Biology subjects

Freitag, M.

Publications and source records attributed to Freitag, M..

15 recordsLinked to original sources

bioRxiv2026

Comparative genomics reveals shared accessory regions between members of two Fusarium species complexes virulent on garden pea

The contribution of accessory or conditionally dispensable chromosomes to host-specific virulence was first demonstrated in members of the Fusarium solani species complex (FSSC) that are pathogens of garden pea, Pisum sativum L. The phenomenon has since been shown to exist in many fungal plant pathogens, including the closely related F. oxysporum species complex (FOSC). Genome analysis of members of the FSSC and FOSC pathogenic on pea revealed a diverse size range of the accessory genome of these fungi. Despite the [~]65 million years of diverging time, regions on a chromosome known to carry host-specific virulence factors for pea, including the cytochrome P450 pisatin demethylase (PDA) and other pea pathogenicity (PEP) genes, were present in all genomes of these pea pathogens. Genes directly involved in virulence on pea - PEP2, PDA, and PEP5- were the most frequently clustered together. Transcriptome analysis of fungal mycelia treated with the pea phytoalexin pisatin, identified 1,155 differentially expressed genes where many were involved in cellular stress responses. As wilt pathogens that invade host xylem, members of the FOSC encode more putative effectors, when compared to those in the FSSC, and several FOSC effectors were identified to confer race specificity. The conservation of part of the accessory genomes across two evolutionarily diverged species complexes suggests a common origin. Horizontal transfer of accessory chromosomes containing genetic loci involved in pathogenesis for garden pea offers a parsimonious explanation of the polyphyletic origin of host specificity.

genomics↗

bioRxiv2026

An aorta to insulin producing cell sensor for internal state in Drosophila

The cellular circuits through which the internal state of an organism is sensed and relayed to the brain, and through which they bring about appropriate physiological and behavioral responses, remain largely unelucidated. Using whole-animal electron microscopy reconstruction of a Drosophila larva, we previously identified an Aorta sensory organ whose somata lie on the periphery of the brain, with dendritic arborizations in the wall of the anterior aorta, and whose axons project to the protocerebrum and synapse onto the insulin-producing cells (IPCs). Here we characterize the full anatomy and connectivity of this sensory organ. We show that the aorta sensory neurons make their strongest direct synaptic contacts onto IPCs and the neurosecretory cells producing Dromyosuppressin (DMS), with only weaker direct contacts to diuretic hormone 44 (DH44). They also make direct contacts to the enteric serotonergic neurons modulating swallowing (Se0ens), and to two single mushroom body neurons, DAN-j1 and MBON-d3, of the learning and memory center of Drosophila. Calcium imaging shows that the neurons are activated by fructose, and optogenetic manipulation reveals that their activity influences peptide content in IPCs, DH44 and DMS cells. Polysynaptic paths to the brain run through two morphologically distinct interneuron families. One, formed by the Hugin protocerebral neurons, targets the neuroendocrine system and is associated with bitter taste and pathogen induced feeding suppression. The other, formed by the BAmas projection neurons, targets dopaminergic input neurons and output neurons of the mushroom body. The Aorta sensory pathway therefore couples internal hemolymph state to two parallel central systems -- endocrine state control and mushroom body-associated value updating -- and provides a candidate substrate for a metabolic memory through which post-ingestive state is fed back into future feeding choice.

neuroscience↗

bioRxiv2026

Inhibition of VP2-mediated entry: a potential antiviral strategy to treat or prevent calicivirus disease

