RESEARCH
Nature is full of diversity. Understanding this natural diversity is important to not only answer how different organisms evolve, but also to improve future conservation and agriculture. Our research is organized into three overarching themes.
Crop Genomics & Domestication
We apply advanced genomic assemblies to understand the history and future of our food. By moving beyond simple reference genomes to haplotype-resolved pangenomes, we are unlocking the genetic potential of established crops and accelerating the domestication of new ones.
The Potato Pan-genome
Craig Dent Sergio Tusso Lisa Baus Ana KurdadzeThe Challenge: Potato is a genetically complex autotetraploid. Standard sequencing collapses its four chromosome copies into one, losing critical variation.
Our Work: We constructed a haplotype-resolved pan-genome of European potato. By resolving all four haplotypes simultaneously, we revealed extraordinarily high sequence diversity between haplotypes — yet surprisingly low haplotype diversity across the continent, the fingerprint of historical breeding bottlenecks stretching back to the crop's introduction to Europe in 1570 and the devastating losses of the Irish Famine.
Nature (2025).
Theoretical and Applied Genetics (2026).
Aardaker: The Protein Potato
Ana KurdadzeWhile nature offers thousands of edible plant species, global agriculture is built around a small set of widely cultivated staple crops. We are working to change that. By harnessing the power of modern genomics, we aim to unlock this untapped potential and revive forgotten crops through de novo domestication.
Meet the Aardaker (L. tuberosus). Native to Eurasia, this member of the Fabaceae family is a nitrogen-fixing powerhouse that produces protein-rich tubers. We are generating a chromosome-scale reference genome and conducting a holistic population genomics analysis to uncover the species' evolutionary origins, characterize its existing genetic architecture, and assess its adaptive potential.
We work directly with breeders and openly share our insights to ensure the Aardaker makes the leap from scientific curiosity to a resilient, stable crop. More on the applied work at Aardaia →
Apple Somatic Evolution
The Mystery of "Sport" Mutations: Many fruit varieties, such as the dark-red 'RubyMac' apple, arise spontaneously as somatic mutations on a single branch of a tree. Understanding these "bud sports" is crucial for breeding improved cultivars with desirable traits.
Genomic Forensics: We sequenced the genome of a single apple tree to identify the specific mutations separating wild-type and mutant branches. We discovered that somatic evolution is driven not just by new mutations, but frequently by gene conversions (loss of heterozygosity) that are specific to individual cell layers in the meristem.
BMC Plant Biology (2024).
Meiotic Dynamics & Evolution
Genetic diversity is driven by the reshuffling of chromosomes during meiosis. We pioneer single-cell sequencing technologies to understand the controlled (recombination) and uncontrolled (mutations) events that drive genomic diversity, and finally build the basis for all the variation in life.
Single-Nucleus Pollen Sequencing
Samija Amar Matthew T. Parker Jonas FreudigmannA Versatile Platform for Haploid Genetics: We are pioneering single-nucleus sequencing technologies to study the haploid life cycle of plants. By isolating and sequencing individual pollen nuclei, we can treat each gamete as an independent "offspring." This allows us to perform high-resolution genetic mapping without the need for time-consuming crosses or large progeny populations.
Beyond Recombination: While our primary focus has been mapping crossover landscapes, this technology is broadly applicable. We develop methods to analyze gene expression dynamics during pollen development, characterize rare cell types, and investigate the transcriptomic consequences of haploid selection. Our group actively maintains the tools (e.g., coelsch) required to analyze these complex, sparse molecular datasets.
preprint (2026).
PLOS Biology (2025).
Natural Variation in Recombination
Matthew T. Parker Raúl Wijfjes Jonas FreudigmannPopulation-Scale Mapping: We investigate how genetic diversity shapes the landscape of meiotic recombination. By extending our single-cell framework to natural populations, we can identify the specific genetic modifiers — like trans-acting factors or local structural variants such as inversions — that control where and how frequently crossovers occur.
