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Schneeberger Lab

@labschneeberger.bsky.social
258 followers 48 following 30 posts

Genome Plasticity and Computational Genetics. We develop cutting-edge technologies to explore genome evolution! Lab Website: schneebergerlab.org

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Schneeberger Lab @labschneeberger.bsky.social · 28/09/2026
Congratulations to first author Xiao Dong and all collaborators across HHU, MPIPZ, LMU, KIT, MPI Tübingen, and the University of Sheffield! 📰 Press release: www.hhu.de/en/news-arti...
hhu.de
Biology: Publication in Nature
Centromeres are crucial for cell division and emerged early in evolution. A research team led by Heinrich Heine University (HHU) Düsseldorf and the Max Planck Institute for Plant Breeding Research (MP...
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Schneeberger Lab @labschneeberger.bsky.social · 28/09/2026
So, can these local mutation patterns generate megabase-scale structures? Yes! Forward simulations parameterized by our mutation spectrum revealed that kb-scale indels and NAGC alone naturally build the megabase homogenized blocks seen in nature. A beautiful example of emergence in genome evolution!
Sequence identity heat maps from forward-in-time simulations of centromere evolution. On the left, the starting point is the Col-0 centromere of chromosome 1, about 2.5 Mb long. Three independent simulations are shown as rows, each at 30,000, 60,000, 90,000, 120,000 and 150,000 generations. Red squares along the diagonal mark homogenized blocks of highly similar repeats. Over time, blocks expand, shrink, disappear and newly emerge, with some reaching megabase sizes similar to those in natural centromeres. Centromere length also varies between simulations, from about 1 to 5 Mb.
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Schneeberger Lab @labschneeberger.bsky.social · 28/09/2026
In lines deficient in the anti-recombinase helicase RTEL1, tandem-repeat-preserving indels became more frequent and longer. One was a 105-kb deletion that still kept repeat periodicity intact! This points to homology-directed DNA repair as a central driver of centromere evolution.
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Schneeberger Lab @labschneeberger.bsky.social · 28/09/2026
Centromeres mutate differently from chromosome arms: • Point mutation rate is ~10x higher • An estimated ~70% of point mutations stem from non-allelic gene conversion (NAGC) • Kilobase-scale indels are frequent, but only add/remove full 178-bp repeat units, keeping periodicity intact
Schematic of centromere evolution in Arabidopsis thaliana. A plant and a chromosome zoom into the centromere, drawn as a row of coloured arrows representing tandem repeat units. Around the central label "Dynamic turnover while preserving tandem repeat structure", a cycle of four mutation types is shown: point mutations in individual repeat units; insertions and deletions that add or remove whole repeat units; sequence copying between repeat units through non-allelic gene conversion; and occasional transposable element insertions.
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Schneeberger Lab @labschneeberger.bsky.social · 28/09/2026
Centromeres proved to be among the most accurately assembled regions of the genome. They make up 8.3% of the sequence but less than 1% of assembly errors, likely because they are depleted of the simple sequence repeats that cause most errors elsewhere.
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Schneeberger Lab @labschneeberger.bsky.social · 28/09/2026
To measure centromeric mutations directly, we generated replicated genome assemblies of Arabidopsis mutation accumulation (MA) lines. Differences between replicate assemblies of the same plant reveal assembly errors, so genuine mutations can be called with confidence!
Experimental design. A single Col-0 plant gives rise to two lineages, A and B, each propagated by single-seed descent over many generations. From the final plant of each lineage, three independent pools of offspring were sequenced and assembled: two with PacBio HiFi (A1, A2, B1, B2) and one with Oxford Nanopore (A3, B3). Differences between replicates of the same lineage indicate assembly errors, and differences between lineages indicate mutations.
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Schneeberger Lab @labschneeberger.bsky.social · 28/09/2026
Centromeres are essential for chromosome segregation, a function conserved across eukaryotes. Yet many centromeres consist of highly variable but internally remarkably homogenized tandem-repeat arrays, whose evolutionary dynamics remain poorly understood.
