Biology subjects

Auxier, B.

Publications and source records attributed to Auxier, B..

11 recordsLinked to original sources

bioRxiv2026

Genetic Association of Somatic Incompatibility and NLR-like Protein Domains in Coprinopsis cinerea

In fungi, hyphal fusion is beneficial within an individual, but fusion between individuals comes with the risks of infection or exploitation. To manage this risk, fungi have developed mechanisms to restrict sustained fusion to be within a genetic individual, called allorecognition. In Ascomycete fungi, this recognition is based on allelic identity at several polymorphic allorecognition genes, often triggering cell death. However, the genetic basis of allorecognition is unknown in basidiomycetes, the clade that includes mushroom-forming fungi. Here, we map the first locus for this trait, which we call somA, in the mushroom-forming fungus Coprinopsis cinerea. We combined F1 offspring phenotypes with independent backcross lines to identify a region on chromosome 5 linked with the production of a barrage zone, a classic allorecognition phenotype. Fine-mapping of this region resulted in a region with a set of kinases and NACHT domain proteins, flanked by a leucine-rich repeat (LRR) protein. While the NACHT and kinase proteins are diverse between the parents, the LRR-encoding protein shows signs of purifying selection. Additional C. cinerea genomes show that this region contains several highly divergent alleles, consistent with long-term balancing selection. These polymorphic alleles all contain a single monomorphic LRR, which may indicate a novel mechanism for fungal nonself recognition. Based on a phylogenetic survey of related Basidiomycetes, this specific locus architecture appears to be restricted to closely related species. This finding of a multiallelic locus may explain the general trend of few nonself recognition loci in basidiomycetes. These results provide a first understanding of how individuality is maintained in basidiomycetes. Significance StatementHow mushroom-forming fungi recognize each other as individuals is an open question. Here, we identify the first genes that trigger this recognition in a mushroom-forming fungus. As these fungi have very distinctive lifecycles compared to mold-forming fungi, it was hypothesized that the process would operate from different mechanisms. Our results show the molecular mechanisms are in fact quite similar. These results provide a first step towards understanding how these fungi can both fuse with themselves and still discriminate against other individuals.

genetics↗

bioRxiv2026

Non-triazole agricultural fungicides indirectly select for triazole resistance in the human pathogen Aspergillus fumigatus

The intensification of agriculture relies on chemical fungicides to manage crop disease1,2, leading to the evolution of resistance in plant pathogens.3 Fungicides have long half-lives, allowing them to remain active well beyond their intended targets and affect downstream ecosystems and agricultural practices. The saprophytic fungus Aspergillus fumigatus is an airborne ubiquitous fungus and an important human pathogen causing severe life-threatening invasive fungal disease.4 Selection pressure from agricultural triazoles, demethylase inhibitors (DMIs), has led to cross-resistance to clinical triazoles, as they share the same target gene, cyp51A.5,6 In the Netherlands7,8, most triazole resistance arises from two cyp51A haplotypes, the TR34 and TR46.9,10 Genomic surveys of A. fumigatus have shown that these triazole-resistance alleles often co-occur with resistance alleles to non-DMI classes, these include some of the dominant fungicide classes used in Europe such as quinone outside inhibitors (QoIs), and succinate dehydrogenase inhibitors (SDHIs).11 Hypothesizing that agricultural environments with non-DMI fungicides can indirectly select for triazole resistance, we used grass mesocosms to compete A. fumigatus isolates. We found that already at low concentrations, commonly found in agricultural residues, DMI, SDHI, and QoI fungicides can each independently increase the proportions of triazole resistant alleles. We show that the resistance alleles for each class are not intrinsically cross-resistant, indicating that their co-occurrences in allelic combinations produce this multi-resistance selection. Consistent with our mesocosms results, environmental samples contained high phenotypic (>20%) triazole resistance in heaps with only non-DMI fungicides. This work provides the first experimental and field evidence of selection for triazole resistance by non-triazole fungicides via genomic hitch-hiking. We thus predict that when novel fungicides are used in the same selective environment, novel resistance alleles will most likely be selected in isolates that have already accumulated resistance alleles to other fungicide classes. Because of linked resistance alleles, tackling selection and spread of environmental triazole resistance will require consideration of all fungicide classes. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC="FIGDIR/small/728463v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@259848org.highwire.dtl.DTLVardef@30bfdeorg.highwire.dtl.DTLVardef@84bb35org.highwire.dtl.DTLVardef@1eb39d_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LITriazole-resistance alleles often co-occur with resistance alleles to non-DMI fungicide classes such as SDHI and QoI. C_LIO_LIDMI, SDHI, and QoI all independently increase the proportions of triazole resistant alleles at low concentrations (0.1 mg/kg) commonly found in agricultural residues. C_LIO_LIThe DMI resistance allele TR46 has a high fitness only under fungicide selective conditions, whereas TR34 maintains its fitness also under fungicide free conditions. C_LIO_LIBeneficial alleles for one fungicide class increase in frequency and hitch-hike with resistance alleles to other fungicide classes. C_LIO_LIResistance alleles to novel fungicide classes will more likely be selected in isolates that already accumulated other fungicide resistance alleles. C_LI

