Sexuality and genetic identity in the Agaricus section Arvenses

Mating-Type Locus Organization and Mating-Type Chromosome Differentiation in the Bipolar Edible Button Mushroom Agaricus bisporus

In heterothallic basidiomycete fungi, sexual compatibility is restricted by mating types, typically controlled by two loci: PR, encoding pheromone precursors and pheromone receptors, and HD, encoding two types of homeodomain transcription factors. We analysed the single mating-type locus of the commercial button mushroom variety, Agaricus bisporus var. bisporus, and of the related variety burnettii. We identified the location of the mating-type locus using genetic map and genome information, corresponding to the HD locus, the PR locus having lost its mating-type role. We found the mip1 and β-fg genes flanking the HD genes as in several Agaricomycetes, two copies of the β-fg gene, an additional HD2 copy in the reference genome of A. bisporus var. bisporus and an additional HD1 copy in the reference genome of A. bisporus var. burnettii. We detected a 140 kb-long inversion between mating types in an A. bisporus var. burnettii heterokaryon, trapping the HD genes, the mip1 gene and fragments of additional genes. The two varieties had islands of transposable elements at the mating-type locus, spanning 35 kb in the A. bisporus var. burnettii reference genome. Linkage analyses showed a region with low recombination in the mating-type locus region in the A. bisporus var. burnettii variety. We found high differentiation between β-fg alleles in both varieties, indicating an ancient event of recombination suppression, followed more recently by a suppression of recombination at the mip1 gene through the inversion in A. bisporus var. burnettii and a suppression of recombination across whole chromosomes in A. bisporus var. bisporus, constituting stepwise recombination suppression as in many other mating-type chromosomes and sex chromosomes.

Evaluating Genetic Diversity of Agaricus bisporus Accessions through Phylogenetic Analysis Using Single-Nucleotide Polymorphism (SNP) Markers

Agaricus bisporus, commonly known as the button mushroom, is widely cultivated throughout the world. To breed new strains with more desirable traits and improved adaptability, diverse germplasm, including wild accessions, is a valuable genetic resource. To better understand the genetic diversity available in A. bisporus and identify previously unknown diversity within accessions, a phylogenetic analysis of 360 Agaricus spp. accessions using single-nucleotide polymorphism genotyping was performed. Genetic relationships were compared using principal coordinate analysis (PCoA) among accessions with known origins and accessions with limited collection data. The accessions clustered into four groups based on the PCoA with regard to genetic relationships. A subset of 67 strains, which comprised a core collection where repetitive and uninformative accessions were not included, clustered into 7 groups following analysis. Two of the 170 accessions with limited collection data were identified as wild germplasm. The core collection allowed for the accurate analysis of A. bisporus genetic relationships, and accessions with an unknown pedigree were effectively grouped, allowing for origin identification, by PCoA analysis in this study.

Molecular characterizations of somatic hybrids developed between Pleurotus florida and Lentinus squarrosulus through inter-simple sequence repeat markers and sequencing of ribosomal RNA-ITS gene

The 12 pfls somatic hybrids and 2 parents of Pleurotus florida and Lentinus squarrosulus were characterized by ISSR and sequencing of rRNA-ITS genes. Five ISSR primers were used and amplified a total of 54 reproducible fragments with 98.14% polymorphism among all the pfls hybrid populations and parental strains. UPGMA-based cluster exhibited a dendrogram with three major groups between the parents and pfls hybrids. Parent P. florida and L. squarrosulus showed different degrees of genetic distance with all the hybrid lines and they showed closeness to hybrid pfls 1m and pfls 1h, respectively. ITS1(F) and ITS4(R) amplified the rRNA-ITS gene with 611-867 bp sequence length. The nucleotide polymorphisms were found in the ITS1, ITS2 and 5.8S rRNA region with different number of bases. Based on rRNA-ITS sequence, UPGMA cluster exhibited three distinct groups between L. squarrosulus and pfls 1p, pfls 1m and pfls 1s, and pfls 1e and P. florida.