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Schneeberger Lab @labschneeberger.bsky.social · 28/09/2026
Thrilled to share our new @nature.com paper from Xiao Dong on the mutational dynamics of centromeres in Arabidopsis thaliana! 🌱 A quick thread on what we found... 🔗 doi.org/10.1038/s415...
doi.org
The mutational dynamics of the Arabidopsis centromeres - Nature
Centromeres in Arabidopsis thaliana evolve through frequent insertions and deletions of repeat units and increased rates of point mutations driven by homology-directed repair, a mutation spectrum that...
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Schneeberger Lab @labschneeberger.bsky.social · 03/03/2026
For the R3a/b locus, we found striking evidence for at least two distinct haplotypes circulating in European breeding 🔍 We also generated a draft genome assembly of S. demissum 'El Desierto', confirming a single sub-genome origin of the introgression.
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Schneeberger Lab @labschneeberger.bsky.social · 03/03/2026
These two high-frequency introgressions trace back to S. tuberosum Group Andigena clone CPC 1673 (H1 nematode resistance, Chr5) and S. demissum (R3a/b late blight resistance, Chr11) - both entering the gene pool through multiple independent lineages.
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Schneeberger Lab @labschneeberger.bsky.social · 03/03/2026
We extended the MCA framework to SNP data 🧬 Using a 20K SNP array, we identified post-1945 introgressed haplotypes and traced their spread through the pedigree. Two introgressions now occur in ~half of all European varieties!
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Schneeberger Lab @labschneeberger.bsky.social · 03/03/2026
We first curated a pedigree database of 12,041 potato varieties 📚 and identified the Major Contributing Ancestors (MCAs) of 1,209 European varieties. Top contributors: Katahdin 🇺🇸, Saskia 🇳🇱, and Agria 🇩🇪, present in the ancestry of the majority of modern European potato!
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Schneeberger Lab @labschneeberger.bsky.social · 03/03/2026
The European potato germplasm traces back to just a few founding genotypes 🌱 Since then, introgressions from wild relatives have reshaped the gene pool. However, how these haplotypes spread through breeding lineages has remained largely unresolved.
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Schneeberger Lab @labschneeberger.bsky.social · 03/03/2026
🥔 We traced the ancestral legacy of modern breeding introgressions in European potato! Combining pedigree records & genome-wide SNPs, we reveal which wild relatives shaped the European gene pool and how. 📄 doi.org/10.1007/s00122-025-05143-z
doi.org
Tracing modern breeding introgressions in European potato - Theoretical and Applied Genetics
The European potato germplasm originated from a few founding genotypes, and its narrow genetic base has since been broadened through introgressions from wild relatives. We combined pedigree records an...
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Schneeberger Lab @labschneeberger.bsky.social · 23/02/2026
🌾 We have an open postdoc position in Plant Genomics in our group at HHU Düsseldorf! If you enjoy computational biology, asking big questions, and the satisfaction of code working on the first try, check out schneebergerlab.org/career/ Apply by Mar. 31 | 3-year postdoc | German skills required
schneebergerlab.org
Career – Schneeberger Lab
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Schneeberger Lab @labschneeberger.bsky.social · 05/02/2026
Finally, we applied our framework to a diversity panel of 34 F₁ hybrids 🌍 This analysis revealed substantial natural variation in recombination rates and uncovered a large ~10 Mb pericentric inversion in the accession Zin-9 - the largest natural inversion reported in A. thaliana to date! 🔍
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Schneeberger Lab @labschneeberger.bsky.social · 05/02/2026
Validating our approach, we analyzed Arabidopsis meiotic mutants ( zyp1, figl1, recq4ab ) 🧬 We successfully recovered known recombination frequencies and landscape alterations, confirming that single-cell haplotyping can measure differences in recombination rates.
