Biology subjects

Johannes, F.

Publications and source records attributed to Johannes, F..

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

GSNOR-dependent nitric oxide homeostasis promotes recovery from repeated climate stress across generations in Arabidopsis thaliana

Climate change exposes plants to recurrent and interacting stresses, yet the extent to which these effects persist across generations, and the mechanisms involved, remain unclear. We propagated Arabidopsis thaliana wild type (WT, Col-0) and nitric oxide homeostasis mutant gsnor1-3 (hereafter, gsnor-ko) for five successive generations. Plants were grown under control, drought, elevated CO2, O3, warm temperature, and combined treatment scenarios for the first three generations (G1-G3), followed by two recovery generations under control conditions (G4-G5). We quantified rosette growth, photosynthetic traits, seed production, and transcriptome dynamics by RNA-seq. Across environments, gsnor-ko showed reduced vegetative growth and reproductive output relative to WT. Transcriptomic responses were strongly scenario- and generation-dependent, with the largest differential expression shifts observed under warm-climate and combined-treatment conditions. Compared with WT, gsnor-ko displayed broader gene overlap across generations and stronger retention or reconfiguration of stress-responsive states after stress withdrawal. Functional enrichment and candidate-gene analyses identified pathways/components linked to DNA methylation, heterochromatin maintenance, histone ubiquitination, m6A RNA regulation, and methyl-donor metabolism. Together, these results support a model in which GSNOR activity promotes transcriptomic recovery after repeated climate stress, whereas impaired GSNOR function shifts responses toward multi-generational persistence and epigenetically associated regulatory reconfiguration. HighlightGSNOR-dependent nitric oxide homeostasis promotes transcriptomic resetting after repeated climate stress, whereas impaired NO homeostasis favours multigenerational persistence and chromatin- and RNA-linked regulatory reconfiguration. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=118 SRC="FIGDIR/small/742973v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@6031c6org.highwire.dtl.DTLVardef@163be5borg.highwire.dtl.DTLVardef@1665e9eorg.highwire.dtl.DTLVardef@1cde833_HPS_FORMAT_FIGEXP M_FIG C_FIG

plant biology↗

bioRxiv2026

Genetic and epigenetic divergence among Arabidopsis thaliana Col-0 laboratory lineages since the 1950s

The model plant Arabidopsis thaliana has been a workhorse of plant biology since the 1950s, when the Columbia-0 (Col-0) accession was widely adopted by the research community as a reference genotype. Since then, Col-0 seeds have been shared among laboratories worldwide and propagated independently, creating a network of related laboratory lineages. Here, we sequenced the genomes and DNA methylomes of 78 Col-0 strains from laboratories and stock centers around the world to assess the genetic and epigenetic variation accumulated during this period and to reconstruct their propagation history from de novo variants. After quality filtering, we identified 1,415 single-nucleotide polymorphisms and 169,677 epimutations across 75 Col-0 lines and used these variants to generate SNP- and epimutation-based phylogenies. The two phylogenies showed highly concordant topologies, but the epimutation-based tree provided greater resolution of relationships among closely related lineages. Divergence-time estimates suggest that many lines have been propagated for approximately one generation per year over several decades, resulting in pairwise divergences of up to approximately 100 generations. We further identified 170 nonsynonymous substitutions and more than 200 candidate epialleles, some of which were associated with gene-expression differences among Col-0 clades and may therefore have functional consequences. Together, these findings show that Col-0 is best viewed not as a single invariant reference genotype, but as a collection of related laboratory lineages that have accumulated genetic, epigenetic, and transcriptional divergence through time, with potential consequences for the reproducibility of experiments across laboratories. Significance StatementThe Arabidopsis Col-0 reference accession is often treated as a single, invariant genotype, yet independently maintained laboratory stocks have accumulated substantial genetic, epigenetic, and transcriptional divergence since the 1950s. Some lineages are separated by more than 100 generations of independent propagation. Mutations and CG epimutations reconstruct nearly identical lineage histories, demonstrating that heritable DNA methylation changes provide a robust record of recent laboratory evolution.

