Genetics of fruit body production in higher basidiomycetes II. Monokaryotic and dikaryotic fruiting in schizophyllum commune

The Pacific Tree-Parasitic Fungus Cyclocybe parasitica Exhibits Monokaryotic Fruiting, Showing Phenotypes Known from Bracket Fungi and from Cyclocybe aegerita

Cyclocybe parasitica is a wood-destroying parasitic edible mushroom growing on diverse broad-leafed trees in New Zealand and other Pacific areas. Recent molecular systematics of European Cyclocybe aegerita, a newly delimited Asian phylum and of related species, corroborated the distinction of the chiefly saprobic cultivated edible mushroom C. aegerita from C. parasitica. Here, we show that C. parasitica exhibits a morpho-physiological trait characteristic to its European cousin, i.e., monokaryotic fruiting sensu stricto (basidiome formation without mating). Monokaryotic fruiting structures formed by C. parasitica ICMP 11668-derived monokaryons were categorized into four phenotypes. One of them displays ulcer-like structures previously reported from bracket fungi. Histology of dikaryotic and monokaryotic C. parasitica fruiting structures revealed anatomical commonalities and differences between them, and towards monokaryotic fruiting structures of C. aegerita. Mating experiments with C. parasitica strains representative of each fruiting phenotype identified compatible sibling monokaryons. Given reports on hypothetically monokaryotic basidiome field populations of ‘C. aegerita sensu lato’, it seems worthwhile to prospectively investigate whether monokaryotic fruiting s.str. occurs in nature. Sampling from such populations including karyotyping, comparative -omics, and competition assays may help to answer this question and provide evidence whether this trait may confer competitive advantages to a species capable of it.

Survival of the basidiomycete Schizophyllum commune in soil under hostile environmental conditions in the Chernobyl Exclusion Zone

Radioactive contamination resulting from major nuclear accidents presents harsh environmental conditions. Inside the Chernobyl exclusion zone, even more than 30 years after the accident, the resulting contamination levels still does not allow land-use or human dwellings. To study the potential of basidiomycete fungi to survive the conditions, a field trial was set up 5 km south-south-west of the destroyed reactor unit. A model basidiomycete, the lignicolous fungus Schizophyllum commune, was inoculated and survival in the soil could be verified. Indeed, one year after inoculation, the fungus was still observed using DNA-dependent techniques. Growth led to spread at a high rate, with approximately 8 mm per day. This shows that also white-rot basidiomycetes can survive the harsh conditions in soil inside the Chernobyl exclusion zone. The unadapted fungal strain showed the ability to grow and thrive in the contaminated soil where both stress from radiation and heavy metals were present.

The genome sequence of the commercially cultivated mushroom Agrocybe aegerita reveals a conserved repertoire of fruiting-related genes and a versatile suite of biopolymer-degrading enzymes

BACKGROUND

Agrocybe aegerita is an agaricomycete fungus with typical mushroom features, which is commercially cultivated for its culinary use. In nature, it is a saprotrophic or facultative pathogenic fungus causing a white-rot of hardwood in forests of warm and mild climate. The ease of cultivation and fructification on solidified media as well as its archetypal mushroom fruit body morphology render A. aegerita a well-suited model for investigating mushroom developmental biology.

RESULTS

Here, the genome of the species is reported and analysed with respect to carbohydrate active genes and genes known to play a role during fruit body formation. In terms of fruit body development, our analyses revealed a conserved repertoire of fruiting-related genes, which corresponds well to the archetypal fruit body morphology of this mushroom. For some genes involved in fruit body formation, paralogisation was observed, but not all fruit body maturation-associated genes known from other agaricomycetes seem to be conserved in the genome sequence of A. aegerita. In terms of lytic enzymes, our analyses suggest a versatile arsenal of biopolymer-degrading enzymes that likely account for the flexible life style of this species. Regarding the amount of genes encoding CAZymes relevant for lignin degradation, A. aegerita shows more similarity to white-rot fungi than to litter decomposers, including 18 genes coding for unspecific peroxygenases and three dye-decolourising peroxidase genes expanding its lignocellulolytic machinery.

CONCLUSIONS

The genome resource will be useful for developing strategies towards genetic manipulation of A. aegerita, which will subsequently allow functional genetics approaches to elucidate fundamentals of fruiting and vegetative growth including lignocellulolysis.

Omics data reveal the unusual asexual-fruiting nature and secondary metabolic potentials of the medicinal fungus Cordyceps cicadae

Background

Ascomycete Cordyceps species have been using as valued traditional Chinese medicines. Particularly, the fruiting bodies of Cordyceps cicadae (syn. Isaria cicadae) have long been utilized for the treatment of chronic kidney disease. However, the genetics and bioactive chemicals in this fungus have been largely unexplored.

