Biology subjects

Habig, M.

Publications and source records attributed to Habig, M..

15 recordsLinked to original sources

bioRxiv2026

Evolutionary trade-offs between antimicrobial resistance and virulence in Pseudomonas aeruginosa

Antibiotics impose strong selection on bacteria, resulting in the emergence and spread of antimicrobial resistance. To date, the consequences of resistance evolution for other traits, especially virulence as a key life-history characteristic of high medical relevance remain poorly understood. A central limitation of existing work is reliance on clinical isolates with complex evolutionary histories, hindering causal inferences on resistance-virulence relationships. Such causal information is critical for our understanding of the distribution of resistance-associated evolutionary trade-offs, which may additionally guide optimization of treatment designs. The objectives of our study are to address these knowledge gaps using an experimental evolution framework with the human pathogen Pseudomonas aeruginosa. We quantified changes in resistance, life-history characteristics, in-vivo virulence with a Caenorhabditis elegans infection model, and whole genome sequences for bacterial clones, which had been independently evolved under three antibiotics with distinct cellular targets. We found that the resistance-virulence trade-off depended on the used antibiotic and was additionally driven by the underlying evolutionary path to resistance. Evolved resistance to the fluoroquinolone ciprofloxacin correlated positively with virulence, dependent on genetic changes in either the antibiotic target or efflux regulation. Conversely, evolved resistance to piperacillin/tazobactam, a {beta}-lactam/{beta}-lactamase inhibitor combination, was negatively correlated with virulence, contingent on the coincidental spread of resistance mutations and a large genomic deletion, containing numerous virulence genes. Lastly, evolved resistance to the aminoglycoside streptomycin led to only minor virulence changes. Overall, these antibiotic-specific evolutionary trajectories challenge the assumption of a universal resistance-virulence trade-off and demonstrate that antibiotic choice itself shapes pathogen virulence potential. Significance StatementAntimicrobial resistance and bacterial virulence are typically studied in isolation, yet they are shaped by the same evolutionary pressures and may directly compete for cellular resources. We addressed a fundamental but unresolved question: does evolution of resistance to an antibiotic make a pathogen more or less dangerous to a host? By characterizing experimentally evolved Pseudomonas aeruginosa, a leading cause of drug-resistant infections, we show that the answer depends on which antibiotic drove resistance. A positive resistance-virulence relationship occurred upon adaptation to a fluoroquinolone antibiotic, whereas it was negative upon {beta}-lactam resistance, and unchanged upon aminoglycoside resistance evolution. These antibiotic-specific evolutionary trajectories challenge the assumption of a universal resistance-virulence trade-off and suggest that antibiotic choice shapes pathogen danger beyond drug susceptibility.

evolutionary biology↗

bioRxiv2025

Evolutionary divergence in sympatric populations of the fungal pathogen Alternaria alternata across wild tomato hosts

Alternaria alternata is a globally distributed fungal pathogen with a broad host range, increasingly affecting both tomato crops and wild tomato relatives. The genomic basis of this ecological breadth in A. alternata remains poorly understood. Here we leverage the opportunity of wild pathosystems to study pathogen evolution and diversity beyond agricultural settings. We sampled isolates from wild tomato species across a 2,500 km range in South America, producing highly contiguous genomes, to investigate population structure. Our comparative genomics analyses reveal that A. alternata sensu stricto consists of two divergent clades. Strikingly, this divergence is not linked to host species, geography, or habitat type. Transposable elements contribute to variation within clades but do not explain their separation. Although some signs of recombination are present, reproductive mode appears stable across clades. Notably, global reference isolates cluster with one clade, while the other, more diverse clade is only found in wild populations. We hypothesize that these wild populations may act as reservoirs of evolutionary potential. These findings challenge prevailing assumptions about the population structure of necrotrophic pathogens and raise new questions about how genetic divergence can persist without ecological or geographic isolation. Media summary (lay abstract)The fungus Alternaria alternata is an emerging threat on tomato and potato crops. In a previous study, we found that it also infects wild tomato plants over a large range in Chile and Peru. Here we sequenced and compared full genomes of the fungi. Surprisingly, they formed two distinct groups that do not reflect different host plant species, geographical locations, or environments. One of those groups is related more closely to global reference samples, while the other group is more diverse. This suggests wild plants may quietly harbour forms of the fungus that could affect crops in the future.