genetics↗

bioRxiv2026

simSOMA: a cell-lineage based simulator of the somatic VAF spectrum in plants

Plants accumulate somatic mutations during growth, and some of these mutations can spread from local cell lineages into branches, organs, or reproductive tissues. There is growing interest in these variants because they can under-lie bud-sport traits in crops, contribute to within-organism somatic selection, and provide genetic variation that may be transmitted vegetatively or sexually to future generations. Recent genomic sequencing of bulk and layer-enriched plant tissues has shown that de novo somatic variants can generate complex variant allele-frequency (VAF) spectra. Interpreting these spectra requires understanding how mutations arising during mitotic cell division are filtered or amplified through shoot growth, branching, and organ formation. Because these processes interact across multiple scales, their combined effects are difficult to derive analytically. Here, we present simSOMA, a modular simulator that links rooted plant topologies to explicit cell-lineage dynamics. simSOMA models somatic mutation accumulation during stem-cell self-renewal in the shoot apical meristem, clonal expansion from the stem-cell niche to the meristem periphery, branch founding, and organ formation. Applying simSOMA across diverse growth scenarios revealed how individual processes can be isolated, varied, and combined to assess their effects on organ-level VAF spectra and among-organ variant sharing. The same simulated spectra can also be transformed to represent bulk or layer-enriched sampling and phased or unphased variant readouts, separating effects of developmental history from those introduced by tissue composition and allele counting. Because simSOMA is organized around modules with defined input-output interfaces, individual developmental components can be replaced or extended as new empirical information becomes available. This makes simSOMA a flexible tool for testing alternative models of somatic mosaicism in plants and for guiding the design and interpretation of VAF-based sequencing studies. The simulator is available at https://github.com/jlab-code/simSOMA.

genomics↗

bioRxiv2026

Brassinosteroid-regulated transcription factors confer epigenetic changes that repress plant immunity

When organisms encounter pathogens, they rapidly activate complex defense programs to ensure survival. While these immune responses are vital, they often also incur trade-offs, such as reduced growth and development and must therefore be tightly controlled 1,2. In this study, we reveal that the steroid hormones brassinosteroids (BRs) contribute to this control in Arabidopsis thaliana by repressing immunity-related genes. We provide evidence that the BR-regulated basic helix-loop-helix (bHLH) transcription factor CESTA (CES), along with its homologs BR ENHANCED EXPRESSION (BEE)1-3, mediate DNA methylation changes at transposable element (TE)-rich loci containing nucleotide-binding leucine-rich-repeat (NLR)-type receptor genes, including SUPPRESSOR OF NPR1-1 CONSTITUTIVE 1 (SNC1). These CES-induced methylation changes correlate with altered splicing of SNC1 pre-mRNA, a process that requires the BR receptor BRASSINOSTEROID INSENSITIVE 1 (BRI1). In support, we show that CES associates with components of the chromatin remodeling and splicing machinery. Together, our findings reveal a previously unrecognized BR-induced mechanism that modulates the epigenetic and post transcriptional regulation of immune genes, enabling plants to prioritize growth over defense. Significance statementSteroid hormones are powerful regulators of growth but also act as potent suppressors of immunity, with well-established clinical applications, for example in treating autoimmune diseases in humans. In plants, the steroid hormones brassinosteroids (BRs) exert similar effects. Here, we uncover that BR-mediated immune suppression involves DNA methylation changes and alternative splicing of a subset of immune receptor genes, that govern resistance responses mediated by the plant hormone salicylic acid. We provide evidence for a function of specific bHLH transcription factors in this process that link BR signaling to chromatin remodelling and RNA processing. Thereby our study reveals a novel mode of steroid hormone activity in immune repression, which involves epigenetic and posttranscriptional adjustment of immune receptor function.

plant biology↗

bioRxiv2026

Somatic DNA methylation heterogeneity predicts extreme transgenerational epimutation hotspots in Arabidopsis

Spontaneous epimutations are stochastic and heritable changes in cytosine methylation that arise independently of DNA sequence alterations. In plants, they occur predominantly at CG sites, accumulate across generations at high and clock-like rates, and contribute substantially to constitutive epigenetic diversity. Although these features are well established, the developmental origin of spontaneous epimutations remains poorly understood. One model proposes that they arise during somatic growth in different cell layers of the shoot apical meristem, where lineage bottlenecks enable nascent epimutations to clonally propagate into developing organs. Such layer-specific dynamics are expected to generate spatial mosaics of methylation states within tissues that manifest as heterogeneity in bulk bisulfite sequencing data. Here, we quantified genome-wide CG methylation heterogeneity in single Arabidopsis leaves using read-level methylation discordance metrics adopted from cancer epigenomics. We identified thousands of highly heterogeneous loci and show that they overlap extreme transgenerational epimutation hotspots. Analysis of multiple leaves from the same individuals further revealed that methylation divergence at these loci scales with developmental distance and recapitulates the branching architecture of the shoot. Together, these results support a meristematic origin of spontaneous epimutations and highlight a shared susceptibility to methylation-maintenance errors in both developmental and transgenerational contexts.