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Schneeberger Lab @labschneeberger.bsky.social · 05/02/2026
We developed coelsch and coelsch_mapping_pipeline to address this 🛠️ We benchmarked droplet-based (scATAC, scRNA) and plate-based (scWGA) methods, quantifying the trade-offs between throughput and coverage sparsity for accurately calling crossovers.
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Schneeberger Lab @labschneeberger.bsky.social · 05/02/2026
Next to traditional progeny sequencing, single-cell sequencing of gametes offers a direct approach to recombination mapping. 🌱 Yet, the effect of technical differences between various single-cell sequencing modalities for crossover detection has remained unclear.
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Schneeberger Lab @labschneeberger.bsky.social · 05/02/2026
Just in time for Karneval, we present coelsch ! 🎭🥳 A platform-agnostic framework for single-cell recombination analysis. We study crossover variation in mutants & natural lines, identifying the largest natural inversion in A. thaliana to date! 📄 doi.org/10.64898/202... 🐱 github.com/schneeberger...
doi.org
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Reposted by Schneeberger Lab
André Marques @amarques.bsky.social · 21/01/2026
3️⃣ Sex without crossovers mimics clonal reproduction in Rhynchospora tenuis 🌱 An extreme meiotic outcome: faithful segregation without crossovers in a holocentric plant. 🔗 doi.org/10.64898/202... #Preprint #GenomeEvolution #Meiosis4eva #centromere #Pangenomics
doi.org
Sex without crossovers mimics clonal reproduction in the holocentric plant Rhynchospora tenuis
Meiotic recombination ensures accurate chromosome segregation and promotes genetic diversity by generating crossovers between homologous chromosomes. While essential in most sexually reproducing organisms, recombination is variably regulated and can be absent in some lineages, a condition known as achiasmy. However, obligate achiasmy in both sexes of a sexual species has not been previously documented. Here, we investigate the beak-sedge Rhynchospora tenuis, a holocentric plant with the lowest known chromosome number among flowering plants (n = 2) and inverted meiosis. Using chromosome-scale genome assemblies from nine accessions, molecular cytogenetics, immunocytochemistry, high-throughput single-gamete sequencing and whole-genome sequencing of controlled crosses, we show that R. tenuis undergoes obligate, genome-wide achiasmy in both male and female meiosis. Despite normal early meiotic axis formation, synapsis fails, crossovers are not detected cytologically or genetically, and univalents persist at metaphase I. Extensive haplotype-specific accumulation of transposable elements (TEs) generates segregation distortion (e.g. meiotic drive), favouring the transmission of larger, TE-rich chromosomes. Remarkably, sexual reproduction is retained with fertilisation producing viable seeds only when translocation-compatible gametes meet, indicating strong post-meiotic selection that eliminates incompatible homozygous combinations. As a result, all surviving offspring are genetically identical to the maternal genotype, effectively restoring heterozygosity each generation and mimicking clonal reproduction. We propose that the combined effects of recombination loss, low chromosome number, holocentricity, inverted meiosis, and selective transmission of longer chromosomes enable faithful segregation and clonal-like inheritance despite sexual reproduction. These findings challenge the boundary between sex and clonality, revealing a unique evolutionary strategy linking genome architecture, recombination loss, and transmission bias. ### Competing Interest Statement The authors have declared no competing interest.
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André Marques @amarques.bsky.social · 21/01/2026
📢 Three new #bioRxiv preprints from our team on holocentric chromosomes. Together, they connect centromere repeat evolution, karyotype dynamics, and meiotic recombination outcomes, revealing how holocentric genomes evolve and function. 🧬👇
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Schneeberger Lab @labschneeberger.bsky.social · 11/11/2025
🌱 Postdoc position in Plant Genomics/Bioinformatics! Love genome plasticity, computational methods, and solving big questions in plant biology? Join our newly established Institute for Crop Biology at HHU Düsseldorf. More info on schneebergerlab.org/career/ Apply by Nov. 30 | 3-year position
schneebergerlab.org
Career – Schneeberger Lab
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Reposted by Schneeberger Lab
PlantEvolution 🌱🌾 @plantevolution.bsky.social · 27/10/2025
1/2 Want to become up to date with pangenomes and genome graphs and their history? Check out this fantastic review by @zbao.bsky.social! Complexity welcome: Pangenome graphs for comprehensive population genomics #pangenomes #plantscience #genomegraphs www.cambridge.org/core/journal...