Antimicrobial Potential, Identification and Phylogenetic Affiliation of Wild Mushrooms from Two Sub-Tropical Semi-Evergreen Indian Forest Ecosystems

The diversity of wild mushrooms was investigated from two protected forest areas in India and 231 mushroom specimens were morphologically identified. Among them, 76 isolates were screened for their antimicrobial potential against seven bacterial and fungal pathogens. Out of 76 isolates, 45 isolates which displayed significant antimicrobial activities were identified using ITS rRNA gene amplification and subsequently phylogenetically characterized using random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers. Sequencing of the ITS rRNA region classified the isolates into 16 genera belonging to 11 families. In total, 11 RAPD and 10 ISSR primers were selected to evaluate genetic diversity based on their banding profile produced. In total 337 RAPD and 312 ISSR bands were detected, among which percentage of polymorphism ranges from 34.2% to 78.8% and 38.6% to 92.4% by using RAPD and ISSR primers respectively. Unweighted Pair-Group Method with Arithmetic Mean (UPGMA) trees of selected two methods were structured similarly, grouping the 46 isolates into two clusters which clearly showed a significant genetic distance among the different strains of wild mushroom, with an similarity coefficient ranges from 0.58 to 1.00 and 0.59 to 1.00 with RAPD and ISSR analysis respectively. This reporthas highlighted both DTR and MNP forests provide a habitat for diverse macrofungal species, therefore having the potential to be used for the discovery of antimicrobials. The report has also demonstrated that both RAPD and ISSR could efficiently differentiate wild mushrooms and could thus be considered as efficient markers for surveying genetic diversity. Additionally, selected six wild edible mushroom strains (Schizophyllum commune BPSM01, Panusgiganteus BPSM27, Pleurotussp. BPSM34, Lentinussp. BPSM37, Pleurotusdjamor BPSM41 and Lentinula sp. BPSM45) were analysed for their nutritional (proteins, carbohydrates, fat and ash content), antioxidant potential. The present findings also suggested that the wild edible mushroom strains do not have only nutritional values but also can be used as an accessible source of natural antioxidants.

Evidence for amphithallism and broad geographical hybridization potential among Agaricus subrufescens isolates from Brazil, France, and Thailand

Agaricus subrufescens is a cultivated edible and medicinal mushroom. Its known geographical distribution encompasses the Americas, Europe, Oceania, and Asia. The objective of this study was to assess mating compatibility and interfertility of strains originating from Brazil, France, and Thailand. Progeny of each strain were analyed with codominant molecular markers. Multilocus genotype tests revealed that the three strains were amphithallic with percentages of heterokaryotic single spore progenies of 75% for the Thai strain and around 40% for the Brazilian and French strains. In mating tests A. subrufescens had a multiallelic unifactorial system of sexual incompatibility. The three parent strains were interfertile based on experimental pairings of single-spore isolates, the recovery of hybrid heterokaryons from compatible matings, and the ability of hybrids to produce mushrooms and fertile spores. This biological approach supports the inclusion of the European strains within the species and the extension of the geographical distribution range to Asia. Our data should help to develop breeding strategies and to better manage and exploit the diversity existing in A. subrufescens.

Carbohydrate utilization and metabolism is highly differentiated in Agaricus bisporus

BACKGROUND

Agaricus bisporus is commercially grown on compost, in which the available carbon sources consist mainly of plant-derived polysaccharides that are built out of various different constituent monosaccharides. The major constituent monosaccharides of these polysaccharides are glucose, xylose, and arabinose, while smaller amounts of galactose, glucuronic acid, rhamnose and mannose are also present.

RESULTS

In this study, genes encoding putative enzymes from carbon metabolism were identified and their expression was studied in different growth stages of A. bisporus. We correlated the expression of genes encoding plant and fungal polysaccharide modifying enzymes identified in the A. bisporus genome to the soluble carbohydrates and the composition of mycelium grown compost, casing layer and fruiting bodies.

