Transmission of mushroom virus X and the impact of virus infection on the transcriptomes and proteomes of different strains of Agaricus bisporus

An agar medium-based method for screening somatic incompatibility in Agaricus bisporus

To visualize the nonself recognition reaction in the cultivated mushroom Agaricus bisporus, we developed a method using the azo dye Evans blue. The use of Evans blue highlights dead mycelial sections, which are produced following nonself recognition in the interaction zone between two individuals. This method can differentiate between distinct heterokaryons, as well as between closely related heterokaryons constructed from siblings. As it is known that co-cultivation of mixed individuals leads to reduced yield, we compared small-scale cultivation experiments to the results of our laboratory assay. Co-cultivation of strains whose interaction produced noticeable Evans blue staining also produced low yield when mixed. However, a combination that did not produce noticeable Evans blue staining still produced an incompatible-like phenotype (reduced yield) when mixed under cultivation conditions. Together, these results suggest that while our Evans blue assay can discriminate between self and nonself pairings, it alone does not encompass all aspects of this interaction. However, this method can facilitate future research into the genetics and physiology of the incompatibility phenotype in this economically important fungus.

Transcriptomics reveals the regulation of the immune system of the mushroom-forming fungus Schizophyllum commune during interaction with four competitors

Mushroom-forming fungi frequently encounter competitors during their lifecycle, but their defense mechanisms remain largely unexplored. We studied the response of the mushroom-forming fungus Schizophyllum commune during interaction with the fungal competitors Trichoderma harzianum, Trichoderma aggressivum and Purpureocillium lilacinum and the bacterial competitor Serratia quinivorans. Transcriptomics revealed 632 up-regulated genes in the direct interaction zone, which were enriched in small secreted proteins and transporters. A set of 26 genes were up-regulated during all interactions, indicating a core transcriptomic defense response. In the non-interacting edge of the mycelium of S. commune, there were 154 up-regulated genes, suggesting that there is a systemic response due to a signal that reaches unaffected areas. The GATA zinc finger transcription factor gene gat1 was up-regulated during interaction and a Δgat1 strain displayed increased colonization by T. harzianum. Previously linked to mushroom development, this transcription factor apparently has a dual role. Moreover, 138 genes were up-regulated during both interaction and mushroom development, indicating priming of the defense response during development to prepare the fruiting body for future interactions. Overall, we unveiled a defensive response of S. commune during interaction with fungal and bacterial competitors and identified a regulator of this response.

Transcriptome Analysis Reveals the Effect of Oyster Mushroom Spherical Virus Infection in Pleurotus ostreatus

Oyster mushroom spherical virus (OMSV) is a mycovirus that inhibits mycelial growth, induces malformation symptoms, and decreases the yield of fruiting bodies in Pleurotus ostreatus. However, the pathogenic mechanism of OMSV infection in P. ostreatus is poorly understood. In this study, RNA sequencing (RNA-seq) was conducted, identifying 354 differentially expressed genes (DEGs) in the mycelium of P. ostreatus during OMSV infection. Verifying the RNA-seq data through quantitative real-time polymerase chain reaction on 15 DEGs confirmed the consistency of gene expression trends. Both Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses highlighted the pivotal role of primary metabolic pathways in OMSV infection. Additionally, significant changes were noted in the gene expression levels of carbohydrate-active enzymes (CAZymes), which are crucial for providing the carbohydrates needed for fungal growth, development, and reproduction by degrading renewable lignocellulose. The activities of carboxymethyl cellulase, laccase, and amylase decreased, whereas chitinase activity increased, suggesting a potential mechanism by which OMSV influenced mycelial growth through modulating CAZyme activities. Therefore, this study provided insights into the pathogenic mechanisms triggered by OMSV in P. ostreatus.

Transmission of Oyster Mushroom Spherical Virus to Progeny via Basidiospores and Horizontally to a New Host Pleurotus floridanus

Mycoviruses are usually transmitted horizontally via hyphal anastomosis and vertically through sporulation in natural settings. Oyster mushroom spherical virus (OMSV) is a mycovirus that infects Pleurotus ostreatus, with horizontal transmission via hyphal anastomosis. However, whether OMSV can be vertically transmitted is unclear. This study aimed to investigate the transmission characteristics of OMSV to progeny via basidiospores and horizontally to a new host. A total of 37 single-basidiospore offspring were obtained from OMSV-infected P. ostreatus and Pleurotus pulmonarius for Western blot detection of OMSV. The OMSV-carrying rate among monokaryotic isolates was 19% in P. ostreatus and 44% in P. pulmonarius. Then, OMSV-free and OMSV-infected monokaryotic isolates were selected for hybridization with harvested dikaryotic progeny strains. Western blot analyses of the offspring revealed that the OMSV transmission efficiency was 50% in P. ostreatus and 75% in P. pulmonarius, indicating vertical transmission via sexual basidiospores. Furthermore, we observed the horizontal transfer of OMSV from P. pulmonarius to Pleurotus floridanus. OMSV infection in P. floridanus resulted in significant inhibition of mycelial growth and yield loss. This study was novel in reporting the vertical transmission of OMSV through basidiospores, and its infection and pathogenicity in a new host P. floridanus.