microbiology↗

bioRxiv2026

Multiple nuclei means multiple chromosome sets in Botrytis cinerea and Neurospora crassa

We often think of fungi as mysterious organisms that do not follow the general principles of other eukaryotes. Thus, when exciting results are found, these organisms do not always receive the rigorous level of scrutiny seen in other fields. For many fungal species, dispersal and reproduction relies on spores, either sexual or asexual. These spores can either have a single nucleus, or multiple nuclei, and the purpose of these presumably mitotic copies was unclear. Recently it was described that the multiple nuclei in these spores are not mitotic duplicates, but instead they share a single haploid set of chromosomes distributed across nuclei. Here, we provide fluorescent microscopy and UV mutagenesis data that is inconsistent with this hypothesis. Contrasting these previous results, we observe multiple sets of chromosomes in spores of both B. cinerea and N. crassa. We also observed a strong linear relationship between the number of nuclei in spores and the total acriflavine fluorescence, further supporting mitotic copies. Genome sequencing of colonies arising from UV-irradiated colonies also recovered variants at intermediate frequences, instead of the fixed 100% expected from the new model proposed. This evidence suggests that, as long suspected, these nuclei are indeed mitotic copies, and that a re-evaluation of fungal biology is not currently necessary.

genetics↗

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

Genetic mapping and nuclear interactions of an incompatibility response in Agaricus bisporus

During cultivation, mixing of different heterokaryotic individuals of the button mushroom, Agaricus bisporus, generally reduces yield. This phenomenon could be caused by direct antagonistic responses and/or reduced synchronization by not forming a chimeric hyphal network. In other fungi, highly divergent alleles for a set of genes affect successful network formation between individuals either by preventing fusion or, more commonly, triggering cell death post-fusion. To understand this process in A. bisporus, it is important to identify the allelic variants allowing these fungi to discriminate self from nonself. We leverage a recently described cell death staining method utilizing Evans Blue to visualize mycelial compatibility. Here, we provide results of a first genetic mapping of incompatibility alleles in A. bisporus. Crossing strains between A. bisporus var. bisporus and A. bisporus var. burnetti we find segregation ratios of compatible progeny generally consistent with three nuclear loci. To identify these regions, we first use a set of single Chromosome Substitution Lines (CSLs), produced by genotyping progeny with recombination skewed to the very chromosome ends. We localize the main effect to be between two and three chromosomes, depending on the common nucleus of interacting heterokaryons. Using genome-wide markers for 167 sexual progeny, we identify loci controlling mycelial compatibility on chromosomes 4, 6 and 7, the same chromosomes as indicated by chromosome substitution lines. Notably, while the choice of a common nucleus seemed to affect the compatibility of CSLs, it did not seem to affect the loci identified in the sexual progeny. The ability to mix different strains of this mushroom-forming fungus could allow additional cultivation approaches, combining strains with complementary characteristics. These results provide a starting point towards understanding the molecular mechanisms underlying this fundamental property of hyphal networks in basidiomycetes.