The Caliciviridae include many notable human and animal pathogens, including norovirus and sapovirus, which cause outbreaks of acute gastroenteritis. We previously demonstrated that, following receptor engagement, feline calicivirus (FCV) assembles a portal structure at a unique capsid three-fold axis. This comprises twelve copies of the minor capsid protein VP2 and is essential for genome delivery. We designed a short peptide based on our structure data that occludes the VP2 binding sites on the capsid surface, to prevent assembly of the VP2 portal and thereby halt the viral entry mechanism. Incubation with low micromolar concentrations of the peptide considerably reduced the infectivity of two laboratory strains and four clinical isolates of FCV associated with respiratory or virulent-systemic disease. Cryo-electron microscopy structures of FCV virions complexed with the peptide confirmed that the peptide occupies the VP2 binding site on the major capsid protein VP1, preventing portal assembly and subsequent genome delivery. Our data show that targeting VP2 is a viable antiviral approach to preventing calicivirus infection, with potential for the treatment or prevention of norovirus disease.

microbiology↗

bioRxiv2025

Tracing spontaneously occurring mutations in Fusarium graminearum laboratory strains resulting in reduced virulence on wheat

BackgroundFusarium graminearum is a well characterized plant pathogenic fungus which is able to infect a broad range of economically relevant crop plants. Besides yield reduction this fungus is also responsible for mycotoxin contamination of food and feed. Upon propagation under laboratory conditions, mutations may occur which would be disadvantageous for fungal fitness in nature but not in the lab where the strains are usually grown on nutrient-rich media under optimal growth conditions. In this study we characterized four phenotypically different Fusarium graminearum strains for fitness traits and compared their genomes to trace down mutations responsible for the phenotypes. ResultsThe four tested F. graminearum PH1-derived strains revealed differences in their phenotypic appearance and also in their secondary metabolite profiles expressed on different growth media. Also, two of the investigated strains (94 and 96) showed significantly reduced virulence on wheat upon point inoculation of flowering wheat. We identified one high impact mutation in each of the two strains. In strain 96 a loss of function mutation occurred in FGSG_00355 which has a high similarity to Ras GTPase activating proteins and consequently may have an impact on the cell cycle. Even though strain 96 showed enhanced DON production in vitro, the strain was no longer able to spread within the wheat ear in infection assays. In strain 94 we identified an insertion of an A rather at the end of FGSG_00052 leading to a frameshift and consequently mutation of the last three amino acids and a shift of the stop codon by seven amino acids. Even though knock-out of this putative transcription factor has been described by Son et al (2011) to have no impact on virulence, changes at the C-terminal region may result in changes of the binding affinity. ConclusionsWe tracked down the mutations which might be responsible for the changes in phenotypic appearance, secondary metabolite profile as well as virulence. Yet, a closer biological characterization is necessary to determine the impact of these mutations on the fungus. Impact statementMutations under laboratory conditions can occur spontaneously. Due to the lack of selection pressure, also potentially deleterious mutations remain unnoticed as long as all nutrients are provided. In this study we analyzed four phenotypically different Fusarium graminearum PH-1 strains among which two showed significantly reduced virulence on wheat. In one strain we identified a loss of function mutation in a Ras-GTPase activating protein resulting in enhanced growth on complete media but at the same time strongly reduced virulence. The mutation in the second strain was an insertion in the C-terminal region of a transcription factor. The exact role of the Ras-GTPase activating protein during infection and the impact C-terminal elongation of a yet uncharacterized transcription factor is yet to be investigated. This study underscores the importance of regularly checking laboratory strains on their traits that such mutations which may have an impact on your research data, do not remain unnoticed. Data summaryThe code used for web scraping is available on github (https://github.com/cicci726/webscraping/tree/main). The sequencing files are deposited at NCBI in the sequence read archive (BioProject ID: PRJNA1293145).

genomics↗

bioRxiv2024

Impact of land-use intensity, productivity, and aboveground richness on seed rain in temperate grasslands