genetics↗

bioRxiv2026

Centromeres are hotspots of cytosine methylation epimutations in a filamentous fungus

Epimutations are changes in chromatin modifications, such as DNA methylation or histone modifications. Some of these epigenetic changes can be inherited for several generations, and they potentially contribute to evolutionary processes. Estimates of epimutation rates now exists in a few species, but the presence and function of epigenetic marks are not conserved across different species. To understand the properties of epimutations in fungi, we performed a mutation accumulation experiment with the filamentous fungus Neurospora crassa and investigated spontaneous changes in DNA methylation and trimethylation of lysine 9 on histone H3 (H3K9me3) in the mutation accumulation lines. We observed that centromeric regions are hotspots of spontaneous DNA methylation changes in N. crassa. In these hotspot regions, DNA methylation changes were transmitted across mitoses, but changes occurring in euchromatin were not maintained. The rate of DNA methylation changes was around 30 000 fold faster than the genetic mutation rate. We did not observe spontaneous changes in H3K9me3 that were transmitted across mitoses. Our results show that while spontaneous epimutations occur in this species, they occur predominantly in gene poor heterochromatic regions, so their impact for evolutionary adaptation may be limited.

genetics↗

bioRxiv2025

Threshold-like transcriptomic responses of European beech to simulated future climates

Beech (Fagus sylvatica) is one of the most important forest tree species in Europe, both in terms of land coverage and ecosystem services. Although it is projected to be strongly affected by climate change, insights into its functional genomic responses to realistic future scenarios are still lacking. We conducted a fully controlled ecotron experiment to examine the transcriptomic responses of 125 young, naturally regenerated beech trees exposed to regionalized dynamic climate series representing a reference period (1987-2016) and two future climate scenarios (Representative Concentration Pathways, RCP2.6 and RCP8.5, for 2071-2100) in Germany. RCPs describe alternative greenhouse gas trajectories established by the IPCC, ranging from strong mitigation (RCP2.6) to high, unmitigated emissions (RCP8.5), the latter representing a worst-case future scenario. Although both scenarios produced substantial transcriptional changes relative to the reference period, RCP8.5 elicited markedly stronger responses than RCP2.6, with nearly twice as many differentially expressed genes and unique transcriptional programs across functional categories that were not predictable from the RCP2.6 transcriptomes. Our study reveals emergent functional responses in European beech under projected late 21st-century climate conditions in Germany and highlights potential biomarkers for monitoring ecosystem responses to climate change.

ecology↗

bioRxiv2025

DNA methylome responses to biotic and abiotic stress in Arabidopsis thaliana: A multi-study analysis

Plants have evolved complex physiological and morphological strategies to cope with biotic and abiotic stress. At the molecular level, these responses are partly mediated by epigenetic mechanisms such as DNA methylation. In Arabidopsis thaliana, numerous studies have examined stress-induced changes in DNA methylation, aiming to elucidate their roles in stress acclimation. However, comparing these studies remains difficult due to variations in analytical methods and focus. To address this, we conducted an integrative analysis of 13 studies (16 datasets) using a unified bioinformatic pipeline to identify common and stress-specific methylation responses. Our results show that the number and distribution of differentially methylated regions (DMRs) vary by stress type and methylation context CG, CHG, and CHH. CG DMRs were primarily located in gene bodies, while CHG and CHH DMRs were enriched in transposable elements (TEs). Gene Ontology analysis revealed consistently enriched stress-related terms across conditions, indicating shared epigenetic regulation. As TEs have been proposed to act as stress sensors and regulators of nearby gene expression, we examined gene-proximal TEs in more detail. We found significant enrichment of stress-responsive methylation changes in LINE/L1, RathE1_ons, and DNA/HAT elements. While stress-induced methylation is often considered transient, many affected CG DMRs overlapped with loci known to accumulate stable epimutations over generations, suggesting that stress may contribute to long-term heritable epigenetic variation. These findings enhance our understanding of epigenetic regulation in plant stress responses, highlighting both shared and stress-specific methylation dynamics. Significance statementWe combined 16 Arabidopsis thaliana Whole-Genome Bisulfite Sequencing datasets to reveal common and stress-specific DNA methylation responses. Although global methylation levels remained stable, specific DMRs varied according to the type of stress and genomics context. Gene Ontology analysis revealed shared stress pathways. Gene-proximal transposable elements (TEs) (e.g. LINE/L1, RathE1_ons, DNA/HAT) were enriched for stress-responsive methylation changes. Notably, a subset of stress-induced CG DMRs overlap with epimutation-prone loci, suggesting an environmental route toward stable, heritable epigenetic variation.