genomics↗

bioRxiv2025

Genome compartmentalization in a host-specific fungal insect pathogen reveals a putative mating type locus on an accessory chromosome

The genomic diversity of many fungal pathogens is driven by rapidly evolving regions harbouring significant amounts of transposable elements. Such genomic regions often contain genes important for pathogenicity and may be sequestered from the core genome on accessory chromosomes, which are variably present in isolates of a species. In this study, we present a pangenomic analysis of a fungal insect pathogen, Metarhizium acridum, using seven chromosome-scale genomes from four different continents. We show that approximately 25% of the M. acridum pangenome is comprised of genes only present in one isolate (singletons) or more than one but not all isolates (accessory). These genes are enriched for functions in secondary metabolite production, nutrient transport, and chromosome organization. We also find evidence of functional compartmentalization of the genome, as the core genome of M. acridum is enriched in carbohydrate-active enzymes, while the accessory components are enriched in effectors that are located in gene-sparse regions of the genome. Furthermore, we identified the first naturally recovered accessory chromosome in M. acridum, which does not harbor effector or secondary metabolite proteins related to host-insect interactions but is enriched in functions related to sexual reproduction. Within the genus Metarhizium, M. acridum is one of few species considered to regularly reproduce sexually. We show that the accessory chromosome contains genes from both the MAT1-1 and MAT1-2 idiomorphs, in addition to the MAT locus found on the core chromosomes. Our findings suggest that the presence of this accessory chromosome may facilitate sexual reproduction, possibly even primary homothallism, in the otherwise heterothallic M. acridum. Overall, our study presents a putative novel mechanism whereby this fungal pathogen may acquire gene recombination and ensure maintenance of the accessory chromosome.

microbiology↗

bioRxiv2025

Transposable elements hitchhike on Starships across fungal genomes

Horizontal transfer (HT) of transposable elements (TEs) is a widespread phenomenon in eukaryotes and is often associated with bursts of TE activity. This process profoundly influences genome evolution by introducing novel genetic material and driving genetic variation. However, the precise mechanisms facilitating these transfers remain largely uncharacterized. Here, we report a recent TE burst in the insect-pathogenic fungus Metarhizium anisopliae. Our analysis reveals that the actively transposing TEs were introduced via hitchhiking on a so-called Starship--a class of large, themselves horizontally transferable transposons found within the fungal subphylum Pezizomycotina. This particular Starship carried 73 TEs, 43 of which exhibited increased copy numbers in the recipient genome, including 508 perfect copies. This expansion triggered extensive structural reshuffling across all chromosomes and led to the formation of a novel chromosome. Remarkably, this structural reorganization was associated with a dramatic phenotypic shift: the loss of pathogenicity. Expanding our analysis to other fungi, we found that Starship-mediated horizontal transfer of TEs is a general phenomenon. A majority (74%) of 618 published Starships also harbor TEs, which can constitute up to 72% of their content. Moreover, Starships serve as sources of actively transposing TEs: 16% of Starships carried at least one TE with a perfect copy found elsewhere in the genome, and identical TEs were observed on Starships from different species. Collectively, our results establish Starships as major vectors of horizontal TE transfer within Pezizomycotina and further highlight their profound impact on recipient fungal genomes through TE piggybacking.

evolutionary biology↗

bioRxiv2025

Resistance variation and bacterial interactions shape the adaptation of a genetically diverse bacterial population to antimicrobial treatment

Bacterial infections are often polymicrobial and subject to the evolution of antimicrobial resistance (AMR). Existing knowledge on AMR in such polymicrobial infections usually relies on observational patient data, for which cause-effect relationships are difficult to infer, or on studying interactions between different bacterial species, ignoring the commonly encountered variation within species. Here, we therefore asked how mixed populations with strains from the same species evolve under antibiotic treatment. We used a genetically diverse population of the high-risk human pathogen Pseudomonas aeruginosa, and first identified strain variation in both AMR and pairwise bacteria-bacteria interactions, the latter ranging from beneficial, neutral, to competitive. Using experimental evolution, we subsequently demonstrate that the response to selection by different antibiotic treatments is significantly influenced by AMR strain variation, bacterial interactions, and also spatial population structure. Moreover, de novo AMR evolution was additionally impacted by variation in resistance rates towards the two considered antibiotics. A second evolution experiment emphasized the central role of strain variation and bacterial interactions in determining the evolutionary outcome. We conclude that ecological dynamics in genetically diverse pathogen populations are key for our general understanding of infection characteristics and AMR evolution, and, therefore, deserve particular attention during treatment of polymicrobial infections.