Results

In this study, we performed comprehensive omics analyses of C. cicadae, and found that, in contrast to other Cordyceps fungi, C. cicadae produces asexual fruiting bodies with the production of conidial spores instead of the meiotic ascospores. Genome sequencing and comparative genomic analysis indicate that the protein families encoded by C. cicadae are typical of entomopathogenic fungi, including the expansion of proteases and chitinases for targeting insect hosts. Interestingly, we found that the MAT1-2 mating-type locus of the sequenced strain contains an abnormally truncated MAT1-1-1 gene. Gene deletions revealed that asexual fruiting of C. cicadae is independent of the MAT locus control. RNA-seq transcriptome data also indicate that, compared to growth in a liquid culture, the putative genes involved in mating and meiosis processes were not up-regulated during fungal fruiting, further supporting asexual reproduction in this fungus. The genome of C. cicadae encodes an array of conservative and divergent gene clusters for secondary metabolisms. Based on our analysis, the production of known carcinogenic metabolites by this fungus could be potentially precluded. However, the confirmed production of oosporein raises health concerns about the frequent consumption of fungal fruiting bodies.

Conclusions

The results of this study expand our knowledge of fungal genetics that asexual fruiting can occur independent of the MAT locus control. The obtained genomic and metabolomic data will benefit future investigations of this fungus for medicinal uses.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-4060-4) contains supplementary material, which is available to authorized users.

Advances in Understanding Mating Type Gene Organization in the Mushroom-Forming Fungus Flammulina velutipes

The initiation of sexual development in the important edible and medicinal mushroom Flammulina velutipes is controlled by special genes at two different, independent, mating type (MAT) loci: HD and PR. We expanded our understanding of the F. velutipes mating type system by analyzing the MAT loci from a series of strains. The HD locus of F. velutipes houses homeodomain genes (Hd genes) on two separated locations: sublocus HD-a and HD-b. The HD-b subloci contained strain-specific Hd1/Hd2 gene pairs, and crosses between strains with different HD-b subloci indicated a role in mating. The function of the HD-a sublocus remained undecided. Many, but not all strains contained the same conserved Hd2 gene at the HD-a sublocus. The HD locus usually segregated as a whole, though we did detect one new HD locus with a HD-a sublocus from one parental strain, and a HD-b sublocus from the other. The PR locus of F. velutipes contained pheromone receptor (STE3) and pheromone precursor (Pp) genes at two locations, sublocus PR-a and PR-b. PR-a and PR-b both contained sets of strain-specific STE3 and Pp genes, indicating a role in mating. PR-a and PR-b cosegregated in our experiments. However, the identification of additional strains with identical PR-a, yet different PR-b subloci, demonstrated that PR subloci can recombine within the PR locus. In conclusion, at least three of the four MAT subloci seem to participate in mating, and new HD and PR loci can be generated through intralocus recombination in F. velutipes.

Fruiting Body Formation in Volvariella volvacea Can Occur Independently of Its MAT-A-Controlled Bipolar Mating System, Enabling Homothallic and Heterothallic Life Cycles

Volvariella volvacea is an important crop in Southeast Asia, but erratic fruiting presents a serious challenge for its production and breeding. Efforts to explain inconsistent fruiting have been complicated by the multinucleate nature, typical lack of clamp connections, and an incompletely identified sexual reproductive system. In this study, we addressed the life cycle of V. volvacea using whole genome sequencing, cloning of MAT loci, karyotyping of spores, and fruiting assays. Microscopy analysis of spores had previously indicated the possible coexistence of heterothallic and homothallic life cycles. Our analysis of the MAT loci showed that only MAT-A, and not MAT-B, controlled heterokaryotization. Thus, the heterothallic life cycle was bipolar. Karyotyping of single spore isolates (SSIs) using molecular markers supported the existence of heterokaryotic spores. However, most SSIs were clearly not heterokaryotic, yet contained structural variation (SV) markers relating to both alleles of both parents. Heterokaryons from crossed, self-sterile homokaryons could produce fruiting bodies, agreeing with bipolar heterothallism. Meanwhile, some SSIs with two different MAT-A loci also produced fruiting bodies, which supported secondary homothallism. Next, SSIs that clearly contained only one MAT-A locus (homothallism) were also able to fruit, demonstrating that self-fertile SSIs were not, per definition, secondary homothallic, and that a third life cycle or genetic mechanism must exist. Finally, recombination between SV markers was normal, yet 10 out of 24 SV markers showed 1:2 or 1:3 distributions in the spores, and large numbers of SSIs contained doubled SV markers. This indicated selfish genes, and possibly partial aneuploidy.