Lessons on fruiting body morphogenesis from genomes and transcriptomes of Agaricomycetes

Fruiting bodies (sporocarps, sporophores or basidiomata) of mushroom-forming fungi (Agaricomycetes) are among the most complex structures produced by fungi. Unlike vegetative hyphae, fruiting bodies grow determinately and follow a genetically encoded developmental program that orchestrates their growth, tissue differentiation and sexual sporulation. In spite of more than a century of research, our understanding of the molecular details of fruiting body morphogenesis is still limited and a general synthesis on the genetics of this complex process is lacking. In this paper, we aim at a comprehensive identification of conserved genes related to fruiting body morphogenesis and distil novel functional hypotheses for functionally poorly characterised ones. As a result of this analysis, we report 921 conserved developmentally expressed gene families, only a few dozens of which have previously been reported to be involved in fruiting body development. Based on literature data, conserved expression patterns and functional annotations, we provide hypotheses on the potential role of these gene families in fruiting body development, yielding the most complete description of molecular processes in fruiting body morphogenesis to date. We discuss genes related to the initiation of fruiting, differentiation, growth, cell surface and cell wall, defence, transcriptional regulation as well as signal transduction. Based on these data we derive a general model of fruiting body development, which includes an early, proliferative phase that is mostly concerned with laying out the mushroom body plan (via cell division and differentiation), and a second phase of growth via cell expansion as well as meiotic events and sporulation. Altogether, our discussions cover 1 480 genes of Coprinopsis cinerea, and their orthologs in Agaricus bisporus, Cyclocybe aegerita, Armillaria ostoyae, Auriculariopsis ampla, Laccaria bicolor, Lentinula edodes, Lentinus tigrinus, Mycena kentingensis, Phanerochaete chrysosporium, Pleurotus ostreatus, and Schizophyllum commune, providing functional hypotheses for ~10 % of genes in the genomes of these species. Although experimental evidence for the role of these genes will need to be established in the future, our data provide a roadmap for guiding functional analyses of fruiting related genes in the Agaricomycetes. We anticipate that the gene compendium presented here, combined with developments in functional genomics approaches will contribute to uncovering the genetic bases of one of the most spectacular multicellular developmental processes in fungi. Citation: Nagy LG, Vonk PJ, Künzler M, Földi C, Virágh M, Ohm RA, Hennicke F, Bálint B, Csernetics Á, Hegedüs B, Hou Z, Liu XB, Nan S, M. Pareek M, Sahu N, Szathmári B, Varga T, Wu W, Yang X, Merényi Z (2023). Lessons on fruiting body morphogenesis from genomes and transcriptomes of Agaricomycetes. Studies in Mycology 104: 1-85. doi: 10.3114/sim.2022.104.01.

Oyster Mushroom Spherical Virus Crosses the Species Barrier and Is Pathogenic to a New Host Pleurotus pulmonarius

Oyster mushroom spherical virus (OMSV) is a mycovirus with a positive-sense single-stranded RNA genome that infects the edible mushroom Pleurotus ostreatus. OMSV is horizontally transferred from an infected strain to a cured strain via mycelia. The infection results in significant inhibition of mycelial growth, malformation of fruiting bodies, and yield loss in oyster mushrooms. This study successfully transferred OMSV from P. ostreatus to Pleurotus pulmonarius. However, transmission was not successful in other Pleurotus species including P. citrinopileatus, P. eryngii, P. nebrodensis, and P. salmoneostramineus. The successful OMSV infection in P. pulmonarius was further verified with Western blot analysis using a newly prepared polyclonal antiserum against the OMSV coat protein. Furthermore, OMSV infection reduced the mycelial growth rate of P. pulmonarius. The OMSV-infected strain demonstrated abnormal performance including twisted mushrooms or irregular edge of the cap as well as reduced yield of fruiting bodies in P. pulmonarius, compared to the OMSV-free strain. This study is the first report on the infection and pathogenicity of OMSV to the new host P. pulmonarius. The data from this study therefore suggest that OMSV is a potential threat to P. pulmonarius.

Application of omics technology in the research on edible fungi

Edible fungus is a large fungus distributed all over the world and used as food and medicine. But people's understanding of edible fungi is not as much as that of ordinary crops, so people have started a number of research on edible fungi in recent years. With the development of science and technology, omics technology has gradually walked into people's vision. Omics technology has high sensitivity and wide application range, which is favored by researchers. The application of omics technology to edible fungus research is a major breakthrough, which has transferred edible fungus research from artificial cultivation to basic research. Now omics technology in edible fungi has been flexibly combined with other research methods, involving multiple studies of edible fungus, such as genetic breeding, growth and development, stress resistance, and the use of special components in edible fungus as pharmaceutical additives. It is believed that in the future, the research of edible fungi will also be brought to a deeper level with the help of omics technology. This paper introduces the application progress of modern omics technology to the study on edible fungi and mentions the application prospect of edible fungi research with the constant development of omics technology, thereby providing ideas for the follow-up in-depth research on edible fungi.