O_LISeed rain, the amount of seeds reaching an area via primary or secondary dispersal, affects the regeneration of plant communities and shapes the trajectory of future community composition. In agricultural grasslands, the composition and density in seed rain are mainly driven by land use, but drivers of seed rain quality and quantity along land-use gradients are poorly understood. We studied the effects of land-use intensity (LUI), its components (i.e. fertilization, mowing, and grazing), productivity, and aboveground vegetation composition and richness on seed rain. C_LIO_LIWe collected the seed rain over a five-month period in 142 grasslands and identified emerging seedlings. Grass seedlings dominated seed rain most likely due to their high abundance in vegetation and intense and early seed set. Only ten species accounted for approximately 80 % of seedlings, with grasses such as Lolium perenne and Alopecurus pratensis being most abundant. Forbs such as Cerastium holosteoides and Veronica arvensis were abundant in seed rain despite lower cover, probably due to early and prolonged flowering and high seed production. C_LIO_LISeed rain of grasses and forbs reacted differently to LUI and vegetation richness, LUI effects on grass seed rain mainly determined total seed density. Seed rain richness first increased with LUI, but decreased at higher LUI levels. Consequently, seed rain richness consistently increased with vegetation richness. This is reflected by a decrease in the abundance of stress strategists and an increase in ruderals in seed rain with increasing LUI and decreasing vegetation richness. C_LIO_LIAmong LUI components, fertilization intensity most strongly affected seed rain density and composition, with negative effects at intermediate fertilization intensities. Mowing once a year increased seed rain density, whereas it decreased at higher mowing frequencies. Grazing intensity reduced overall seed density and richness by reducing grass seed density, while forb seed density remained unaffected. C_LI Synthesis: Land-use intensity and aboveground productivity significantly influence the species composition and seed densities in the seed rain of temperate agricultural grasslands. Higher land-use intensity and productivity increased seed production but reduced taxonomic and functional diversity in seed rain and may negatively impact ecosystem stability and resilience.

ecology↗

bioRxiv2024

LINE-1 ribonucleoprotein complexes bind DNA to enable nuclear entry during mitosis

Long Interspersed Nuclear Element-1 (LINE-1) is an autonomous retrotransposon that makes up a significant portion of the human genome, contributing to genetic diversity and genome evolution. LINE-1 encodes two proteins, ORF1p and ORF2p, both essential for successful retrotransposition. ORF2p has endonuclease and reverse transcription activity, while ORF1p binds RNA. Many copies of ORF1p assemble onto the LINE-1 RNA to form a ribonucleoprotein complex (RNP). However, the functional role of RNPs in the LINE-1 life cycle is unclear. Using reconstitution assays on DNA curtains, we show that L1 RNPs gain DNA binding activity only when RNA is super-saturated with ORF1p. In cells, L1 RNPs bind to chromosomes during mitosis. Mutational analysis reveals that DNA binding is crucial for nuclear entry and LINE-1 retrotransposition activity. Thus, a key function of ORF1p is to form an RNP that gains access to the genome through DNA binding upon nuclear envelope breakdown.

biophysics↗

bioRxiv2024

Unraveling Morphogenesis, Starvation, and Light Responses in a Mushroom-Forming Fungus, Coprinopsis cinerea, Using Long Read Sequencing and Extensive Expression Profiling

Mushroom-forming fungi (Agaricomycetes) are emerging as pivotal players in several fields, as drivers of nutrient cycling, sources of novel applications, and the group includes some of the most morphologically complex multicellular fungi. Genomic data for Agaricomycetes are accumulating at a steady pace, however, this is not paralleled by improvements in the quality of genome sequence and associated functional gene annotations, which leaves gene function notoriously poorly understood in comparison with other fungi and model eukaryotes. We set out to improve our functional understanding of the model mushroom Coprinopsis cinerea by integrating a new, chromosome-level assembly with high-quality gene predictions and functional information derived from gene-expression profiling data across 67 developmental, stress, and light conditions. The new annotation has considerably improved quality metrics and includes 5- and 3-untranslated regions (UTRs), polyadenylation sites (PAS), upstream ORFs (uORFs), splicing isoforms, conserved sequence motifs (e.g., TATA and Kozak boxes) and microexons. We found that alternative polyadenylation is widespread in C. cinerea, but that it is not specifically regulated across the various conditions used here. Transcriptome profiling allowed us to delineate core gene sets corresponding to carbon starvation, light-response, and hyphal differentiation, and uncover new aspects of the light-regulated phases of life cycle. As a result, the genome of C. cinerea has now become the most comprehensively annotated genome among mushroom-forming fungi, which will contribute to multiple rapidly expanding fields, including research on their life history, light and stress responses, as well as multicellular development.

