Genome sequence of the oyster mushroom Pleurotus ostreatus strain PC9

Pleurotus ostreatus as a model mushroom in genetics, cell biology, and material sciences

Pleurotus ostreatus, also known as the oyster mushroom, is a popular edible mushroom cultivated worldwide. This review aims to survey recent progress in the molecular genetics of this fungus and demonstrate its potential as a model mushroom for future research. The development of modern molecular genetic techniques and genome sequencing technologies has resulted in breakthroughs in mushroom science. With efficient transformation protocols and multiple selection markers, a powerful toolbox, including techniques such as gene knockout and genome editing, has been developed, and numerous new findings are accumulating in P. ostreatus. These include molecular mechanisms of wood component degradation, sexual development, protein secretion systems, and cell wall structure. Furthermore, these techniques enable the identification of new horizons in enzymology, biochemistry, cell biology, and material science through protein engineering, fluorescence microscopy, and molecular breeding. KEY POINTS: • Various genetic techniques are available in Pleurotus ostreatus. • P. ostreatus can be used as an alternative model mushroom in genetic analyses. • New frontiers in mushroom science are being developed using the fungus.

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.

A carnivorous mushroom paralyzes and kills nematodes via a volatile ketone

The carnivorous mushroom Pleurotus ostreatus uses an unknown toxin to rapidly paralyze and kill nematode prey upon contact. We report that small lollipop-shaped structures (toxocysts) on fungal hyphae are nematicidal and that a volatile ketone, 3-octanone, is detected in these fragile toxocysts. Treatment of Caenorhabditis elegans with 3-octanone recapitulates the rapid paralysis, calcium influx, and neuronal cell death arising from fungal contact. Moreover, 3-octanone disrupts cell membrane integrity, resulting in extracellular calcium influx into cytosol and mitochondria, propagating cell death throughout the entire organism. Last, we demonstrate that structurally related compounds are also biotoxic to C. elegans, with the length of the ketone carbon chain being crucial. Our work reveals that the oyster mushroom has evolved a specialized structure containing a volatile ketone to disrupt the cell membrane integrity of its prey, leading to rapid cell and organismal death in nematodes.

Introducing multiple-gene mutations in Pleurotus ostreatus using a polycistronic tRNA and CRISPR guide RNA strategy

The white-rot fungus Pleurotus ostreatus is an agaricomycete that is frequently used in molecular genetics studies as many useful tools are applicable to the fungus. In particular, efficient gene targeting using homologous recombination and CRISPR/Cas9 enables the introduction of a mutation in the gene of interest for functional analysis. Multiple genes encoding various lignocellulose-degrading enzymes are predicted to be present in the genome; therefore, analyses of multiple-gene mutants are required to elucidate the mechanisms underlying lignocellulose degradation by P. ostreatus. Conventional tools for generating multiple-gene mutations in P. ostreatus are laborious and time-consuming. Therefore, more efficient and practical methods are needed. In this study, we introduced CRISPR/Cas9-assisted multiple-gene mutations using a polycistronic tRNA and CRISPR guide RNA approach. The frequency (triple-gene mutation in fcy1, vp2, and   62347) was only 3.3% when a tetracistronic tRNA-sgRNA containing four different sgRNAs targeting fcy1, vp2, vp3, or   62347 was expressed. It increased to 20% (triple-gene mutation in vp1, vp2, and vp3) after a tricistronic tRNA-sgRNA was expressed with replaced/modulated promoter and tRNA sequences. This study demonstrated, for the first time, the applicability of a strategy to induce multiple-gene mutations in P. ostreatus in a transformation experiment.

The wtf meiotic driver gene family has unexpectedly persisted for over 100 million years

Meiotic drivers are selfish elements that bias their own transmission into more than half of the viable progeny produced by a driver+/driver- heterozygote. Meiotic drivers are thought to exist for relatively short evolutionary timespans because a driver gene or gene family is often found in a single species or in a group of very closely related species. Additionally, drivers are generally considered doomed to extinction when they spread to fixation or when suppressors arise. In this study, we examine the evolutionary history of the wtf meiotic drivers first discovered in the fission yeast Schizosaccharomyces pombe. We identify homologous genes in three other fission yeast species, S. octosporus, S. osmophilus, and S. cryophilus, which are estimated to have diverged over 100 million years ago from the S. pombe lineage. Synteny evidence supports that wtf genes were present in the common ancestor of these four species. Moreover, the ancestral genes were likely drivers as wtf genes in S. octosporus cause meiotic drive. Our findings indicate that meiotic drive systems can be maintained for long evolutionary timespans.

