Biology subjects

Schneeberger, K.

Publications and source records attributed to Schneeberger, K..

At least 19 recordsLinked to original sources

bioRxiv2026

The alpine Edelweiss genome reveals a recent allotetraploid origin and localized subgenome dominance

Few plants symbolize the European Alps as profoundly as Edelweiss (Leontopodium nivale subsp. alpinum), yet its evolutionary origin and genomic constitution has remained elusive. We present a haplotype-resolved, chromosome-scale assembly of an L. n. alpinum accession from the Central Alps. The 3.15-Gb genome resolved 48 chromosomes in four phased sets with balanced gene and repeat landscapes. Phylogenomics partitioned these sets into two progenitor-derived subgenomes, DE and FG, demonstrating an allotetraploid origin. Comparison with the diploid subspecies L. n. nivale from Southern European Mountains (Appennines) linked DE to this sampled southern lineage, whereas FG derives from another distinct, unresolved diploid progenitor. Chloroplast genomes placed the plastid split between central Alps and Apennine samples in the recent Pleistocene, approximately 20,000 years ago, and LTR insertion-age profiles revealed recent retrotransposon activity consistent with genome shock following allopolyploidization. Although the subgenomes are broadly balanced,large inversions and elevated divergence concentrate on three chromosome groups. On Chromosome 3, structural complexity coincides with FG hypermethylation and DE-biased expression, revealing localized subgenome dominance. Together, these results support previous studies that suggested a westward expansion from the Asian centre of Leontopodium diversity, followed by differentiation and hybridization of closely related European lineages. Our assembly positions Edelweiss as an alpine model for recent allotetraploidy and enables genomic studies of demography, selection and high-alpine adaptation.

evolutionary biology↗

bioRxiv2026

Evolutionary diversification of the SymRK receptor family in land plants

Plant receptor-like kinases (RLKs) are involved in diverse processes, ranging from growth and reproduction to interactions with microbes. Variation in the extracellular domains delineates several RLKs subfamilies, including the malectin-like domain leucine-rich repeat receptor-like kinases (MLD-LRR-RLKs). Symbiosis Receptor-like Kinase (SymRK) is the prototypical member of MLD-LRR-RLKs and is required for microbial accommodation in host roots during root endosymbiosis. Yet, comparative phylogenetic analysis of SymRK orthologs in the broader context of MLD-LRR-RLK subfamily evolution remains limited. In this study, we examined the inventory, phylogeny and clade-specific evolutionary and transcriptional characteristics of this receptor group. SymRK and its closest homologs are present in most land plant lineages and group into four major clades and six additional species-specific clades. These clades can be distinguished by their evolutionary characteristics as either conserved with reduced gene copy number changes (including SymRK) or expanded and diversified, as observed in clade IV. Clade IV dynamics are largely driven by tandem gene duplications, which often arise within gene clusters. We further analysed the evolutionary characteristics of MLD-LRR-RLKs at the population level in Arabidopsis thaliana accessions. We found that some genes are conserved across accessions and are therefore likely to be functionally important, whereas a subset of genes, often located within tandem clusters, are highly diverse and likely contribute to accession-specific adaptations. Finally, most MLD-LRR-RLKs in the A. thaliana Col-0 accession are expressed in roots and respond broadly to biotic stimuli at the transcriptional level. Notably, clustered genes frequently exhibited divergent expression profiles, suggesting transcriptional diversification. Together, we revealed two contrasting evolutionary characteristics among members of the MLD-LRR-RLK subfamily, potentially associated with their functions in plants.

plant biology↗

bioRxiv2026

Optimization of isolation, expansion, and differentiation of canine intestinal organoids

Intestinal organoids are three-dimensional in vitro structures derived from stem cells and serve as a valuable model for studying intestinal biology and pathophysiology. This study optimized the isolation, expansion, and differentiation of canine intestinal organoids from duodenum and colon. Organoids were generated from canine intestinal crypts and cultured in Matrigel with a growth factor cocktail. The impact of prostaglandin E2 (PGE2) concentration on organoid growth was evaluated, and a two-phase differentiation protocol--comprising patterning and differentiation media--was implemented, including interleukin (IL)-22 in the duodenal differentiation phase. Organoids cultured with 100 nM PGE2 exhibited increased crypt budding and organoid-forming efficiency, indicative of enhanced stem cell proliferation. Differentiated organoids expressed key intestinal markers (VIL1, SI, CHGA, MUC2), and forskolin-induced swelling demonstrated functional Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) activity. Although the sample size (n=2) limits generalizability, this optimized protocol provides a relevant in vitro model for studying canine intestinal function. The model can be used in future research for disease modelling and translational applications, supporting downstream studies in gastrointestinal disease, drug permeability, and comparative One Health research.