evolutionary biology↗

bioRxiv2025

The nematode Caenorhabditis elegans can benefit from its coexisting fungal microbiome member Barnettozyma californica

The nematode Caenorhabditis elegans is known to feed on and interact with bacteria in its environment and has become a model organism for microbiome studies. However, whether and how C. elegans interacts with co-occurring fungi remains largely unknown, despite the presence of many fungal species in its natural habitat. Here, we isolate the yeast Barnettozyma californica from a mesocosm experiment with C. elegans and characterize its genome and interaction with the nematode. We find that B. californica is ingested by C. elegans and can serve as a sole, albeit poor, food source. Yet, when present together with Escherichia coli OP50, the fungus can lead to higher population growth and altered foraging behavior, suggesting that this fungi-bacteria mixture provides a better food source than bacteria alone. This effect varied between different natural C. elegans strains, suggesting a genomic basis for the nematodes interaction with B. californica. The fully assembled and annotated genome of the isolated B. californica strain does not indicate any obvious candidate genes for its interaction with C. elegans and/or E. coli OP50. Overall, our results provide an intriguing example of the complexity and multi-level relationship between naturally interacting fungi, bacteria, and animals. Graphical AbstractBarnettozyma californica is a member of the fungal microbiome of the model nematode Caenorhabditis elegans and can serve as food for worms. When combined with E. coli, this fungus can increase population growth and reduce foraging behaviour dependent on C. elegans genotype, revealing a genetic influence on host-fungus-bacterium interactions. O_FIG O_LINKSMALLFIG WIDTH=189 HEIGHT=200 SRC="FIGDIR/small/638710v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@184b29eorg.highwire.dtl.DTLVardef@eabb71org.highwire.dtl.DTLVardef@b810ceorg.highwire.dtl.DTLVardef@5745c7_HPS_FORMAT_FIGEXP M_FIG C_FIG

ecology↗

bioRxiv2024

Horizontal transfer of accessory chromosomes in fungi - a regulated process for exchange of genetic material?

Horizontal transfer of entire chromosomes has been reported in several fungal pathogens, often significantly impacting the fitness of the recipient fungus. All documented instances of horizontal chromosome transfers (HCTs) showed a marked propensity for accessory chromosomes, consistently involving the transfer of an accessory chromosome while other chromosomes were seldom, if ever, co-transferred. The mechanisms underlying HCTs, as well as the factors regulating the specificity of HCTs for accessory chromosomes, remain unclear. In this perspective, we provide an overview of the observed propensity in reported cases of horizontal chromosome transfers. We hypothesize the existence of a signal that distinguishes mobile, i.e., horizontally transferred, accessory chromosomes from the rest of the donor genome. Recent findings in Metarhizium robertsii and Magnaporthe oryzae, suggest that a mobile accessory chromosome may contain putative histones and/or histone modifiers, which could generate such a signal. Based on this, we propose that mobile accessory chromosomes may encode the machinery required for their own horizontal transmission, implying that HCT could be a regulated process. Finally, we present evidence of substantial differences in codon usage bias between core and accessory chromosomes in 14 out of 19 analysed fungal species and strains. Such differences in codon usage bias could indicate past horizontal transfers of these accessory chromosomes. Interestingly, HCT was previously unknown for many of these species, suggesting that the horizontal transfer of accessory chromosomes may be more widespread than previously thought and, therefore, an important factor in fungal genome evolution.