The Aa-Pri4 gene, specifically expressed during fruiting initiation in the Agrocybe aegerita complex, contains an unusual CT-rich leader intron within the 5' uncoding region

The Aa1-Pri4 gene was cloned from the edible mushroom Agrocybe aegerita. The gene, specifically expressed during fruiting initiation, encodes a glycine-rich protein of 116 amino acids, with no homology to already known proteins. Homologous genes were amplified from two other strains belonging to the Agr. aegerita complex and originating from South-East Asia; and a comparison of the three genes revealed a high conservation of the coding sequences (72.8-97.8%). The PRI4 putative protein sequences were highly similar (87.5-100.0%); and all of them contained two protein kinase C sites, suggesting a potential supplementary regulation by phosphorylation at the protein level. The 5' uncoding regions all presented a leader intron, very variable in sequence (45.7% identity), but with a high C+T content (74.5-79.0%). The presence of such CT-rich sequences previously described in the promoter of highly expressed fungal genes suggests that the leader intron of the Aa1-Pri4 gene could be involved in the high-level, stage-specific expression.

Haploid fruiting in Cryptococcus neoformans is not mating type alpha-specific

Under appropriate conditions, haploid Cryptococcus neoformans cells can undergo a morphological switch from a budding yeast form to develop hyphae and viable basidiospores, which resemble those produced by mating. This process, known as haploid fruiting, was previously thought to occur only in MATalpha strains. We identified two new strains of C. neoformans var. neoformans serotype D that are MATa type and are able to haploid fruit. Further, a MATa reference strain, B-3502, also produced hyphae and fruited after prolonged incubation on filament agar. Over-expression of STE12a dramatically enhanced the ability of all MATa strains tested to filament. Segregation analysis of haploid fruiting ability confirmed that haploid fruiting is not MATalpha-specific. Our results indicate that MATa cells are intrinsically able to haploid fruit and previous observations that they do not were probably biased by the examination of a small number of genetically related isolates that have been maintained in the laboratory for many years.

Tetrapolar fungal mating types: sexes by the thousands

In order to achieve genetic rearrangement in a sexual cycle, eukaryotes go through the processes of meiosis and mating. Different mating types assure that mating is only possible between two genetically diverse individuals. Basidiomycetous fungi display thousands of different mating types that are determined by two genetically unlinked loci. One locus is multiallelic and contains genes for homeodomain transcription factors which are able to form heterodimers. The activation of target genes is dependent on heterodimers formed from the monomeric transcription factor proteins originating from different alleles of this genetic locus. The interactions between the two monomeric transcription factors and the activation of target genes by the heterodimeric proteins make this regulatory system both complex and interesting. The second locus contains a pheromone receptor system: the pheromone receptor is similar to the G protein-linked serpentine receptors in Saccharomyces cerevisiae that activate the pheromone response via a phosphorylation signal transduction cascade in S. cerevisiae. This pheromone perception is a trigger of sexual development and not, as with yeast, itself under control of mating type genes. Rather it directly senses diversity at the mating type loci. Whereas heterobasidiomycetes display a bi-allelic structure for this locus with recognition between one receptor and the opposite pheromone, homobasidiomycetes contain multiple specificities for pheromone receptors and pheromones.

Genetic regulation of emergent growth in Schizophyllum commune

After a period of juvenile growth, Schizophyllum commune starts to transcribe genes for a number of abundant cell-wall proteins that are excreted into the medium by submerged hyphae but become part of the cell wall in emergent structures. The dikaryon transcribes the genes SC1, SC3, SC4, and SC6 that encode hydrophobins and SC7 and SC14 that encode hydrophilic wall proteins of unknown function. Of these, only the SC3 gene is highly transcribed in the monokaryon. The SC3p hydrophobin forms an insoluble hydrophobic rodlet layer by interfacial self-assembly at the outer surface of aerial hyphae of both monokaryon and dikaryon. The SC4p hydrophobin forms an insoluble membrane separating the extracellular matrix surrounding dikaryotic hyphae of the plectenchyma from air cavities in the fruit bodies while the product of the SC7 gene is found within the extracellular matrix. However, these plectenchyma hyphae do not express the SC3 gene. Because SC3 activity is suppressed in a MATA = MATB≠ heterokaryon and a MATAx matBCon homokaryon, interaction between different B mating-type gene products appears responsible for suppression of SC3 in the hyphae that form the plectenchyma. On the other hand, in aerial hyphae of the MATA ≠ MATB≠ heterokaryon the binucleate state of the hyphae appears disrupted and this is accompanied by expression of SC3 only, as in the monokaryon. This suggests that regulation of specific genes by the products of different MATB genes only occurs when these genes are present in closely paired nuclei. Thus, spatial differences in gene expression during emergent growth in the MATA ≠ MATB≠ heterokaryon may occur by regulation of the nuclear distribution. Key words: Schizophyllum commune development, hydrophobins in development, mating-type genes in Schizophyllum, fruit-body development, emergent growth.