genetics↗

bioRxiv2024

Widely dispersed clonal expansion of multi-fungicide-resistant Aspergillus fumigatus limits genomic epidemiology prospects

BackgroundAspergillus fumigatus is a ubiquitous fungus that causes a range of diseases in animals, including humans. The most lethal manifestation is invasive aspergillosis for which treatment relies on triazoles. Triazole-resistant A. fumigatus can be recovered from decaying plant material and so-called hotspots containing triazole fungicide residues. Although observations have shown clonal isolates between the environment and clinical samples, a direct link between a specific environment and cases of triazole-resistant invasive aspergillus disease in an individual patient has not yet been demonstrated. MethodsTo understand where patients acquire A. fumigatus isolates causing disease, we used a genomic epidemiology approach with 157 Dutch A. fumigatus isolates, based on whole genome sequencing. Isolates were from three well-characterized environmental hotspots and two hospitals between 2016 and 2019. FindingsIn the Dutch dataset, A. fumigatus isolates from six patients showed near-identical genomes compared to five environmental isolates. One environmental isolate matched three probable cases of triazole-resistant invasive aspergillosis, including one fatal case. Patient isolates were recovered up to 34 months later than near-identical environmental isolates. Comparison to over 1{middle dot}2K global publicly available A. fumigatus genomes showed hundreds of clonal groups spread across three continents. In addition, finding variants associated with resistance to non-triazole fungicides such as benzimidazole, succinate dehydrogenase inhibitor and quinone outside inhibitor classes, strongly suggests an exposure history to multiple agricultural fungicides in these environmental hotspots. InterpretationEnvironmental hotspots represent highly selective habitats for multi-fungicide-resistant A. fumigatus, which we can now directly link to probable cases of aspergillus disease, including a triazole-resistant case. However, geographically widely dispersed clonal expansion limits the utility of genomic epidemiology to identify the source of a particular patients isolate. Furthermore, reducing a single class of fungicides in agriculture may not effectively reduce resistance selection when other classes are still in use. FundingNWO.Groen2019.002 Research in contextO_ST_ABSEvidence before this studyC_ST_ABSTriazole fungicides that exhibit activity against Aspergillus fumigatus have been shown to be a major source of resistant aspergillus disease in humans. However, the route of transmission from environmental hotspot to human remains poorly understood. Isolates of A. fumigatus can be recovered from both environmental samples and clinical specimens that harbour the same resistance signature haplotypes, e.g., TR34/L98H and TR46/Y121F/T289A, in the cyp51A-gene. We searched the literature for evidence using high resolution whole genome sequencing (WGS) to link environmental isolates to human infection. We searched PubMed for articles using the search terms Aspergillus fumigatus AND azole resistance AND whole genome sequencing on 15 April 2024. This search retrieved 32 articles describing different evolutionary routes to select for triazole-resistant A. fumigatus or population structure of whole-genome sequenced isolates. Twenty-six articles used whole-genome sequencing, but none focused on identifying clonal groups to identify direct cases of transmission between the environment and clinical cases of aspergillus disease. By using the additional search term transmission, no other records were retrieved. Added value of this studyOur study links triazole-resistant A. fumigatus isolates cultured from three environmental hotspots to cases of aspergillus disease in two hospitals in the Netherlands. Genome comparisons of isolates from environmental hotspots and patients showed multiple near-identical linked genotypes, consistent with a route of transmission from the environment to patients. Although a naive expectation may be a higher probability of matches of the hotspots located in the northwest of the Netherlands with the hospital located in the west of the country, in fact, more patient isolates from the far southeast were linked to the hotspots. Integrating the Dutch data set into a global data set showed 205 clonal groups spread across the Netherlands, Germany, the United Kingdom (UK), the United States of America (USA) and Japan. Our demonstration of a large number of geographically dispersed clonal groups suggests that current sampling is insufficient to definitively identify the source of an individual patients infection. A genetically highly diverse population combined with a wide global distribution of clones can make it impossible to definitively identify the source of an individual patients infection even with much more sampling. Implications of all the available evidenceOur study provides evidence that triazole-resistant A. fumigatus isolates with multi-fungicide resistance profiles cause aspergillus disease in at-risk patients and may contribute to treatment failure and mortality. The risk of infection due to these triazole-resistant isolates is not confined to the geographic vicinity of the environmental hotspot since clonal spread can be detected across great distances. The finding of linked cases without clear transmission routes limits epidemiological studies and underscores the need to better understand the ecology and environmental niches of this fungus. As it is highly unlikely that each patient visited the rural agricultural areas where a hotspot was located, research should address the complex and long-distance transmission routes of resistant isolates, which involves airborne dispersal of conidia or habitats of this fungus outside the agricultural environment. Furthermore, because of the multi-fungicide resistance phenotype of the triazole-resistant A. fumigatus, involving several classes of fungicides, reducing one class of fungicides in the environment may not effectively reduce resistance selection. Effective interventions should instead aim to reduce the burden of environmental resistance by modifying environments that currently favour the massive outgrowth of fungicide-resistant A. fumigatus to limit the escape of aerial spores from these environmental hotspots.