evolutionary biology↗

bioRxiv2023

Frequent horizontal chromosome transfer between asexual fungal insect pathogens

Entire chromosomes are typically only transmitted vertically from one generation to the next. The horizontal transfer of such chromosomes has long been considered improbable, yet gained recent support in several pathogenic fungi where it may affect the fitness or host specificity. To date, it is unknown how these transfers occur, how common they are and whether they can occur between different species. In this study, we show multiple independent instances of horizontal transfers of the same accessory chromosome between two distinct strains of the asexual entomopathogenic fungus Metarhizium robertsii during experimental co-infection of its insect host, the Argentine ant. Notably, only the one chromosome - but no other - was transferred from the donor to the recipient strain. The recipient strain, now harboring the accessory chromosome, exhibited a competitive advantage under certain host conditions. By phylogenetic analysis we further demonstrate that the same accessory chromosome was horizontally transferred in a natural environment between M. robertsii and another congeneric insect pathogen, M. guizhouense. Hence horizontal chromosome transfer is not limited to the observed frequent events within species during experimental infections but also occurs naturally across species. The transferred accessory chromosome contains genes that might be involved in its preferential horizontal transfer, encoding putative histones and histone-modifying enzymes, but also putative virulence factors that may support its establishment. Our study reveals that both intra- and interspecies horizontal transfer of entire chromosomes is more frequent than previously assumed, likely representing a not uncommon mechanism for gene exchange. Significance StatementThe enormous success of bacterial pathogens has been attributed to their ability to exchange genetic material between one another. Similarly, in eukaryotes, horizontal transfer of genetic material allowed the spread of virulence factors across species. The horizontal transfer of whole chromosomes could be an important pathway for such exchange of genetic material, but little is known about the origin of transferable chromosomes and how frequently they are exchanged. Here, we show that the transfer of accessory chromosomes - chromosomes that are non-essential but may provide fitness benefits - is common during fungal co-infections and is even possible between distant pathogenic species, highlighting the importance of horizontal gene transfer via chromosome transfer also for the evolution and function of eukaryotic pathogens.

genomics↗

bioRxiv2023

The apoplastic space of two wheat genotypes provide highly different environment for pathogen colonization: Insights from proteome and microbiome profiling

The intercellular space comprising the plant apoplast harbors a diverse range of microorganisms. The apoplastic interface represents the main compartment for interactions between proteins produced and secreted by the plant and the microbial endophytes. The outcomes of these interactions can play a role in plant cell wall metabolism, stress tolerance, and plant-pathogen resistance. So far the underlying factors that determine microbiota composition in the apoplast are not fully understood. However, it is considered that cell wall composition, nutrient availability, and the plant immune system are main determinants of microbiota composition. The plant immune system is considered to play a crucial role in modulating microbiota composition through the recognition of specific microbe-associated molecular patterns and the activation of defense responses. Hereby the plant may restrict non-beneficial microbial members and facilitate the propagation of beneficial ones. In this study, we investigated changes in the apoplastic environment during pathogen invasion using wheat as a model system. Infection of wheat with Zymoseptoria tritici, a fungal pathogen, resulted in notable alterations in the apoplast composition, reduced microbial diversity, and the accumulation of antimicrobial defense metabolites. Intriguingly, certain core microbial members persisted even in the presence of pathogen-induced immune responses, indicating their ability to evade or tolerate host immune defenses. To further explore these dynamics, we developed a protocol for extracting apoplastic fluids from wheat leaves and conducted proteome analyses to characterize the dynamic environment of the wheat leaves. Our findings uncovered a highly variable apoplastic environment that selects for microbes with specific adaptations. Notably, a core microbial community enriched in the resistant wheat cultivar exhibited antagonistic activity against Z. tritici, suggesting a potential role in conferring pathogen defense. This study advances our understanding of the dynamic interactions and adaptations of the wheat apoplastic microbiota during pathogen invasion, emphasizing the pivotal role of microbial interactions in pathogen defenses.

microbiology↗

bioRxiv2022

Repeat-induced point mutation and gene conversion coinciding with heterochromatin shape the genome of a plant pathogenic fungus