cell biology↗

bioRxiv2026

coelsch: Platform-agnostic single-cell analysis of meiotic recombination events

BackgroundMeiotic recombination creates genetic diversity through reciprocal exchange of haplotypes between homologous chromosomes. Scalable and robust methods for mapping recombination breakpoints are essential for understanding meiosis and for genetic mapping. Single cell sequencing of gametes offers a direct approach to recombination mapping, yet the effect of technical differences between single-cell sequencing methods for crossover detection remains unclear. ResultsWe benchmark single cell methods for droplet-based chromatin accessibility and RNA sequencing and plate-based whole-genome amplification for mapping meiotic recombination in Arabidopsis thaliana. For this purpose we introduce two novel open-source tools coelsch_mapping_pipeline and coelsch for haplotype-aware alignment and per-cell crossover detection, using them to recover known recombination frequencies and quantify the effects of coverage sparsity. We subsequently apply our approach to a panel of 40 recombinant F hybrids derived from crosses of 22 diverse natural accessions, successfully recovering genetic maps for 34 F1s in a single dataset. This analysis reveals substantial variation in recombination rate and identifies a [~]10 Mb pericentric inversion in the accession Zin-9, the largest natural inversion reported in A. thaliana to date. ConclusionsThese results demonstrate the applicability and scalability of single-cell gamete sequencing for high-throughput mapping of meiotic recombination, and highlight the strengths and limitations of different single-cell modalities. The accompanying open-source tools provide a framework for haplotyping and crossover detection analysis using sparse single-cell sequencing data. Our methodology enables parallel analysis of large numbers of hybrids in a single dataset, removing a major technical barrier to large-scale studies of natural variation in recombination rate.

bioinformatics↗

bioRxiv2026

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 chromosomes1. While essential in most sexually reproducing organisms, recombination is variably regulated and can be absent in some lineages, a condition known as achiasmy2. 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 meiosis3. 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.

evolutionary biology↗

bioRxiv2025

The mutational dynamics of the Arabidopsis centromeres

Centromeres are specialized chromosomal regions essential for sister chromatid cohesion and spindle attachment during cell division. Although many centromeres consist of highly variable tandem repeat arrays, the mutational processes driving this variability remain poorly understood. Here, using replicated genome assemblies of Arabidopsis thaliana mutation accumulation (MA) lines, we define the centromeric mutation spectrum. We find that point mutations occur at an almost tenfold higher rates than in chromosome arms, largely driven by non-allelic gene conversion between closely linked repeat units. Large kilobase-scale indels are also frequent and consistently preserve the tandem repeat array by adding or removing only complete repeat units. Analysis of MA lines deficient in the helicase RTEL1 supports the involvement of homology-directed DNA repair in these mutational processes. Moreover, simulations of sequence turnover using the centromere-specific mutation spectrum recapitulate the emergence of homogenized repeat blocks characteristic of natural centromeres. Together, our results show that centromere evolution is driven by a distinct mutational spectrum shaped by homology-directed DNA repair, providing a quantitative framework for how local mutational processes generate and maintain the large-scale architecture of centromeric DNA.

genomics↗

bioRxiv2025

Genomic basis of adaptation to serpentine soil in two Alyssum species shows convergence with Arabidopsis across 20 million years of divergence

Background and AimsSerpentine outcrops, characterized by low nutrient availability, high heavy metal concentrations, propensity to drought, and island-like distributions, offer valuable systems to study parallelisms in repeated adaptation to extreme environments. While shared phenotypic manifestation of adaptation to serpentine environments has been investigated in many species, it is still unclear whether there may be a common genetic basis underlying such responses. Here we assess local adaptation to serpentine soil and infer the parallel genetic signatures of local adaptation to serpentine environments in two thus far unexplored closely related species, Alyssum gmelinii and Alyssum spruneri (Brassicaceae). Then we measure gene- and function-level convergence with the previously explored Arabidopsis arenosa, to reveal candidate shared adaptive strategies within Brassicaceae. MethodsWe tested for adaptation using a reciprocal substrate-transplant experiment in A. gmelinii. Then, after assembling a reference genome, we generated population-level sequencing data of four population pairs and performed genome scans for directional selection to infer serpentine adaptive candidate genes in Alyssum. Finally, we compared candidate gene lists with those inferred in similar experiments in Arabidopsis arenosa and used protein-protein interaction networks to discern functional convergence in serpentine adaptation. Key ResultsIndependent colonization of serpentine environments by Alyssum populations is associated with footprints of selection on genes related to ion transport and homeostasis, nutrient and water uptake, and life-history traits related to germination and reproduction. Reciprocal transplant experiments demonstrated that adapted plants germinate sooner and exhibit better growth in serpentine conditions while excluding heavy metals and increasing Ca uptake in their tissues. Finally, a significant fraction of such genes and molecular pathways is shared with Arabidopsis arenosa. ConclusionsWe show that genetic adaptation to the multi-factorial challenge imposed by serpentine environments involves key pathways that are shared not only between closely related species, but also between Brassicaceae tribes of [~]20 Mya divergence.

