Biology subjects

Baars, J. J. P.

Publications and source records attributed to Baars, J. J. P..

3 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↗

bioRxiv2022

Feeding Growing Mushrooms

A number of experiments were done to further our understanding of the substrate utilization in button mushroom crops (Agaricus bisporus). An analysis of the degradation of dry matter of the substrate during a crop cycle revealed that for pin formation the upper layer is used, for the production of flush one all layers are involved and for flush two mainly the lower layer is used. A reduction in substrate depth leads to a decrease in yield/m2 but an apparent increase in yield per ton of substrate but with a lower mushroom quality. A short daily interruption of the connection between the casing soil with all the substrate results in a delay of the first flush. Repetitive interruption of the connection with all or only part of the substrate leads to a shift in yield from flush one to flush two but the total yield remains unchanged. The mycelial biomass in the substrate increases from filling up to pinning, a steeper increase during flush one, levelling off during flush two, indicating that in the period of venting and up to/including flush one, enzymes are secreted by growing hyphae generating nutrients to feed a fixed amount of mushroom biomass for two flushes. A sidewise extension of the substrate (without casing soil, thus not producing mushrooms) showed that the substrate at a distance more than 20-50 cm away from the casing soil does not contribute to feeding mushrooms in the first two flushes. The observations are discussed with respect to relevant previous research. ImportanceButton mushrooms (Agaricus bisporus) are cultivated on a substrate prepared of composted wheat straw, chicken and/or horst manure and gypsum. This manuscript describes a number of experiments indicating that in a harvesting strategy towards quality mushrooms there is a fixed amount of nutrients prepared/available to feed two flushes. The increase of mycelial biomass in the substrate after venting and especially during the development of flush one indicates that likely a branching of mycelium occurs during this period, leading to a substantial number of growing hyphal tips excreting lignocellulolytic enzymes that degrade substrate and make nutrients available during flush one which are utilised in flush one and two. The presently used substrate seems to have reached its limits and there are hardly opportunities for further improvement. Research on alternative, more energy dense, substrates are needed to improve the efficiency of the present production system.

microbiology↗

bioRxiv2017

Nucleus Specific Expression In The Multinucleated Mushroom-Forming Fungus Agaricus bisporus Reveals Different Nuclear Regulatory Programs

MotivationFungi are essential in nutrient recycling in nature. They also form symbiotic, commensal, parasitic and pathogenic interactions with other organisms including plants, animals and humans. Many fungi are polykaryotic, containing multiple nuclei per cell. In the case of heterokaryons, there are even different nuclear types within a cell. It is unknown what the different nuclear types contribute in terms of mRNA expression levels in fungal heterokaryons. Each cell of the cultivated, mushroom forming basidiomycete Agaricus bisporus contains 2 to 25 nuclei of two nuclear types, P1 or P2, that originate from two parental strains. Using RNA-Seq data, we wish to assess the differential mRNA contribution of individual nuclear types in heterokaryotic cells and its functional impact.\n\nResultsWe studied differential expression between genes of the two nuclear types throughout mushroom development of A. bisporus in various tissue types. The two nuclear types, produced specific mRNA profiles which changed through development of the mushroom. The differential regulation occurred at a gene and multi-gene locus level, rather than the chromosomal or nuclear level. Although the P1 nuclear type dominates the mRNA production throughout development, the P2 type showed more differentially upregulated genes in important functional groups including genes involved in metabolism and genes encoding secreted proteins. Out of 5,090 karyolelle pairs, i.e. genes with different alleles in the two nuclear types, 411 were differentially expressed, of which 246 were up-regulated by the P2 type. In the vegetative mycelium, the P2 nucleus up-regulated almost three-fold more metabolic genes and cazymes than P1, suggesting phenotypic differences in growth. A total of 10% of the differential karyollele expression is associated with differential methylation states, indicating that epigenetic mechanisms may be partly responsible for nuclear specific expression.\n\nConclusionWe have identified widespread transcriptomic variation between the two nuclear types of A. bisporus. Our novel method enables studying karyollelle specific expression which likely influences the phenotype of a fungus in a polykaryotic stage. This is thus relevant for the performance of these fungi as a crop and for improving this species for breeding. Our findings could have a wider impact to better understand fungi as pathogens. This work provides the first insight into the transcriptomic variation introduced by genomic nuclear separation.

microbiology↗