microbiology↗

bioRxiv2023

Community diversity affects functionality and species sorting during propagation of a natural microbial community

The influence of community diversity on community function has long been a central question in ecology. Particularly, the dynamics over time of this relationship as a function of levels of diversity remains unclear. Natural populations may vary in levels of species diversity, for instance after they experience disturbances that remove significant amounts of their genetic and species variation, including rare but functionally unique guilds. We investigated the influence of diversity on associated community function by propagating natural microbial communities from a traditionally fermented milk beverage diluted to various levels. Specifically, we assessed the influence of less abundant microbial types such as yeast and rarer bacterial types on community functionality and species sorting trajectories over approximately 100 generations. We observed repeatable changes in bacterial community compositions, metabolic profiles, and acidity related to starting diversity levels. The influence of a single ecological guild, yeast in our study, played a dramatic role on function, but interestingly not on long-term species sorting trajectories of the remaining bacterial community. Our results together evidence ecological selection on the microbial communities in our system and suggest an unexpected niche division between yeast and bacterial communities.

ecology↗

bioRxiv2022

Identification of heterokaryon incompatibility genes in Aspergillus fumigatus highlights a narrow footprint of ancient balancing selection

In fungi, a phenomenon termed heterokaryon incompatibility restricts hyphal fusion to occur within an individual since fusion between individuals leads to cell death. Generally, the genes involved are found to be under balancing selection from negative frequency dependent fitness. Here, we assess this in Aspergillus fumigatus, a human pathogenic fungus with an extremely high crossover rate. Using auxotrophic markers we screened sexual progeny for compatibility to identify genes involved in this process, the so-called het genes. In total, 5/148 (3.4%) offspring were compatible with a parent and 166/2142 (7.7%) sibling pairs were compatible, consistent with several segregating incompatibility loci. Genetic mapping resulted in five loci, four of which could be fine mapped to individual genes, of which we tested three through heterologous expression, confirming their causal relationship. Surprisingly, a population-level analysis of two available independent datasets did not show an increase in Tajimas D near these loci, normally a hallmark of balancing selection. However, analysis of closely related species did show trans-species polymorphisms across >10 million years, and equal allele frequencies within A. fumigatus. Using available de novo assemblies, we show that these balanced polymorphisms are restricted to within several hundred base pairs flanking the coding sequence, potentially due to this species high crossover rate. In addition to identifying the first het genes in an Aspergillus species, this work highlights the interaction of long-term balancing selection with a high recombination rate. Future mechanistic work on these het genes may provide novel routes for clinical therapies, as well as opportunities for strain improvement in biotechnology.