The mushroom-inducing gene Frt1 of Schizophyllum commune encodes a putative nucleotide-binding protein

Fruiting bodies (mushrooms) can be induced to form in unmated, normally non-fruiting strains of the basidiomycete fungus Schizophyllum commune by the ectopic genomic integration of a cloned gene called Frt1. Thus, the normal requirement of mating for mushroom formation is bypassed. Sequence analysis of genomic and cDNA clones revealed that the Frt1 gene encodes a predicted polypeptide of 192 amino acids, interrupted by three short introns. The FRT1 protein is predicted to be of M(r) 21,625 and does not have significant overall similarity to any known proteins. Analysis of the predicted amino acid sequence revealed the presence of a P-loop motif, a conserved sequence found in nucleotide-binding proteins. A potential site for Mg2+ binding is predicted to reside next to the P-loop at Thr24. The possible functional significance of these and other residues within FRT1 was examined using site-directed mutagenesis, followed by transformation of these mutant alleles of Frt1 back into S. commune. Mutation of the middle glycine of the P-loop completely abolished the fruit-inducing activity of cloned Frt1. Substitution of an alanine residue for Thr24 also resulted in mutant clones with no fruit-inducing activity. The possibility of an interaction between two closely spaced threonine residues within FRT1 was suggested by transformation experiments utilizing mutant Frt1 alleles with specific combinations of mutations at these sites. Taken together, the results of our mutagenesis experiments suggest the possibility that activity of the predicted FRT1 protein could be altered by nucleotide binding and coordination of Mg2+. Northern blot hybridization experiments indicate that Frt1 activity is probably not controlled at the transcriptional level.

On the taxonomy of the entomogenous fungus Filobasidiella arachnophila

The taxonomic status of Filobasidiella arachnophila Malloch et al. was investigated. The carbohydrate profile of two strains revealed basidiomycetous affinities. However, the vast majority of the mycelial cells are monokaryotic, demonstrating that F. arachnophila is not a typical basidiomycete. The morphological resemblance to the two teleomorph species of Filobasidiella is noteworthy and therefore the accommodation in Filobasidiella is maintained. F. arachnophila proved to be identical with Aspergillus depauperatus Petch and the new combination Filobasidiella arachnophila (Petch) Samson et al. is made.

Two morphological markers indicating dikaryosis in Schizophyllum commune

In the wood destroying basidiomycete Schizophyllum commune a method is described to recognize the onset of dikaryosis rapidly in using recessive genetic markers. The gene ai (+)/ai causes in its mutant recessive allele (ai) the production of dark coloured fruit bodies. This can be made use of to evaluate macroscopically the formation of a dikaryon. Another useful marker is the gene rd (+)/rd. The recessive allele (rd) causes phenotypically the formation of a round looking mycelium instead of the fringed looking mycelium, the wild type. This genetic marker which is closely linked to the A-incompatibility factor is therefore also qualified to detect the onset of dikaryosis without much effort.

Genetic studies of the basisdiomycete Agrocybe aegerita : Part 2: Genetic control of fruit body formation and its practical implications

In the edible white rot fungus Agrocybe aegerita the threshold from mycelial growth to fruit body formation is under control of a single gene in both monokaryons and dikaryons.The allele su opens the pathway for fruiting and allows the subsequent expression of the fruiter genes fi(+) (fruit body initials) and fb (+) (fruit bodies). Its allele, su (+), suppresses monokaryotic fruiting completely and restricts dikaryotic fruiting drastically.The detection of this threshold gene su (+)/su and its action and interactions has practical implication in that an opportunity for concerted breeding is created.First results indicate that the fruiter genes are involved in two essential parameters of productivity. Both time of fruiting and biomass production depend on the two fruiter genes fi (+) and fb (+).Comparable results obtained with two other basidiomycetes suggest that the genetic control of fruiting in Agrocybe aegerita is a general mechanism which may be made use of in breeding work with other basidiomycetes of economic value.

Inbreeding for isogeneity by backcrossing to a fixed parent in haploid and diploid eukaryotes

The consequences of repeated backcrossing to a fixed parent are examined for haploid eukaryotes having a transitory diploid phase. The isogenicity attained in the absence of selected markers depends on the number of chromosomes and the total genetic map length, while the isogenicity of a chromosome carrying a selected marker increases more slowly and depends on the size of the chromosome. As inbreeding proceeds, the remaining non-isogenic material is not distributed evenly to all of the progeny. Instead, the majority of the progeny are completely isogenic with the fixed parent (with the exception of a region surrounding each selected marker), while the non-isogenic material is concentrated in a minority of the progeny. Even when the average isogenicity of the progeny and the fixed parent exceeds 99%, a significant proportion of the progeny will contain tracts of non-isogenic material which average several map units in length. Minor modifications enable these results to be applied to diploide. Examples show how to determine the degree of isogenicity produced by a given number of backcrosses in several specific situations.