genomics↗

bioRxiv2023

Segment Anything for Microscopy

We present Segment Anything for Microscopy, a tool for interactive and automatic segmentation and tracking of objects in multi-dimensional microscopy data. Our method is based on Segment Anything, a vision foundation model for image segmentation. We extend it by training specialized models for microscopy data that significantly improve segmentation quality for a wide range of imaging conditions. We also implement annotation tools for interactive (volumetric) segmentation and tracking, that speed up data annotation significantly compared to established tools. Our work constitutes the first application of vision foundation models to microscopy, laying the groundwork for solving image analysis problems in these domains with a small set of powerful deep learning architectures.

bioinformatics↗

bioRxiv2022

H4K20me3 controls Ash1-mediated H3K36me3 and transcriptional silencing in facultative heterochromatin

Facultative heterochromatin controls development and differentiation in many eukaryotes. In metazoans, plants, and many filamentous fungi, facultative heterochromatin is characterized by transcriptional repression and enrichment with nucleosomes that are trimethylated at histone H3 lysine 27 (H3K27me3). While loss of H3K27me3 results in derepression of transcriptional gene silencing in many species, additional up- and downstream layers of regulation are necessary to mediate control of transcription in chromosome regions enriched with H3K27me3. Here, we investigated the effects of one histone mark on histone H4, namely H4K20me3, in the fungus Zymoseptoria tritici, a globally important pathogen of wheat. Deletion of kmt5, the gene encoding the sole methyltransferase responsible for H4K20 methylation, resulted in global derepression of transcription, especially in regions of facultative heterochromatin. Reversal of silencing in the absence of H4K20me3 not only affected genes but also a large number of novel, previously undetected, non-coding transcripts generated from regions of facultative heterochromatin on accessory chromosomes. Transcriptional activation in kmt5 deletion strains was accompanied by a complete loss of Ash1-mediated H3K36me3 and chromatin reorganization affecting H3K27me3 and H3K4me2 distribution in regions of facultative heterochromatin. Strains with a H4K20M mutation in the single histone H4 gene of Z. tritici recapitulated these chromatin changes, suggesting that H4K20me3 is essential for Ash1-mediated H3K36me3. The {Delta}kmt5 mutants we obtained are more sensitive to genotoxic stressors and both, {Delta}kmt5 and {Delta}ash1, showed greatly increased rates of accessory chromosome loss. Taken together, our results provide insights into a novel, and unsuspected, mechanism controlling the assembly and maintenance of facultative heterochromatin. SignificanceFacultative heterochromatin contains genes important for specific developmental or life cycle stages. Transcriptional regulation of these genes is influenced by chromatin structure. Here, we report that a little studied histone modification, trimethylation of lysine 20 on histone H4 (H4K20me3), is enriched in facultative heterochromatin and important for transcriptional repression in these regions in an important agricultural pathogen. Furthermore, normal levels of H4K20me3 are essential for deposition of another repressive histone mark, Ash1-mediated H3K36me3, and affect the distribution of other marks including H3K27me3. We conducted the first genome-wide assessment of H4K20 methylation levels in a fungus, and our discoveries reveal that multiple chromatin modifications are required to establish transcriptional silencing, providing the framework to understand epistasis relationships among these histone marks.

genetics↗

bioRxiv2020

Recent loss of the Dim2 cytosine DNA methyltransferase impacts mutation rate and evolution in a fungal plant pathogen