Experimental Outcrossing in Agaricus bisporus Revealed a Major and Unexpected Involvement of Airborne Mycelium Fragments

Agaricus bisporus var. bisporus, the button mushroom, has a predominantly pseudohomothallic life cycle. Most of its spores are heterokaryotic and give rise to fertile heterokaryons. However, previous studies have suggested that outcrossing should not be rare in wild populations. In order to discover how outcrossing occurs, we experimentally favored it between aerial propagules of a fruiting donor mycelium and a delayed receiver mycelium that only invaded culture trays. Two donor/receiver pairs were studied, and potentially hybrid basidiomata collected on the receiver trays were analyzed with a mitochondrial marker, two unlinked nuclear CAPS markers, then haplotype markers based on DNA sequences obtained after PCR cloning of the rDNA ITS region and the fruk gene. For one of the two pairs, most basidiomata were hybrids between the donor and the receiver. Genotyping of the hybrids revealed only two genotypes consistent with outcrossing involving airborne mycelium fragments rather than basidiospores. The resident receiver heterokaryon that provided its mitochondria to the hybrid basidiomata is suspected to have had a trophic contribution to their growth and successful fruiting. The high level of heterozygosity and the cultivar introgression previously revealed in wild populations of this pseudohomothallic species may result from outcrossing involving airborne pieces of mycelium.

Interspecific spread of dsRNA mycoviruses in entomogenous fungi Beauveria spp

Mycoviruses can spread interspecifically and intraspecifically in plant pathogenic fungi, as well as spreading intraspecifically in entomogenous fungi, especially Beauveria bassiana. However, whether mycoviruses are common in Beauveria spp. and can spread interspecifically between Beauveria species are unclear. Herein, four Beauveria species, but not B. bassiana, were randomly selected for double stranded RNA (dsRNA) detection. Furthermore, two previously reported dsRNA mycoviruses from B. bassiana, BbCV-2 and BbPmV-4, were used to study the interspecific transmission among B. bassiana, B. amorpha, and B. aranearum, using hyphal anastomosis and a novel insect coinfection transmission method. The results showed that dsRNA mycoviruses exist universally in Beauveria spp. and could spread interspecifically between different Beauveria species. The transmission efficiency from B. bassiana to the other two Beauveria species was significantly higher than that of the reverse transmission. Both viruses could stably and vertically spread in B. amorpha and B. aranearum, which affected their growth rate and colony morphology.

Pseudo-Chromosomal Genome Assembly in Combination with Comprehensive Transcriptome Analysis in Agaricus bisporus Strain KMCC00540 Reveals Mechanical Stimulus Responsive Genes Associated with Browning Effect

Agaricus bisporus is one of the world's most popular edible mushrooms, including in South Korea. We performed de novo genome assembly with a South Korean white-colored cultivar of A. bisporus, KMCC00540. After generating a scaffold-level genomic sequence, we inferred chromosome-level assembly by genomic synteny analysis with the representative A. bisporus strains H97 and H39. The KMCC00540 genome had 13 pseudochromosomes comprising 33,030,236 bp mostly covering both strains. A comparative genomic analysis with cultivar H97 indicated that most genomic regions and annotated proteins were shared (over 90%), ensuring that our cultivar could be used as a representative genome. However, A. bisporus suffers from browning even from only a slight mechanical stimulus during transportation, which significantly lowers its commercial value. To identify which genes respond to a mechanical stimulus that induces browning, we performed a time-course transcriptome analysis based on the de novo assembled genome. Mechanical stimulus induces up-regulation in long fatty acid ligase activity-related genes, as well as melanin biosynthesis genes, especially at early time points. In summary, we assembled the chromosome-level genomic information on a Korean strain of A. bisporus and identified which genes respond to a mechanical stimulus, which provided key hints for improving the post-harvest biological control of A. bisporus.

Diversity of mycoviruses in edible fungi

Mycoviruses (fungal viruses) are widespread in all major taxonomic groups of fungi. Although most mycovirus infections are latent, some mycoviruses, such as La France isometric virus, mushroom virus X, and oyster mushroom spherical virus, can cause severe diseases in edible fungi and lead to significant production losses. Recently, deep sequencing has been employed as a powerful research tool to identify new mycoviruses and to enhance our understanding of virus diversity and evolution. An increasing number of novel mycoviruses that can infect edible fungi have been reported, including double-stranded (ds) RNA, positive-sense ( +)ssRNA, and negative-sense (-)ssRNA viruses. To date, approximately 60 mycoviruses have been reported in edible fungi. In this review, we summarize the recent advances in the diversity and evolution of mycoviruses that can infect edible fungi. We also discuss mycovirus transmission, co-infections, and genetic variations, as well as the methods used to detect and control of mycoviruses in edible fungi, and provide insights for future research on mushroom viral diseases.