Investigations on the Fusants From Wide Cross Between White-Rot Fungi and Saccharomyces cerevisiae Reveal Unknown Lignin Degradation Mechanism

The degradation of lignocellulose by fungi, especially white-rot fungi, contributes a lot to carbon cycle, bio-fuel production, and many other bio-based applications. However, the existing enzymatic and non-enzymatic degradation mechanisms cannot be unequivocally supported by in vitro simulation experiment, meaning that additional mechanisms might exist. Right now, it is still very difficult to discover new mechanisms with traditional forward genetic approaches. To disclose novel lignin degradation mechanisms in white-rot fungi, a series of fusants from wide cross by protoplast fusion between Pleurotus ostreatus, a well-known lignin-degrading fungus, and Saccharomyces cerevisiae, a well-known model organism unable to degrade lignocellulose, was investigated regarding their abilities to degrade lignin. By analyzing the activity of traditional lignin-degrading enzyme, the ability to utilize pure lignin compounds and degrade corn stalk, a fusant D1-P was screened out and proved not to contain well-recognized lignin-degrading enzyme genes by whole-genome sequencing. Further investigation with two-dimension nuclear magnetic resonance (NMR) shows that D1-P was found to be able to degrade the main lignin structure β-O-4 linkage, leading to reduced level of this structure like that of the wild-type strain P. ostreatus after a 30-day semi-solid fermentation. It was also found that D1-P shows a degradation preference to β-O-4 linkage in Aβ(S)-threo. Therefore, wide cross between white-rot fungi and S. cerevisiae provides a powerful tool to uncover novel lignocellulose degradation mechanism that will contribute to green utilization of lignocellulose to produce bio-fuel and related bio-based refinery.

Gene age shapes the transcriptional landscape of sexual morphogenesis in mushroom forming fungi (Agaricomycetes)

Multicellularity has been one of the most important innovations in the history of life. The role of gene regulatory changes in driving transitions to multicellularity is being increasingly recognized; however, factors influencing gene expression patterns are poorly known in many clades. Here, we compared the developmental transcriptomes of complex multicellular fruiting bodies of eight Agaricomycetes and Cryptococcus neoformans, a closely related human pathogen with a simple morphology. In-depth analysis in Pleurotus ostreatus revealed that allele-specific expression, natural antisense transcripts, and developmental gene expression, but not RNA editing or a ‘developmental hourglass,’ act in concert to shape its transcriptome during fruiting body development. We found that transcriptional patterns of genes strongly depend on their evolutionary ages. Young genes showed more developmental and allele-specific expression variation, possibly because of weaker evolutionary constraint, suggestive of nonadaptive expression variance in fruiting bodies. These results prompted us to define a set of conserved genes specifically regulated only during complex morphogenesis by excluding young genes and accounting for deeply conserved ones shared with species showing simple sexual development. Analysis of the resulting gene set revealed evolutionary and functional associations with complex multicellularity, which allowed us to speculate they are involved in complex multicellular morphogenesis of mushroom fruiting bodies.

Chromosomal genome and population genetic analyses to reveal genetic architecture, breeding history and genes related to cadmium accumulation in Lentinula edodes

BACKGROUND

Lentinula edodes (Berk.) is the second most productive mushroom in the world. It contains compounds effective for antiviral, antitumor, antioxidant and immune regulation. Although genomes have previously been reported for this species, a high-quality chromosome-level reference for L. edodes is unavailable. This hinders detailed investigation of population genetics, breeding history of strains and genes related to environmental stress responses.

RESULTS

A high-quality chromosome-level genome was constructed. We separated a monokaryon from protoplasts of the commercial L. edodes strain L808 and assembled the genome of L. edodes using PacBio long-read and Illumina short-read sequencing, along with the high-throughput chromatin conformation capture (Hi-C) technique. We assembled a 45.87 Mb genome, and 99% of the sequences were anchored onto 10 chromosomes. The contig and scaffold N50 length were 2.17 and 4.94 Mb, respectively. Over 96% of the complete Benchmarking Universal Single-Copy Orthologs (BUSCO) were identified, and 9853 protein-coding genes were predicted. We performed population genome resequencing using 34 wild strains and 65 commercial cultivars of L. edodes originating from China, Japan, the United States and Australia. Based on whole-genome variants, we showed substantial differences in the Chinese wild population, which divided into different branches according to the main areas of their geographical distribution. We also determined the breeding history of L. edodes at the molecular level, and demonstrated that the cultivated strains in China mainly originated from wild strains from China and Northeast Asia. Phenotypic analysis showed that 99 strains exhibited differences on the Cd accumulation. Three significant loci in the of L. edodes genome were identified using the genome-wide association study (GWAS) of Cd accumulation traits. Functional genes associated with Cd accumulation traits were related to DNA ligase and aminoacyl tRNA synthetase, indicating that DNA damage repair and in vivo protein translation may be responses to Cd stress.

