herbarium collections. (postdoc project Yannick Woudstra)
• Botanical records through a social lens. In this project, which is led by the Meertens Institute, we explore if historical botanical records can reveal which plant species are winners and which are losers of the urbanization process.

Intraspecific variation and adaptation in plant - soil and plant - microbiome interactions. Can plants show rapid adaptation based on microbiome-mediated plant traits?

• Intraspecific variation in grass microbiome interaction. Capacity for rapid adaptation depends on the levels of relevant standing genetic variation. Is there genetic variation in ryegrass for soil microbiome interactions, and can we pinpoint plant genes that control the composition of root microbiomes? (PhD project Paola Rallo)

Lab alumni

• Purva Kulkarni (postdoc, 2017-2018, co-supervised with Dr. Paolina Garbeva at NIOO - Microbial Ecology). Developing bioinformatics tools for metabolomics data analysis. Currently bioinformatics Postdoc at the Translational Metabolic Laboratory, RUMC Nijmegen.
• Julie Ferreira de Carvalho (postdoc, 2013-2017). Heritable gene expression and transposable element divergence within apomictic dandelion lineages. Currently a Marie Curie fellow at INRA Rennes, France.
• Jun Shi (PhD student, 2013-2016, co-supervised with Dr. Mirka Macel at Tübingen University). Effects of population admixture on plant performance and plant chemistry in the invasive plant Lythrum salicaria. Currently a Researcher at the Ningbo Academy of Agricultural Sciences, China.
• Thomas van Gurp (PhD student, 2011-2016). Measuring stress-induced DNA methylation in apomictic Dandelions. Currently a Bioinformatics scientist at Naktuinbouw, Roelofarendsveen, and founding owner of Deena Bioinformatics.
• Veronica Preite (PhD student, 2011-2015). Epigenetic inheritance in apomictic dandelions: stress-induced and heritable modifications in DNA methylation and small RNA. Currently a Postdoc at Ruhr-Universität Bochum, Germany.
• Maartje Groot (PhD student, 2011-2015, co-supervised with Dr. Philippine Vergeer and Prof. Joop Ouborg at Radboud University Nijmegen). A plant warned is half saved: Effects of non-genetic environmentally induced variation across generations on plant adaptation. Currently a Data scientist at Bayer Crop Science.
• Eveline Verhulst (postdoc, 2013-2014, co-supervised with Prof. Kees van Oers at NIOO - Animal Ecology). Coping epigenetically: the role of methylation in animal personality. Currently Assistant Professor at the Lab of Entomology, Wageningen University.
• Carla Oplaat (Research assistant in VIDI project, 2011-2014). Plasticity and general-purpose genotypes in Dandelion. Currently working as Plant Virologist at NVWA, the Netherlands food and consumer product safety authority.