CONCLUSIONS

The compost grown vegetative mycelium of A. bisporus consumes a wide variety of monosaccharides. However, in fruiting bodies only hexose catabolism occurs, and no accumulation of other sugars was observed. This suggests that only hexoses or their conversion products are transported from the vegetative mycelium to the fruiting body, while the other sugars likely provide energy for growth and maintenance of the vegetative mycelium. Clear correlations were found between expression of the genes and composition of carbohydrates. Genes encoding plant cell wall polysaccharide degrading enzymes were mainly expressed in compost-grown mycelium, and largely absent in fruiting bodies. In contrast, genes encoding fungal cell wall polysaccharide modifying enzymes were expressed in both fruiting bodies and vegetative mycelium, but different gene sets were expressed in these samples.

Anaerobically digested food waste in compost for Agaricus bisporus and Agaricus subrufescens and its effect on mushroom productivity

BACKGROUND

Source-separated food waste is increasingly being treated by means of hygienisation followed by anaerobic digestion. The fibrous digester residue (digestate) is a potential mushroom substrate, while heat from the biogas can provide steam for the cultivation process. Using bag experiments the present study explored digestate as a full substitute for chicken manure conventionally used in mushroom composts.

RESULTS

After mixing, a rapid temperature development in the compost was stimulated by a small amount of chicken manure, as aerobic microbial seeding. Mechanical elimination of lumps was essential for full mycelial colonisation. Three straw digestate composts had Agaricus bisporus mushroom yields above 370 g kg⁻¹ substrate. The optimal compost water content was 600 g kg⁻¹ at inoculation, and high digestate content (up to 500 g kg⁻¹ by dry weight) did not affect yield for this species. High yields of A. subrufescens (200 g kg⁻¹) were related to drier composts of lower digestate content (more straw) and lower pH values at inoculation.

CONCLUSION

Digestate successfully substituted chicken manure in straw composts without affecting mushroom yields for both species. There were no clear differences between straw digestate and control composts in terms of mushroom dry matter, size, nitrogen or ash content.

Transcriptomic analysis of the interactions between Agaricus bisporus and Lecanicillium fungicola

Agaricus bisporus is susceptible to a number of diseases, particularly those caused by fungi, with Lecanicillium fungicola being the most serious. Control of this disease is important for the security of crop production, however given the lack of knowledge about fungal-fungal interactions, such disease control is rather limited. Exploiting the recently released genome sequence of A. bisporus, here we report studies simultaneously investigating both the host and the pathogen, focussing on transcriptional changes associated with the cap spotting lesions typically seen in this interaction. Forward-suppressive subtractive hybridisation (SSH) analysis identified 68 A. bisporus unigenes induced during infection. Chitin deacetylase showed the strongest response, with almost 1000-fold up-regulation during infection, so was targeted for down-regulation by silencing to see if it was involved in defence against L. fungicola. Transgenic lines were made expressing hairpin RNAi constructs, however no changes in susceptibility to L. fungicola were observed. Amongst the other up-regulated genes there were none with readily apparent roles in resisting infection in this susceptible interaction. Reverse-SSH identified 72 unigenes from A. bisporus showing reduced expression, including two tyrosinases, several genes involved in nitrogen metabolism and a hydrophobin. The forward-SSH analysis of infected mushrooms also yielded 64 unigenes which were not of A. bisporus origin and thus derived from L. fungicola. An EST analysis of infection-mimicking conditions generated an additional 623 unigenes from L. fungicola including several oxidoreductases, cell wall degrading enzymes, ABC and MFS transporter proteins and various other genes believed to play roles in other pathosystems. Together, this analysis shows how both the pathogen and the host modify their gene expression during an infection-interaction, shedding some light on the disease process, although we note that some 40% of unigenes from both organisms encode hypothetical proteins with no ascribed function which highlights how much there is still to discover about this interaction.

A phylogenetic reconstruction and emendation of Agaricus section Duploannulatae

Agaricus section Duploannulatae comprises the group of species allied with A. bisporus and A. bitorquis. Disagreement exists in the literature regarding the composition of this group. We used DNA sequence data from the ITS segments of the nuclear ribosomal DNA region, in a sample of European and North American isolates, to identify characters shared by this group, to further delimit species-level taxa within the section, and to develop a phylogenetic hypothesis. Shared polymorphisms that suggest a natural limit for section Duploannulatae were found. ITS1 data were assessed using parsimony, distance and maximum likelihood methods of phylogeny. The section Duploannulatae comprised six robust clades. Five clades corresponded to well characterized species from the temperate Northern Hemisphere (A. bisporus, A. subfloccosus, A. bitorquis, A. vaporarius, A. cupressicola). The sixth clade encompassed an A. devoniensis complex. Species concepts, nomenclature, and relationships are discussed and compared with prior reports.