plant biology↗

bioRxiv2025

Polymer-derived distance penalties improve chromatin interaction predictions from single-cell data across crop genomes

Scalable proxies for 3D genome contacts - such as single-cell co-accessibility and deep learning predictions - have emerged as powerful alternatives to chromatin capture-based methods, but predictions systematically overestimate long-range interactions. Here we show how to correct this bias using distance-based penalty functions informed by Gaussian mixture modeling and polymer-physics scaling. Using Hi-C datasets from maize, rice, and soybean, we derive tissue-specific and global consensus penalties parameterized by multi-regime power-law exponents. Applying these corrections to scATAC-seq co-accessibility scores improves their distance profiles in concordance with Hi-C and reduces long-range false positives by an average of 73% with tissue-specific penalties and 66% with the global consensus. We provide open-source code and fitted parameters to support adoption in maize, rice, and soybean.

bioinformatics↗

bioRxiv2025

Mapping genetic modifiers of epimutation rates reveals a punctuated-equilibrium model of CG methylome evolution

Spontaneous epimutations--stochastic changes in cytosine methylation--can persist across generations in plants and are thought to contribute to phenotypic variation. Although epimutations are increasingly studied for their potential long-term effects, it remains unclear why their accumulation varies across genotypes. Here, we tracked DNA methylation across ten generations in [~]400 mutation accumulation lineages derived from [~]70 Arabidopsis Ler x Cvi recombinant inbred lines. Treating epimutation rates as quantitative molecular traits, we mapped a major QTL to a Cvi-derived deletion near VIM2 and VIM4, two genes involved in CG methylation (mCG) maintenance. We show that this deletion rapidly reduces genome-wide methylation to a lower steady-state and compromises mCG maintenance fidelity across generations, resulting in a [~]1.5-fold increase in epimutation rates. Genotypes with elevated rates exhibited accelerated epigenetic drift and phenotypic divergence. Our findings support a punctuated-equilibrium model of mCG evolution, in which sudden disruptions to methylation homeostasis can destabilize epigenetic inheritance over longer time-scales.

genetics↗

bioRxiv2025

Branching architecture limits the rate of somatic mutation accumulation in trees

Trees are long-lived plants that develop highly branched shoot systems over time. During growth, somatic mutations accumulate along these branching structures and can become fixed in reproductive tissues such as flowers and fruits. Because mature trees produce tens of thousands of terminal branches, each harboring potentially mutated gametes, limiting the accumulation of somatic mutations is critical to avoid mutational meltdown and inbreeding depression. Although recent evidence suggests that long-lived plants have evolved mechanisms to suppress mutation accumulation, the developmental basis for this remains unclear. Here we develop a theoretical model that connects crown development with cell lineage sampling to show that branching architecture can strongly suppress somatic mutation accumulation in trees, often to the same extent as reducing the mutation rate itself. Specifically, tree forms that promote developmental path-sharing among branches suppress the number of unique mutational lineages in the crown. We find that this architectural effect can alter mutation burden by orders of magnitude, even when mutation rates and terminal branch numbers remain constant. These insights suggest that branching strategies may evolve not only to optimize growth and resource allocation, but also to limit the accumulation of somatic variants during ontogeny.

genetics↗

bioRxiv2025

Somatic evolution of stem cell mutations in long-lived plants

Long-lived perennial plants accumulate numerous somatic mutations with age. Mutations originating in stem cells at the shoot apex often become fixed in large sectors of the plant body due to cell lineage drift during repeated branching. Understanding the somatic evolution of such mutations requires knowledge of the effective stem cell population size, the cellular bottleneck strength during branch initiation, and the mutation rate. Here we show that these parameters can be estimated directly from cell-layer-enriched DNA sequencing data, thus filling a gap where no other in vivo method exists.

evolutionary biology↗

bioRxiv2024

Multi-generational biotic stress increases the rate of spontaneous epimutations in a ROS1-dependent manner