Genetics of the Haploid Phase: Beyond recombination, we map the regulatory networks of the gamete itself. Using single-nucleus eQTL mapping, we uncover how cis- and trans-regulatory variation drives gene expression in pollen. For example, we recently identified DUO3 as a master regulator of sperm cell development by linking haplotype inheritance to transcriptomes in single nuclei.
Interspecific variation in recombination: Species of the Brassicaceae family vary in genome structure and ecological characteristics, while their core meiotic genes are well-conserved. We aim to identify how this variation drives differences in recombination landscape between species and the degree to which specific factors (mating system, ploidy, chromosome number, translocations) contribute.
preprint (2026).
PLOS Biology (2025).
Centromere Evolution
Xiao DongDeciphering Centromere Dynamics: Centromeres are essential for cell division but evolve rapidly. We use replicated, error-free genome assemblies to track the "birth" of mutations in these repetitive regions. Our work reveals a unique mutational spectrum dominated by non-allelic gene conversions and small, structure-preserving indels.
From Chaos to Order: We model how these fundamental processes shape genome architecture. Our simulations demonstrate that simple, small-scale mutations are sufficient to drive the self-organization of complex, megabase-scale Higher-Order Repeat (HOR) structures, providing a unified theory for centromere evolution.
bioRxiv (2025).
Methods & Computational Tools
Modern biology is data-driven. We develop the algorithms required to analyze complex structural variations and graph genomes, while simultaneously establishing wet-lab protocols for next-generation sequencing applications.
Pan-genomics
Raúl Wijfjes Craig Dent Leon Rauschning Lisa BausReference Bias: A single linear reference genome captures only a fraction of a species' genetic diversity. It introduces reference bias, causing us to miss genes and structural variants present in the population but absent from the reference.
Aggregating Diversity: Our group develops pan-genomic approaches to comprehensively characterize variation across plant populations and species. By combining long-read sequencing with advanced phasing methods, we construct haplotype-resolved assemblies that reveal the full spectrum of genetic variation.
Evolution of Gene Synteny: Conservation or loss of gene synteny between species can affect gene expression, and subsequently phenotype. Using a panel of diverse Brassicaceae genomes, we investigate conservation of gene synteny across 20 million years of evolution and its implications for gene function.
From chromosome-level pan-genomes of Arabidopsis to phased assemblies of tetraploid potato and comparative resources across the Brassicaceae, our work connects natural variation to phenotypic diversity.
Nature (2025).
Nature Genetics (2024).
Software Infrastructure
Manish Goel Matthew T. Parker Leon RauschningWe develop methods that leverage genomic differences from SNPs to large chromosomal rearrangements. Our most popular tools include:
- SyRI: Synteny and Rearrangement Identifier — finds inversions, translocations, and duplications between whole-genome assemblies.
- plotsr: Visualizes structural similarities and rearrangements between multiple genomes in a single, publication-ready figure.
- coelsch: A set of tools for identifying recombination events at the single nucleus/cell level.
Genome Biology (2019).
Bioinformatics (2022).
preprint (2026).
PLOS Biology (2025).
Advanced Sequencing Methods
Lisa Baus Samija Amar Xiao Dong Sergio Tusso Craig DentA core part of our work is the continuous development and optimization of sequencing protocols and analytical pipelines, ensuring our datasets push the boundaries of what genome assembly can resolve.
Long- and ultra-long-read sequencing: We work to improve nanopore-based sequencing workflows for generating longer, more contiguous reads — a critical step for assembling the highly repetitive regions, centromeres, and structural variants that short-read methods miss entirely.
Single-cell and single-nucleus methods: We develop and refine protocols for single-cell and single-nucleus sequencing applications, from library preparation through to computational analysis. This includes both transcriptomic and genomic approaches tailored for sparse, low-input data.
Crucially, we do not limit these efforts to tractable model organisms. We actively scale and adapt our methods for complex crop genomes — including the highly polyploid potato and the emerging crop Lathyrus tuberosus (Aardaker) — where the genomic complexity demands purpose-built solutions rather than off-the-shelf pipelines.
All assemblies, annotations, and pipelines are shared openly to support the broader community in trait discovery, evolutionary genomics, and plant breeding.
Our Funding