Molecular diversity assessment of arctic and boreal Agaricus taxa

We provide a phylogenetic diversity assessment study in genus Agaricus as part of our ongoing work to saturate ITS and LSU rDNA sequence diversity of soil-dwelling fungi in Alaska. Pairwise sequence similarity-based groupings and statistical parsimony analyses were applied to delimit operational taxonomic unit (OTU) and were compared to results of full phylogenetic analyses. Our results show that the proportion of section Arvenses taxa is particularly high in the boreal forest and hypo-arctic (low arctic) regions, whereas the genus is represented by section Agaricus in high arctic habitats. Furthermore our findings suggest that the commercially important A. bisporus occurs naturally in the boreal region of interior Alaska, substantially expanding the known northern limit of the species. Delimitations of OTU varied greatly with different methods. In general 95% similarity-based grouping proved to be the least sensitive method, often resulting in section- and subsection-level groups. The 95% connection-limit statistical parsimony separated far more groups. The 98% similarity-based groups and the 98% connection limit networks recognized respectively 11 and 13 OTU containing our specimens. The 98% connection limit statistical parsimony was the only method in which all recognized OTU consisted of members grouped by branches with significant (> .95) posterior probabilities, providing an independent support for the groups. Our results also point out that considerable additional efforts will be needed to elucidate the evolution of this diverse genus and to assess its phylogenetic diversity, given that most taxa in our analyses could not be placed convincingly within well characterized species using ITS/LSU data.

GC-MS studies of the chemical composition of two inedible mushrooms of the genus Agaricus

Background

Mushrooms in the genus Agaricus have worldwide distribution and include the economically important species A. bisporus. Some Agaricus species are inedible, including A. placomyces and A. pseudopratensis, which are similar in appearance to certain edible species, yet are known to possess unpleasant odours and induce gastrointestinal problems if consumed. We have studied the chemical composition of these mushrooms using GC-MS.

Results

Our GC-MS studies on the volatile fractions and butanol extracts resulted in the identification of 44 and 34 compounds for A. placomyces and A. pseudopratensis, respectively, including fatty acids and their esters, amino acids, and sugar alcohols. The most abundant constituent in the volatiles and butanol were phenol and urea respectively. We also identified the presence of ergosterol and two Δ⁷-sterols. In addition, 5α,8α-Epidioxi-24(ξ)-methylcholesta-6,22-diene-3β-ol was isolated for the first time from both mushrooms. Our study is therefore the first report on the chemical composition of these two species.

Conclusion

The results obtained contribute to the knowledge of the chemical composition of mushrooms belonging to the Agaricus genus, and provide some explanation for the reported mild toxicity of A. placomyces and A. pseudopratensis, a phenonomenon that can be explained by a high phenol content, similar to that found in other Xanthodermatei species.

DNA-fingerprinting (AFLP and RFLP) for genotypic identification in species of the Pleurotus eryngii complex

Wild populations of edible species are important source of genetic variability for cultivated lines that can undergo a drastic loss of diversity resulting from man's selection. The development of tools aimed at the clear-cut and safe identification and assessment of genetic variability of the wild and cultivated strains is thus a fundamental goal of molecular genetic research. In this study, we used two polymerase chain reaction (PCR)-based fingerprinting methods-amplified fragment length polymorphism (AFLP) and restriction fragment length polymorphism (RFLP) of laccase and manganese peroxidase genes-to assess genetic differences among strains and independently evolving lineages belonging to the Pleurotus eryngii complex. Both laccase RFLP and AFLP have been proved to distinguish unambiguously the three taxa studied: Pleurotus ferulae, P. eryngii, and P. eryngii var. nebrodensis. AFLP also showed enough sensitivity to detect polymorphisms among the strains, proving to be an efficient DNA fingerprinting tool in studies of strain assignment. The divergent RFLP laccase and manganese peroxidase patterns are also discussed in relation to the role played by these genes in the interaction between these fungi and their host plants.