evolutionary biology↗

bioRxiv2024

The 1001G+ project: A curated collection of Arabidopsis thaliana long-read genome assemblies to advance plant research

Arabidopsis thaliana was the first plant for which a high-quality genome sequence became available. The publication of the first reference genome sequence almost 25 years ago was already accompanied by genome-wide data on sequence polymorphisms in another accession, or naturally occurring strain. Since then, inventories of genome-wide diversity have been generated at increasingly precise levels. High-density genotype data for A. thaliana, including those from the 1001 Genomes Project, were key to demonstrating the enormous power of GWAS in inbred populations of wild plants, and the comparison of intraspecific polymorphism with interspecific divergence has illuminated many aspects of plant genome evolution. Over the past decade, an increasing number of nearly complete genome sequences have been published for many more accessions. Here, we highlight the diversity of a curated collection of previously published and so far unpublished genome sequences assembled using different types of long reads, including PacBio Continuous Long Reads (CLR), PacBio High Fidelity (HiFi) reads, and Oxford Nanopore Technologies (ONT) reads. This 1001 Genomes Plus (1001G+) resource is being made available at http://1001genomes.org. We invite colleagues with yet unpublished genome assemblies from A. thaliana accessions to contribute to this effort.

genomics↗

bioRxiv2024

Expression quantitative trait locus mapping in recombinant gametes using single nucleus RNA sequencing

Phenotypic differences between individuals of a species are often caused by differences in gene expression, which are in turn caused by genetic variation. Expression quantitative trait locus (eQTL) analysis is a methodology by which we can identify such causal variants. Scaling eQTL analysis is costly due to the expense of generating mapping populations, and the collection of matched transcriptomic and genomic information. We developed a rapid eQTL analysis approach using single-cell/nucleus RNA sequencing of gametes from a small number of heterozygous individuals. Patterns of inherited polymorphisms are used to infer the recombinant genomes of thousands of individual gametes and identify how different haplotypes correlate with variation in gene expression. Applied to Arabidopsis pollen nuclei, our approach uncovers both cis- and trans-eQTLs, ultimately mapping variation in a master regulator of sperm cell development that affects the expression of hundreds of genes. This establishes snRNA-sequencing as a powerful, cost-effective method for the mapping of meiotic recombination, addressing the scalability challenges of eQTL analysis and enabling eQTL mapping in specific cell-types.

bioinformatics↗

bioRxiv2024

Mass Generation and Long-term Expansion of Hepatobiliary Organoids from Adult Primary Human Hepatocytes

Adult primary human hepatocytes (PHHs) are the gold standard in ex vivo toxicological studies and possess the clinical potential to treat patients with liver disease as advanced therapy medicinal products (ATMPs). However, the utility of this valuable cell type has been limited by short-term functionality and limited expansion potential in vitro. While notable advances have been made in the long-term maintenance of primary hepatocytes, there has been limited success in driving the efficient generation and expansion of adult PHH-derived organoids which recapitulate both liver tissue architecture and function, hampering in vitro studies and regenerative medicine applications. Here we describe the mass generation and long-term expansion of hepatobiliary organoids with functionally interconnected hepatic and biliary-like structures from adult primary human hepatocytes. Hepatobiliary organoids retain the expression of lineage and functional markers, closely resembling PHH, while also acquiring the expression of regeneration, fetal and biliary markers. Organoids perform key hepatocyte functions while proliferating and can be matured to enhance their functionality. As a proof-of-principle, we demonstrate that hepatobiliary organoids can recapitulate hallmarks of cholestasis and steatosis in vitro. Moreover, we show that hepatocytes can be transfected, transduced and gene edited in 3D prior to organoid generation, facilitating a wide range of applications. Our novel hepatobiliary organoid system bridges the gap between short-term functionality of primary human hepatocytes and the need for scalable, long-term organoid models of the adult liver, offering immense potential for drug testing, disease modeling, and advanced therapeutic applications.

cell biology↗

bioRxiv2024

Epigenetic and transcriptional consequences of chemically induced transposon mobilization in the endosperm