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PlantEvolution 🌱🌾 @plantevolution.bsky.social · 06/06/2025
Awesome new work from @labschneeberger.bsky.social (with a small contribution from the Weigel lab). Experimentally observed mutational patterns in centromeres underpin a model that recapitulates intra-specific centromere divergence! www.biorxiv.org/content/10.1...
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Schneeberger Lab @labschneeberger.bsky.social · 06/06/2025
New preprint out from our lab, showing how mutations drive centromere evolution! 🧬 Check out this thread from Xiao Dong to learn more.
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CEPLAS - Cluster of Excellence on Plant Sciences @ceplas.bsky.social · 23/04/2025
🍹In our new #PlantersPunch CEPLAS Postdoc Craig Dent from @labschneeberger.bsky.social @mpipz.bsky.social pz.bsky.social explains why the DNA of the European potato is at the same time diverse...and not diverse🤔! Very exciting story! One question remains: which one tastes best 🥔🍟😜? ➡️ bit.ly/42Mys6F
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Schneeberger Lab @labschneeberger.bsky.social · 16/04/2025
Interested in hearing more about the story behind our latest paper? Check out our blog post and the latest @naturepodcast.bsky.social episode! 📝 go.nature.com/3G73vT7 🎙️ www.nature.com/articles/d41...
go.nature.com
A Recipe for Complexity: Building the Potato Pan-Genome
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Schneeberger Lab @labschneeberger.bsky.social · 16/04/2025
🌱 This resource provides a foundation for genomics-assisted breeding in this challenging autotetraploid crop that feeds over a billion people globally, with particular utility for complex traits governed by multiple loci across different haplotypes! 7/7
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Schneeberger Lab @labschneeberger.bsky.social · 16/04/2025
🍟 We demonstrate this by generating megabase-scale pseudo-genome assemblies for modern cultivars using only cost-effective short reads - including for 'Russet Burbank', THE famous French Fries potato! 6/7
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Schneeberger Lab @labschneeberger.bsky.social · 16/04/2025
📊 Yet, our assemblies already cover ~85% of all European potato genetic diversity, indicating most haplotype diversity in Europe is already captured. To demonstrate practical utility, we converted the pan-genome into a haplotype-graph that enables megabase-scale phasing from short reads only! 5/7
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Schneeberger Lab @labschneeberger.bsky.social · 16/04/2025
🌎 The explanation? While multiple bottlenecks during the potato’s journey from South America to Europe – and later the Irish Potato Famine – reduced haplotype diversity, the high sequence diversity likely stems from wild species introgressions during domestication. 4/7
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Schneeberger Lab @labschneeberger.bsky.social · 16/04/2025
🧩 Paradoxically, despite the high sequence diversity, haplotype diversity was remarkably constrained. From 40 potential distinct haplotypes, we found an average of only 9 unique haplotypes per genomic region. 3/7
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Schneeberger Lab @labschneeberger.bsky.social · 16/04/2025
🧬 We observed extreme sequence diversity between haplotypes of ~ 1 variant per 56 bp between haplotype pairs – the highest reported in any domesticated crop so far! 2/7
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Schneeberger Lab @labschneeberger.bsky.social · 16/04/2025
📢 Excited to share our work out now in @nature.com! 📢 We present the phased pan-genome of tetraploid European potato, based on 10 historical cultivars representing 85% of European potato diversity. Learn more below! 🔗 www.nature.com/articles/s41... 1/7
nature.com
The phased pan-genome of tetraploid European potato - Nature
A haplotype-resolved pan-genome of autotetraploid European potato founder lines shows high nucleotide diversity at remarkably low haplotype diversity, which is probably the result of hybridization eve...
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