CONCLUSIONS

A high-quality chromosome-level genome and population genetic data of L. edodes provide genetic resources for functional genomic, evolutionary and artificial breeding studies for L. edodes.

Genetic Linkage and Physical Mapping for an Oyster Mushroom (Pleurotus cornucopiae) and Quantitative Trait Locus Analysis for Cap Color

Oyster mushrooms are grown commercially worldwide, especially in many developing countries, for their easy cultivation and high biological efficiency. Pleurotus cornucopiae is one of the main oyster mushroom species because of its gastronomic value and nutraceutical properties. Cap color is an important trait, since consumers prefer dark mushrooms, which are now represented by only a small portion of the commercial varieties. Breeding efforts are required to improve quality-related traits to satisfy various demands of consumers. Here, we present a saturated genetic linkage map of P. cornucopiae constructed by using a segregating population of 122 monokaryons and 3,449 single nucleotide polymorphism (SNP) markers generated by the 2b-RAD approach. The map contains 11 linkage groups covering 961.6 centimorgans (cM), with an average marker spacing of 0.27 cM. The genome of P. cornucopiae was de novo sequenced, resulting in 425 scaffolds (>1,000 bp) with a total genome size of 35.1 Mb. The scaffolds were assembled to the pseudochromosome level with the assistance of the genetic linkage map. A total of 97% SNP markers (3,357) were physically localized on 140 scaffolds that were assigned to 11 pseudochromosomes, with a total of 32.5 Mb, representing 92.5% of the whole genome. Six quantitative trait loci (QTL) controlling cap color of P. cornucopiae were detected, accounting for a total phenotypic variation of 65.6%, with the highest value for the QTL on pseudochromosome 5 (18%). The results of our study provide a solid base for marker-assisted breeding for agronomic traits and especially for studies on biological mechanisms controlling cap color in oyster mushrooms. IMPORTANCE Oyster mushrooms are produced and consumed all over the world. Pleurotus cornucopiae is one of the main oyster mushroom species. Dark-cap oyster mushrooms are becoming more and more popular with consumers, but dark varieties are rare on the market. Prerequisites for efficient breeding programs are the availability of high-quality whole genomes and genetic linkage maps. Genetic studies to fulfill some of these prerequisites have hardly been done for P. cornucopiae. In this study, we de novo sequenced the genome and constructed a saturated genetic linkage map for P. cornucopiae. The genetic linkage map was effectively used to assist the genome assembly and identify QTL that genetically control the trait cap color. As well, the genome characteristics of P. cornucopiae were compared to the closely related species Pleurotus ostreatus. The results provided a basis for understanding the genetic background and marker-assisted breeding of this economically important mushroom species.

Overexpressing Pleurotus ostreatus rho1b results in transcriptional upregulation of the putative cellulolytic enzyme-encoding genes observed in ccl1 disruptants

The transcriptional expression pattern of lignocellulolytic enzyme-encoding genes in white-rot fungi differs depending on the culture conditions. Recently, it was shown that 13 putative cellulolytic enzyme-encoding genes were significantly upregulated in most Pleurotus ostreatus ligninolysis-deficient mutant strains on beech wood sawdust medium. However, the mechanisms by which this transcriptional shift is triggered remain unknown. In this study, we identified one mechanism. Our previous study implied that histone H3 N-dimethylation at lysine 4 level possibly affects the shift; therefore, we analysed the expression pattern in the disruptants of P. ostreatus ccl1, which encodes a putative component of the COMPASS complex mediating the methylation. The results showed upregulation of 5 of the 13 cellulolytic enzyme-encoding genes. We also found that rho1b, encoding a putative GTPase regulating signal transduction pathways, was upregulated in the ccl1 disruptants and ligninolysis-deficient strains. Upregulation of at least three of the five cellulolytic enzyme-encoding genes was observed in rho1b-overexpressing strains but not in ccl1/rho1b double-gene disruptants, during the 20-day culture period. These results suggest that Rho1b may be involved in the upregulation of cellulolytic enzyme-encoding genes observed in the ccl1 disruptants. Furthermore, we suggest that Mpk1b, a putative Agaricomycetes-specific mitogen-activated protein kinase, functions downstream of Rho1b.