Research overview
Research Profile & General Overview
The lab investigates fast genomic change in plants – on individual and evolutionary time-scales, in populations, and as response to external stimuli. For this, we recognize repetitive DNAs as agents of genomic change. Although they impact evolution, chromosome setup, gene regulation and adaptation, their repetitive nature impairs straight-forward analysis. Hence, repetitive DNAs are barely understood. This needs to change urgently as they can inform breeding of resilient crops, needed to buffer climate change.
Please see Projects and Publications for defined research examples.
Research Pillars
What is the molecular basis of fast genomic change -- and how can we use this? We explore these questions in four research pillars, targeting DNA (🧬), DNA methylation (📍) and chromosomes (🧶), as well as their application in breeding (🌱):
🧬(pillar I): repetitive DNAs as agents of fast genomic change;
📍(pillar II): the epigenetic basis of clonal change, heritability and adaptivity;
🧶(pillar III): the evolutionary trajectory of chromosomes and genomes; &
🌱(pillar IV): applications in (epi)marker development and genotype selection for breeding of resilient crops and trees.
FAQs
Which plants do we work with?
As the genome is at the center of our research, we occasionally switch/add research plants, if we think that we can make a worthwhile contribution. Our experience spans model and non-model plants, including Arabidopsis thaliana as well as crops (beets, quinoa, saffron crocus), trees (poplars, willows, mangos, larches, spruces), and horti- and floriculturally relevant species (camellias, cranberries, bananas).
As we hope to contribute to finding solutions for mitigating the problems of climate change, we take care to always include plants from agricultural and forest ecosystems into our research portfolio.
🌹. 🥀. 🌺. 🌻. 🌼. 🌷. 🌱. 🪴. 🌲. 🌳. 🌴. 🌵. 🌾. 🌿. ☘. 🍀. 🍁. 🍂. 🍃 🍇. 🍈. 🍉. 🍊. 🍋. 🍌. 🍍. 🥭. 🍎. 🍏. 🍐. 🍑. 🍒. 🍓. 🥝. 🍅. 🥥
Why is research on repetitive DNAs relevant and timely?
Repetitive DNAs (1) drive genome evolution, (2) rewire gene-regulatory networks, and (3) form the structural backbones of chromosomes. Due to their fast impact on genome evolution and regulation, they carry large roles in adaptation to the effects of climate change. The molecular basis for understanding and modifying plant adaptation is urgently needed to provide food/wood/environmental security. With long-read sequencing and emerging cytogenomics, there has never been a time more fitting to address repeat-derived genomic divergence and impact.
Which repetitive DNAs do we investigate?
We focus on transposable elements (TEs) that are dispersed through the genome. Besides TE identification and annotation, we assess their activation to understand their potential to modify genomes. As TEs can carry promoters or stress-responsive domains, they may hold one of the keys of understanding the molecular basis of adaptation. Measuring the impact of TEs on surrounding genes contributes to understanding and modifying regulatory networks.
Being critical components of chromosomes, we also investigate tandem repeats, especially satellite DNAs and ribosomal genes. Tandem repeats build chromosomal structures, such as the centromere, and are among the fastest-evolving genome components. Hence, their dynamics give insights into speciation, hybridization, and polyploidization processes.
What are our methods?
To investigate molecular and evolutionary mechanisms, we develop and integrate methods from genomics, cytogenetics, epigenetics, and bioinformatics, often in collaborations.
Cytogenetic techniques include fluorescence in situ hybridization along mitotic and meiotic chromosomes, followed by microscopy. Cytogenetics profits increasingly from omics data and allows developing of new techniques, e.g. for chromosome painting.
(Epi)genomics includes high-throughput, long read and enrichment strategies.
We also develop software (pipelines) for DNA analysis and transposon annotation and distribute those under open licences.