evolutionary biology↗

bioRxiv2022

Meiosis in the human pathogen Aspergillus fumigatus has the highest known number of crossovers

Evidence from both population genetics and a laboratory sexual cycle indicate that sex is common in the fungus Aspergillus fumigatus. However, the impact of sexual reproduction has remained unclear. Here, we show that meiosis in A. fumigatus involves the highest known recombination rate, producing ~29 crossovers per chromosome. This represents the highest known crossover rate for any Eukaryotic species. We validate this recombination rate by mapping resistance to acriflavine, a common genetic marker. We further show that this recombination rate can produce the commonly encountered TR34/L98H azole-resistant cyp51A haplotype in each sexual event, facilitating its rapid and global spread. Understanding the consequences of this unparalleled crossover rate will not only enrich our genetic understanding of this emergent human pathogen, but of meiosis in general. One-Sentence SummaryGenetic exchange between chromosomes during sex in Aspergillus fumigatus is higher than in any other known organism.

genetics↗

bioRxiv2021

Recombinant haplotypes reflect sexual reproduction in symbiotic arbuscular mycorrhizal fungi

Arbuscular mycorrhizal fungi (AMF) are part of the most widespread fungal-plant symbiosis. They colonize at least 80% of plant species, promote plant growth and plant diversity. These fungi are multinucleated and contain either one or two haploid nuclear genotypes (monokaryon and dikaryon) identified by the alleles at a putative mating-type locus. This taxon has been considered as an ancient asexual scandal because of the lack of observable sexual structures. Despite identification of a putative mating-type locus and functional activation of genes related to mating when two isolates co-exist, it remains unknown if AMF take part in a mainly sexual life cycle. We used publicly available genome sequences to test if dikaryon genomes display signatures of sexual reproduction in the form of reciprocal recombination patterns, or if they display signatures of parasexual reproduction involving gene conversion. We used short-read and long-read sequence data to identify nucleus genotype-specific haplotypes within dikaryons and then compared them to orthologous gene sequences from related monokaryon isolates displaying the same putative MAT-types. We observed that these genotype-specific haplotypes display reciprocal recombination and not gene conversion. These results are consistent with a sexual origin of the dikaryon rather than a parasexual origin and provides an important step to understand the life cycle of these globally important symbiotic fungi.

evolutionary biology↗

bioRxiv2020

Nuclear selection is effectively policed by mating restrictions of the dikaryotic life cycle of mushrooms.

Generally, sexual organisms contain two haploid genomes, one from each parent, united in a single diploid nucleus of the zygote which links their fate during growth. A fascinating exception to this are Basidiomycete fungi, where the two haploid genomes remain separate in a dikaryon, retaining the option to fertilize subsequent monokaryons encountered. How the ensuing nuclear competition influences the balance of selection within and between individuals is largely unexplored. We test the consequences of the dikaryotic lifecycle for mating success and mycelium-level fitness components. We assume a tradeoff between mating fitness at the level of the haploid nucleus and fitness of the fungal mycelium. We show that the maintenance of fertilization potential by dikaryons leads to a higher proportion of fertilized monokaryons, but that the ensuing intra-dikaryon selection for increased nuclear mating fitness leads to reduced mycelium fitness relative to a diploid life cycle. However, this fitness reduction is lower compared to a hypothetical life cycle where dikaryons can also exchange nuclei. Prohibition of fusion between dikaryons therefore reduces the level of nuclear parasitism. The number of loci influencing fitness is an important determinant of the degree to which average mycelium-level fitness is reduced. The results of this study crucially hinge upon a tradeoff between nucleus and mycelium-level fitness. We discuss the evidence for this assumption and the implications of an alternative that there is a positive relationship between nucleus and mycelium-level fitness.

evolutionary biology↗