Differential expression of a putative riboflavin-aldehyde-forming enzyme (raf) gene during development and post-harvest storage and in different tissue of the sporophore in Agaricus bisporus

Cloning and characterisation of a putative riboflavin-aldehyde-forming enzyme gene (raf) from the cultivated mushroom Agaricus bisporus and its expression during morphogenesis are described. Three cDNA clones were isolated following differential screening of cDNA libraries from rapidly expanding sporophores and post-harvest stored sporophores. The cDNA sequence and predicted translation analysis revealed an open reading frame (ORF) of 348 nucleotides encoding a polypeptide of 115 amino acids, with three introns (56-66 bases) interrupting the genomic ORF. Blast X searches of the databases with the gene sequence showed homology (40% identity and 56% similarity) to the riboflavin-aldehyde-forming enzyme gene from Schizophyllum commune. In A.bisporus, the raf gene sequence upstream of the ORF contained a large CT-rich putative regulatory element (-64 to -24 bases) found in highly expressed genes in various mushrooms, and a 6-base motif present in the 3' end of the genomic sequence, but not in the corresponding 3' non-coding part of the cDNA, was identified. The raf gene transcripts increased abundantly in rapidly developing sporophores as well in post-harvest stored sporophores. Differential expression of the raf gene transcripts in different tissues of the sporophore was also observed, with higher levels in the stipe compared with the cap and gills. The temporal and spatial expression patterns observed suggest transcriptional regulation of the raf gene during A. bisporus morphogenesis.

Evolution in action: molecular evidence for recent emergence of secotioid genera Endxoptychum, Gyrophragmium and Longula from Agaricus ancestors

Phylogenetic analyses of 29 Agaricus species and one representative from genera Endoptychum, Gyrophragmium and Longula each were conducted based on sequence data of the entire internal transcribed spacers and partial large subunit of ribosomal DNA. The Agaricus species formed several distinct clades both confirming and challenging previous morphological sections in several cases. Endoptychum depressum, Gyrophragmium dunalii and Longula texensis were nested among species of the genus Agaricus. This study provides evidence for independent emergence of these secotioid fungi from Agaricus ancestors, most likely from species placed in the section Arvenses as inferred from molecular data.

Differentiation of Agaricus species and other homobasidiomycetes based on volatile production patterns using an electronic nose system

Comparisons of the qualitative volatile production patterns between seven species of Agaricus, and between two of Volvariella and Pleurotus and one Coprinus species when grown at 25 degrees C on agar media for 14 d were made. There was good reproducibility between the volatile production patterns of the same species using an electronic nose unit with a 14 conducting sensor polymer array. Principle Component Analysis (PCA) showed that it was possible to discriminate between five of the seven Agaricus species, but that some overlap occurred between the others. Cluster analysis showed that there was also overlap between some species with the tropical collection of A. bitorquis separating out from the others. The volatile production profile of the commercial A. bisporus was close to that of a wild species, A. campestris. A. bisporus could be readily differentiated from other non-Agaricus species. This study demonstrates the potential for using electronic nose systems to rapidly differentiate mycelial cultures of homobasidiomycete mushrooms.

Agaricus bisporus and Coprinus bilanatus TRP2 genes are tri-functional with conserved intron and domain organisations

Cloned homobasidiomycete TRP2 genes for Agaricus bisporus and Coprinus bilanatus were sequence-characterised. Both genes encode tri-functional proteins with activity domains for glutamine amidotransferase (GAT; G domain), indole glycerol phosphate synthase (InGP; C domain) and phosphoribosyl anthranilate isomerase (F domain). A conserved intron disrupts the GAT-coding sequence in both genes. Consensus amino acid (aa) signatures were identified for GAT and InGP, but in the latter 15-aa signature, one residue did not fit the previously defined consensus. Protein architecture and parsimony analysis with analogous proteins indicate domain organisation (NH(2)-G-C-F-COOH) was as for other filamentous fungi. The data do not support earlier suggestions that the three activity domains are detached in A. bisporus.