Biology subjects

Walkemeier, B.

Publications and source records attributed to Walkemeier, B..

5 recordsLinked to original sources

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↗

bioRxiv2025

Monopolar orientation of kinetochores at meiosis is enforced by COHESINS and their regulators, CENP-C, and the deSUMOylase SPF2

The first division of meiosis is unique in its capacity to halve the ploidy of the future gametes. To this end, one key innovation compared to mitosis is the monopolar orientation of the pairs of sister kinetochores required for the proper separation of homologs at meiosis I. How monopolar orientation is imposed is unclear and seems to vary in eukaryotes. Here we performed a forward genetic screen in Arabidopsis thaliana, specifically designed to identify the molecular components imposing monopolar orientation, based on mutants ability to restore fertility in spo11 osd1 haploid plants. We show that monopolar orientation involves all four cohesin subunits (REC8, SCC3, SMC1, SMC3), the cohesion establishment factors CTF18 and DCC1, and the cohesin protectors SGO1/2 and PANS1, the inner kinetochore protein CENP-C, and the desumoylase SPF2. The mutants show bipolar orientation of achiasmatic chromosomes, but monopolar orientation is maintained in the presence of crossovers despite splitting of sister kinetochores at metaphase I and reduced levels of cohesin. Taken together, the findings demonstrate that cohesion establishment and protection, kinetochore function, and deSUMOylation, together with crossovers, enforce monopolar orientation in plants and support a cohesion-driven model of kinetochore orientation at meiosis I that is conserved across kingdoms.

cell 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↗

bioRxiv2022

HEIP1 is required for efficient meiotic crossover implementation and is conserved from plants to humans

Crossovers (CO) shuffle genetic information and physically connect homologous chromosome pairs, ensuring their balanced segregation during meiosis. COs arising from the major class I pathway require the activity of a well-conserved ZMMs group of proteins which, in conjunction with MLH1, facilitate the maturation of DNA recombination intermediates specifically into COs. The HEIP1 protein was identified in rice and proposed to be a new, plant-specific member of the ZMM group. Here we establish and decipher the function of the Arabidopsis thaliana HEIP1 homolog in meiotic crossover formation and report its wide conservation in eukaryotes. We show that the loss of Arabidopsis HEIP1 elicits a marked reduction in meiotic COs and their redistribution towards chromosome ends. Epistasis analysis showed that AtHEIP1 acts specifically in the class I CO pathway. Further, we show that HEI1P acts both prior to crossover designation, as the number of MLH1 foci is reduced in heip1, and at the maturation step of MLH1-marked sites into COs. Despite the HEIP1 protein being predicted to be primarily unstructured and very divergent at the sequence level, we identified homologs of HEIP1 in an extensive range of eukaryotes, including mammals.

genetics↗

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↗