DNA methylation is found throughout all domains of life, yet the extent and function of DNA methylation differ between eukaryotes. Strains of the plant pathogenic fungus Zymoseptoria tritici appeared to lack cytosine DNA methylation (5mC) because gene amplification followed by Repeat-Induced Point mutation (RIP) resulted in the inactivation of the dim2 DNA methyltransferase gene. 5mC is, however, present in closely related sister species. We demonstrate that inactivation of dim2 occurred recently as some Z. tritici isolates carry a functional dim2 gene. Moreover, we show that dim2 inactivation occurred by a different path than previously hypothesized. We mapped the genome-wide distribution of 5mC in strains with and without functional dim2. Presence of functional dim2 correlates with high levels of 5mC in transposable elements (TEs), suggesting a role in genome defense. We identified low levels of 5mC in strains carrying inactive dim2 alleles, suggesting that 5mC is maintained over time, presumably by an active Dnmt5 DNA methyltransferase. Integration of a functional dim2 allele in strains with mutated dim2 restored normal 5mC levels, demonstrating de novo cytosine methylation activity of dim2. To assess the importance of 5mC for genome evolution, we performed an evolution experiment, comparing genomes of strains with high levels of 5mC to genomes of strains lacking dim2. We found that the presence of dim2 alters nucleotide composition by promoting C to T transitions (C[->]T) specifically at CpA (CA) sites during mitosis, likely contributing to TE inactivation. Our results show that 5mC density at TEs is a polymorphic trait in Z. tritici populations that can impact genome evolution. Author SummaryCytosine DNA methylation (5mC) is known to silence transposable elements in fungi and thereby appears to contribute to genome stability. The genomes of plant pathogenic fungi are highly diverse, differing substantially in transposon content and distribution. Here, we show extensive differences of 5mC levels within a single species of an important wheat pathogen. These differences were caused by inactivation of the DNA methyltransferase Dim2 in the majority of studied isolates. Presence of widespread 5mC increased point mutation rates in regions with active or mutated transposable elements during mitosis. The mutation pattern is dependent on the presence of Dim2 and resembles a mitotic version of Repeat-Induced Point mutation (RIP). Thus, loss of 5mC may represent an evolutionary trade-off offering adaptive potential at the cost of transposon control.

genetics↗

bioRxiv2019

Genome compartmentalization predates species divergence in the plant pathogen genus Zymoseptoria

BackgroundAntagonistic co-evolution can drive rapid adaptation in pathogens and shape genome architecture. Comparative genome analyses of several fungal pathogens revealed highly variable genomes, for many species characterized by specific repeat-rich genome compartments with exceptionally high sequence variability. Dynamic genome architecture may enable fast adaptation to host genetics. The wheat pathogen Zymoseptoria tritici with its highly variable genome and has emerged as a model organism to study the genomic evolution of plant pathogens. Here, we compared genomes of Z. tritici isolates and genomes of sister species infecting wild grasses to address the evolution of genome composition and structure. ResultsUsing long-read technology, we sequenced and assembled genomes of Z. ardabiliae, Z. brevis, Z. pseudotritici and Z. passerinii, together with two isolates of Z. tritici. We report a high extent of genome collinearity among Zymoseptoria species and high conservation of genomic, transcriptomic and epigenomic signatures of compartmentalization. We identify high gene content variability both within and between species. In addition, such variability is mainly limited to the accessory chromosomes and accessory compartments. Despite strong host specificity and non-overlapping host-range between species, effectors are mainly shared among Zymoseptoria species, yet exhibiting a high level of presence-absence polymorphism within Z. tritici. Using in planta transcriptomic data from Z. tritici, we suggest different roles for the shared orthologs and for the accessory genes during infection of their hosts. ConclusionDespite previous reports of high genomic plasticity in Z. tritici, we describe here a high level of conservation in genomic, epigenomic and transcriptomic signatures of genome architecture and compartmentalization across the genus Zymoseptoria. The compartmentalized genome may reflect purifying selection to retain a functional core genome and relaxed selection on the accessory genome allowing a higher extent of polymorphism.