Genomic imprinting, an epigenetic phenomenon leading to parent-of-origin-specific gene expression, has independently evolved in the endosperm of flowering plants and the placenta of mammals--tissues crucial for nurturing embryos. While transposable elements (TEs) frequently colocalize with imprinted genes and are implicated in imprinting establishment, direct investigations of the impact of de novo TE transposition on genomic imprinting remain scarce. In this study, we explored the effects of chemically induced transposition of the Copia element ONSEN on genomic imprinting in Arabidopsis thaliana. Through the combination of chemical TE mobilization and doubled haploid induction, we generated a line with 40 new ONSEN copies. Our findings reveal a preferential targeting of maternally expressed genes (MEGs) for transposition, aligning with the colocalization of H2A.Z and H3K27me3 in MEGs-- both previously identified as promoters of ONSEN insertions. Additionally, we demonstrate that chemically-induced DNA hypomethylation induces global transcriptional deregulation in the endosperm, leading to the breakdown of MEG imprinting. This study provides insights into the consequences of chemically induced TE remobilization in the endosperm, underscoring the need for cautious interpretation of the connection between TEs and genomic imprinting.

plant biology↗

bioRxiv2024

The majority of somatic mutations in fruit trees are layer-specific

BackgroundAll plant tissues and organs develop from meristems. Plant meristems are structured organs consisting of distinct layers of stem cells. Somatic mutations occurring in one of these layers can propagate into large sectors of the plant. However, the frequency and characteristics of meristematic mutations that form the basis of somaclonal phenotypic variation remain unclear. ResultsHere, we analysed the frequency and distribution of somatic mutations in an individual Apricot tree. For this, we sequenced the genomes of fruit samples corresponding to distinct meristematic cell layers selected across the entire tree. Most somatic mutations (>90%) were specific to individual layers. Genotyping the somatic mutations in leaves sampled next to the fruits confirmed their meristematic origin. Interestingly, layer 1 (epidermis) had a higher mutation load than layer 2 (mesocarp), implying differential mutational dynamics between the layers. The somatic mutations followed the branching pattern of the tree. These factors led to the unexpected observation that the layer 1 samples from different branches were more similar to each other than to layer 2 samples of the same branch. Further, using single-cell RNA sequencing, we demonstrated that the layer-specific mutant alleles could only be found in the transcripts of the respective, layer-specific cell clusters and could form the basis for somaclonal phenotypic variation. ConclusionsHere, we analyzed the prevalence and distribution of somatic mutations with meristematic origin. Our insights into the yet unexplored layer-specificity of such somatic mutations outlined how they can be identified and how they impact the breeding of clonally propagated crops.

genomics↗

bioRxiv2023

Meiotic recombination dynamics in plants with repeat-based holocentromeres shed light on the primary drivers of crossover patterning

Centromeres strongly affect (epi)genomic architecture and meiotic recombination dynamics influencing the overall distribution and frequency of crossovers. Here, we studied how recombination is regulated and distributed in the holocentric plant Rhynchospora breviuscula, a species lacking localised centromeres. Combining immunocytochemistry, chromatin analysis and high-throughput single-pollen sequencing, we discovered that crossover frequency is higher at ends related to centred chromosomal regions. Contrasting the diffused distribution of (epi)genetic features and hundreds of repeat-based centromeric units. Remarkably, we found that crossovers were abolished at core centromeric units but not at their vicinity indicating the absence of a centromere effect across repeat-based holocentromeres. We further show that telomere-led pairing and synapsis of homologous chromosomes appear to be the primary force determining the observed U-shaped recombination landscape. While centromere and (epi)genetic properties only affect crossover positioning locally. Our results suggest that the conserved U-shaped crossover distribution of eukaryotes is independent of chromosome compartmentalisation and centromere organisation.

genomics↗

bioRxiv2023

The identification and analysis of meristematic mutations within the apple tree that developed the RubyMac sport mutation

Understanding the molecular basis of sport mutations in fruit trees can accelerate breeding of novel cultivars. For this, we analyzed the DNA of the apple tree that evolved the RubyMac phenotype through a sport mutation that introduced changes in fruit coloration in upper branches of the tree. Unexpectedly, we not only found 46 de novo mutations, but also 54 somatic gene conversions (i.e., loss-of-heterozygosity mutations) distinguishing the mutant and wild-type branches of the tree. Approximately 30% of the de novo mutations and 80% of the gene conversions were observed only in specific cells layers suggesting that they occurred in the corresponding meristematic layers. Interestingly, the de novo mutations were enriched for GC=>AT transitions, while the gene conversions showed the opposite bias for AT=>GC transitions suggesting that GC-biased gene conversions have the potential to counteract the AT-bias of de novo mutations. By comparing the gene expression patterns in fruit skins from mutant and wild-type branches, we found 56 differentially expressed genes including 18 that were involved in anthocyanin biosynthesis. While none of the differently expressed genes harbored a mutation, we found that some of the mutations affected the integrity of candidate genes in regions of the genome that were recently associated with natural variation in fruit coloration.