Meiosis is associated with genetic changes in the genome - via recombination, gene conversion, and mutations. The occurrence of gene conversion and mutations during meiosis may further be influenced by the chromatin conformation, in analogy to what is known for mutations during mitosis. To date, however, the exact distribution and type of meiosis-associated changes and the role of the chromatin conformation in this context is largely unexplored. Here, we determine recombination, gene conversion, and de novo mutations using whole-genome sequencing of all meiotic products of 23 individual meioses in Zymoseptoria tritici, an important pathogen of wheat. We could confirm a high genome-wide recombination rate of 65 cM/Mb and see higher recombination rates on the accessory compared to core chromosomes. A substantial fraction of 0.16% of all polymorphic markers was affected by gene conversions, showing a weak GC-bias, and occurring at higher frequency in regions of constitutive heterochromatin, indicated by the histone modification H3K9me3. The de novo mutation rate associated with meiosis was approx. three orders of magnitude higher than the corresponding mitotic mutation rate. Importantly, repeat-induced point mutation (RIP), a fungal defense mechanism against duplicated sequences, is active in Z. tritici and responsible for the majority of these de novo meiotic mutations. Our results indicate that the genetic changes associated with meiosis are a major source of variability in the genome of an important plant pathogen and shape its evolutionary trajectory. ImportanceThe impact of meiosis on the genome composition via gene conversion and mutations is mostly poorly understood, in particular for non-model species. Here, we sequenced all four meiotic products for 23 individual meioses and determined the genetic changes caused by meiosis for the important fungal wheat pathogen Zymoseptoria tritici. We found a high rate of gene conversions and an effect of the chromatin conformation on gene conversion rates. Higher conversion rates were found in regions enriched with the H3K9me3 - a mark for constitutive heterochromatin. Most importantly, meiosis was associated with a much higher frequency of de novo mutations than mitosis. 78% of the meiotic mutations were caused by repeat-induced point mutations - a fungal defense mechanism against duplicated sequences. In conclusion, the genetic changes associated with meiosis are therefore a major factor shaping the genome of this fungal pathogen.

genomics↗

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

The transcription factor Zt107320 affects the dimorphic switch, growth and virulence of the fungal wheat pathogen Zymoseptoria tritici

Zymoseptoria tritici is a filamentous fungus causing Septoria tritici blotch in wheat. The pathogen has a narrow host range and infections of grasses other than susceptible wheat are blocked early after stomatal penetration. During these abortive infections the fungus shows a markedly different expression pattern. However, the underlying mechanisms causing differential gene expression during host and non-host interaction are largely unknown, but likely include transcriptional regulators responsible for the onset of an infection program in compatible hosts. In the rice blast pathogen Magnaporthe oryzae, MoCOD1, a member of the fungal Zn(II)2Cys6 transcription factor family, has been shown to directly affect pathogenicity. Here, we analyse the role of the putative transcription factor Zt107320, a homolog of MoCOD1, during infection of compatible and incompatible hosts by Z. tritici. We show for the first time that Zt107320 is differentially expressed in host versus non-host infections and that lower expression corresponds to an incompatible infection of non-hosts. Applying reverse genetics approaches we further show that Zt107320 regulates the dimorphic switch as well as the growth rate of Z. tritici and affects fungal cell wall composition in vitro. Moreover, {Delta}Zt107320 mutants showed reduced virulence during compatible infections of wheat. We conclude that Zt107320 directly influences pathogen fitness and propose that Zt107320 regulates growth processes and pathogenicity during infection. Our results suggest that this putative transcription factor is involved in discriminating compatible and non-compatible infections.

microbiology↗

bioRxiv2018

Meiotic drive of female-inherited supernumerary chromosomes in a pathogenic fungus

Meiosis is a key cellular process of sexual reproduction involving the pairing of homologous sequences. In many species however, meiosis can also involve the segregation of supernumerary chromosomes, which can lack a homolog. How these unpaired chromosomes undergo meiosis is largely unknown. In this study we investigated chromosome segregation during meiosis in the haploid fungus Zymoseptoria tritici that possesses a large complement of supernumerary chromosomes. We used isogenic whole chromosome deletion strains to compare meiotic transmission of chromosomes when paired and unpaired. Unpaired chromosomes inherited from the male parent as well as paired supernumerary chromosomes showed Mendelian inheritance. In contrast, unpaired chromosomes inherited from the female parent showed non-Mendelian inheritance but were amplified and transmitted to all meiotic products. We concluded that the supernumerary chromosomes of Z. tritici show a meiotic drive and propose an additional feedback mechanism during meiosis which initiates amplification of unpaired female-inherited chromosomes.

molecular biology↗

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↗