genomics↗

bioRxiv2019

Less is more! Rapid increase in plant species richness after reduced mowing of urban grasslands

Urban lawns provide space for recreation in cities, and they are an important part of urban green infrastructures. However, most lawns are intensively managed. As only few plant species can survive the frequent mowing, urban lawns typically harbor only a limited number of plant species. To improve the biodiversity of urban lawns, it is often suggested to reduce the mowing frequency. Here, we studied the plant diversity of urban grasslands that have recently undergone management changes from mowing every few weeks to mowing only once or twice per season and compared them to intensively managed lawns. Within six years after the management changes, the grasslands with reduced mowing frequency indeed hosted 30% more plant species than intensively managed lawns, and they were more heterogeneous both within and between grasslands. Additionally, the species composition of less frequently mown grasslands shifted from common mowing-tolerant lawn species to typical meadow species. Our study thus shows that the reduction of mowing is a simple and effective tool for increasing the biodiversity in urban grasslands.

ecology↗

bioRxiv2018

The multi-speed genome of Fusarium oxysporum reveals association of histone modifications with sequence divergence and footprints of past horizontal chromosome transfer events

Fusarium oxysporum is an economically important pathogen causing wilting or rotting disease symptoms in a large number of crops. It is proposed to have a structured, \"two-speed\" genome: i.e. regions containing genes involved in pathogenicity cluster with transposons on separate accessory chromosomes. This is hypothesized to enhance evolvability. Given the continuum of adaptation of all the genes encoded in a genome, however, one would expect a more complex genome structure. By comparing the genome of reference strain Fol4287 to those of 58 other Fusarium oxysporum strains, we found that some Fol4287 accessory chromosomes are lineage-specific, while others occur in multiple lineages with very high sequence similarity - but only in strains that infect the same host as Fol4287. This indicates that horizontal chromosome transfer has been instrumental in past host-switches. Unexpectedly, we found that the sequence of the three smallest core chromosomes (Chr. 11, 12 and 13) is more divergent than that of the other core chromosomes. Moreover, these chromosomes are enriched in genes involved in metabolism and transport and genes that are differentially regulated during infection. Interestingly, these chromosomes are -like the accessory chromosomes- marked by histone H3 lysine 27 trimethylation (H3K27me3) and depleted in histone H3 lysine 4 dimethylation (H3K4me2). Detailed genomic analyses revealed a complex, \"multi-speed genome\" structure in Fusarium oxysporum. We found a strong association of H3K27me3 with elevated levels of sequence divergence that is independent of the presence of repetitive elements. This provides new leads into how clustering of genes evolving at similar rates could increase evolvability.\n\nAuthor summaryFungi that cause disease on plants are an increasingly important threat to food security. New fungal diseases emerge regularly. The agricultural industry makes large investments to breed crops that are resistant to fungal infections, yet rapid adaptation enables fungal pathogens to overcome this resistance within a few years or decades. It has been proposed that genome compartmentalization of plant pathogenic fungi, in which infection-related genes are clustered with transposable elements (or jumping genes) into separate, fast-evolving regions, enhances their adaptivity. Here, we aimed to shed light on the possible interplay between genome organization and adaptation. We measured differences in sequence divergence and dispensability between and within individual chromosomes of the important plant pathogen Fusarium oxysporum. Based on these differences we defined four distinct chromosomal categories. We then mapped histone modifications and gene expression levels under different conditions for these four categories. We found a division of labor between chromosomes, where some are pathogenicity chromosomes - specialized towards infection of a specific host, while others are enriched in genes involved in more generic infection-related processes. Moreover, we confirmed that horizontal transfer of pathogenicity chromosomes likely plays an important role in gain of pathogenicity. Finally, we found that a specific histone modification is associated with increased sequence divergence.