genomics↗

bioRxiv2022

plotsr: Visualising structural similarities and rearrangements between multiple genomes

SummaryThird-generation genomic technologies have led to a sharp increase in the number of high-quality genome assemblies. This allows the comparison of multiple assembled genomes of individual species and demands for new tools for visualising their structural properties. Here we present plotsr, an efficient tool to visualize structural similarities and rearrangements between multiple genomes. It can be used to compare genomes on chromosome level or to zoom in on any selected region. In addition, plotsr can augment the visualisation with regional identifiers (e.g. genes or genomic markers) or histogram tracks for continuous features (e.g. GC content or polymorphism density). Availability and implementationplotsr is implemented as a python package and uses the standard matplotlib library for plotting. It is freely available under the MIT license at GitHub (https://github.com/schneebergerlab/plotsr) and bioconda (https://anaconda.org/bioconda/plotsr). ContactManish Goel (manish.goel@lmu.de), Korbinian Schneeberger (k.schneeberger@lmu.de)

bioinformatics↗

bioRxiv2022

The megabase-scale crossover landscape is independent of sequence divergence

Meiotic recombination frequency varies along chromosomes and strongly correlates with sequence divergence. However, the causality underlying this correlation is unclear. To untangle the relationship between recombination landscapes and polymorphisms, we characterized the genome-wide recombination landscape in the absence of polymorphisms, using Arabidopsis thaliana homozygous inbred lines in which a few hundred genetic markers were introduced through mutagenesis. We found that megabase-scale recombination landscapes in inbred lines are strikingly similar to the recombination landscapes in hybrids, with the sole exception of heterozygous large rearrangements where recombination is prevented locally. In addition, we found that the megabase-scale recombination landscape can be accurately predicted by chromatin features. Our results show that polymorphisms are not causal for the shape of the megabase-scale recombination landscape, rather, favor alternative models in which recombination and chromatin shape sequence divergence across the genome.

genetics↗

bioRxiv2021

Chromosome-scale and haplotype-resolved genome assembly of a tetraploid potato cultivar

Potato is the most important tuber crop in the world. However, separate reconstruction of the four haplotypes of its autotetraploid genome remained an unsolved challenge. Here, we report the 3.1 Gb haplotype-resolved (at 99.6% precision), chromosome-scale assembly of the potato cultivar Otava using high-quality long reads coupled with single-cell sequencing of 717 pollen genomes and Hi-C data. Unexpectedly, almost 50% of the genome were found to be identical-by-descent due to recent inbreeding, which contrasted by highly abundant structural rearrangements involving around 20% of the genome. Among 38,214 genes, only 54% were present in four haplotypes with an average of 3.2 copies per gene. Analyzing the leaf transcriptome as example, we found that 11% of the genes featured differently expressed alleles in at least one of the haplotypes, of which 25% are likely regulated through allele-specific DNA methylation. Our work sheds light on the recent breeding history of potato, the functional organization of its tetraploid genome and has the potential to strengthen the future of genomics-assisted breeding.

genomics↗

bioRxiv2020

The evolutionary dynamics of genetic incompatibilities introduced by duplicated genes in Arabidopsis thaliana

Although gene duplications provide genetic backup and allow genomic changes under relaxed selection, they may potentially limit gene flow. When different copies of a duplicated gene are pseudo-functionalized in different genotypes, genetic incompatibilities can arise in their hybrid offspring. While such cases have been reported after manual crosses, it remains unclear whether they occur in nature and how they affect natural populations. Here we identified four duplicated-gene based incompatibilities including one previously not reported within an artificial Arabidopsis intercross population. Unexpectedly, however, for each of the genetic incompatibilities we also identified the incompatible alleles in natural populations based on the genomes of 1,135 Arabidopsis accessions published by the 1001 Genomes Project. Using the presence of incompatible allele combinations as phenotypes for GWAS, we mapped genomic regions which included additional gene copies which likely rescue the genetic incompatibility. Reconstructing the geographic origins and evolutionary trajectories of the individual alleles suggested that incompatible alleles frequently co-exist, even in geographically closed regions, and that their effects can be overcome by additional gene copies collectively shaping the evolutionary dynamics of duplicated genes during population history.

evolutionary biology↗