Mistakes in the maintenance of CG methylation are a source of spontaneous epimutations in plants that can be inherited across generations. The extent to which these stochastic events are affected by prolonged exposure to biotic and abiotic stress remains poorly characterized. Here, we grew Arabidopsis Mutation Accumulation (MA) lines for 12 generations in the presence of two biotic stressors: Pseudomonas syringae (Pst) and salicylic acid (SA). We found that multi-generational exposure to Pst and SA led to an 18%-32% and 23%-61% increase in the genome-wide epimutation rate, respectively. These rate increases were mainly targeted to subsets of genes characterized by low steady-state methylation (LM), on average, and a lack of transcriptional responsiveness to stress. We show that these effects are mediated by the DNA demethylase Repressor of Silencing 1 (ROS1). Loss of ROS1 not only buffers transcriptional responses to biotic stress, but also stabilizes epimutation rates, particularly in LM genes, rendering them insensitive to environmental perturbations. Taken together, our data demonstrates that stress can induce heritable epimutations and highlights a ROS1-mediated link between transcriptional plasticity and DNA methylation maintenance fidelity over generations.

evolutionary biology↗

bioRxiv2024

The genetic architecture of cell-type-specific cis-regulation

AbstractGene expression and complex phenotypes are determined by the activity of cis-regulatory elements. However, an understanding of how extant genetic variants affect cis regulation remains limited. Here, we investigated the consequences of cis-regulatory diversity using single-cell genomics of >0.7 million nuclei across 172 Zea mays (maize) inbreds. Our analyses pinpointed cis-regulatory elements distinct to domesticated maize and revealed how historical transposon activity has shaped the cis-regulatory landscape. Leveraging population genetics principles, we fine-mapped [~]22,000 chromatin accessibility-associated genetic variants with widespread cell-type-specific effects. Variants in TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR binding sites were the most prevalent determinants of chromatin accessibility. Finally, integrating chromatin accessibility-associated variants, organismal trait variation, and population differentiation revealed how local adaptation has rewired regulatory networks in unique cellular context to alter maize flowering.

genetics↗

bioRxiv2024

Allometric scaling of somatic mutation and epimutation rates in trees

How long-lived trees escape "mutational meltdown" despite centuries of continuous growth remains puzzling. Here we integrate recent studies to show that the yearly rate of somatic mutations and epimutations (Y) scales inversely with generation time (G), and follows the same allometric power law found in mammals (Y{propto}G-1). Deeper insights into the scaling function will permit predictions of somatic (epi)mutation rates from life-history traits without the need for genomic data.

evolutionary biology↗

bioRxiv2024

Accelerated growth increases the somatic epimutation rate in trees

Trees are critical components of ecosystems and of major economic importance. Due to their extraordinary longevity and well-defined modular architecture they have also emerged as model systems to study the long-term accumulation of somatic mutations in plants. Coupled with retrospective life-history and environmental data, trees can offer unique insights into mutational processes that would be difficult to obtain with prospective studies. In addition to genetic mutations, somatic epimutations in the form of stochastic gains and losses of DNA cytosine methylation have been shown to accumulate rapidly during ontogeny. One hypothesis is that somatic epimutations originate from DNA methylation maintenance errors during mitotic cell divisions, which would predict that their rate of accumulation scales with growth rate, rather than with age. Here we test this hypothesis in European beech. We analyzed one of the oldest continuously measured experimental plots in the world. The plot contains an even-aged beech stand that was established in 1822 and monitored for growth at regular intervals until the present. Starting [~]150 years ago, alternative thinning strategies were applied to subplots of this experiment, resulting in differential stem growth rates among trees. We show that accelerated growth significantly increased the per-year somatic epimutation rate at CG dinucleotides, and that this effect is accompanied by differences in cell division rates. Hence, faster growth elevates the chances for methylation maintenance errors during DNA replication per unit time. As somatic CG epimutations can be stably inherited to subsequent generations in plants, our insights have direct ecological and evolutionary implications.

genomics↗

bioRxiv2024

GenomicLinks: Deep learning predictions of 3Dchromatin loops in the maize genome

Gene regulation in eukaryotes is partly shaped by the 3D organization of chro]matin within the cell nucleus. Distal interactions between cis-regulatory elements and their target genes are widespread and many causal loci underlying heritable agricultural traits have been mapped to distal non-coding elements. The biology underlying chromatin loop formation in plants is poorly understood. Dissecting the sequence features that mediate distal interactions is an important step toward identifying putative molecular mechanisms. Here, we trained GenomicLinks, a deep learning model, to identify DNA sequence features predictive of 3D chromatin interactions in maize. We found that the presence of binding motifs of specific Transcription Factor classes, especially bHLH, are predictive of chromatin interaction specificities. Using an in silico mutagenesis approach we show the removal of these motifs from loop anchors leads to reduced interaction probabilities. We were able to validate these predictions with single-cell co-accessibility data from different maize genotypes that harbor natural substitutions in these TF binding motifs. GenomicLinks is currently implemented as an open-source web tool, which should facilitate its wider use in the plant research community.

genomics↗