genomics↗

bioRxiv2018

Destabilization of chromosome structure by histone H3 lysine 27 methylation

Chromosome and genome stability are important for normal cell function as instability often correlates with disease and dysfunction of DNA repair mechanisms. Many organisms maintain supernumerary or accessory chromosomes that deviate from standard chromosomes. The pathogenic fungus Zymoseptoria tritici has as many as eight accessory chromosomes, which are highly unstable during meiosis and mitosis, transcriptionally repressed, show enrichment of repetitive elements, and enrichment with heterochromatic histone methylation marks, e.g., trimethylation of H3 lysine 9 or lysine 27 (H3K9me3, H3K27me3). To elucidate the role of heterochromatin on genome stability in Z. tritici, we deleted the genes encoding the methyltransferases responsible for H3K9me3 and H3K27me3, kmt1 and kmt6, respectively, and generated a double mutant. We combined experimental evolution and genomic analyses to determine the impact of these deletions on chromosome and genome stability, both in vitro and in planta. We used whole genome sequencing, ChIP-seq, and RNA-seq to compare changes in genome and chromatin structure, and differences in gene expression between mutant and wildtype strains. Analyses of genome and ChIP-seq data in H3K9me3-deficient strains revealed dramatic chromatin reorganization, where H3K27me3 is mostly relocalized into regions that are enriched with H3K9me3 in wild type. Many genome rearrangements and formation of new chromosomes were found in the absence of H3K9me3, accompanied by activation of transposable elements. In stark contrast, loss of H3K27me3 actually increased the stability of accessory chromosomes under normal growth conditions in vitro, even without large scale changes in gene activity. We conclude that H3K9me3 is important for the maintenance of genome stability because it disallows H3K27me3 in these regions. In this system, H3K27me3 reduces the overall stability of accessory chromosomes, generating a \"metastable\" state for these quasi-essential regions of the genome.\n\nAuthor SummaryGenome and chromosome stability are essential to maintain normal cell function and viability. However, differences in genome and chromosome structure are frequently found in organisms that undergo rapid adaptation to changing environmental conditions, and in humans are often found in cancer cells. We study genome instability in a fungal pathogen that exhibits a high degree of genetic diversity. Regions that show extraordinary diversity in this pathogen are the transposon-rich accessory chromosomes, which contain few genes that are of unknown benefit to the organism but maintained in the population and thus considered \"quasi essential\". Accessory chromosomes in all fungi studied so far are enriched with markers for heterochromatin, namely trimethylation of H3 lysine 9 and 27 (H3K9me3, H3K27me3). We show that loss of these heterochromatin marks has strong but opposing effects on genome stability. While loss of the transposon-associated mark H3K9me3 destabilizes the entire genome, presence of H3K27me3 favors instability of accessory chromosomes. Our study provides insight into the relationship between chromatin and genome stability and why some regions are more susceptible to genetic diversity than others.

genetics↗

bioRxiv2018

Extraordinary genome instability and widespread chromosome rearrangements during vegetative growth

The haploid genome of the pathogenic fungus Zymoseptoria tritici is contained on \"core\" and \"accessory\" chromosomes. While 13 core chromosomes are found in all strains, as many as eight accessory chromosomes show presence/absence variation and rearrangements among field isolates. We investigated chromosome stability using experimental evolution, karyotyping and genome sequencing. We report extremely high and variable rates of accessory chromosome loss during mitotic propagation in vitro and in planta. Spontaneous chromosome loss was observed in 2 to >50 % of cells during four weeks of incubation. Similar rates of chromosome loss in the closely related Z. ardabiliae suggest that this extreme chromosome dynamic is a conserved phenomenon in the genus. Elevating the incubation temperature greatly increases instability of accessory and even core chromosomes, causing severe rearrangements involving telomere fusion and chromosome breakage. Chromosome losses do not impact the fitness of Z. tritici in vitro, but some lead to increased virulence suggesting an adaptive role of this extraordinary chromosome instability.

genomics↗