Influence of light on the morphological changes that take place during the development of the Flammulina velutipes fruit body

Effects of Light on the Fruiting Body Color and Differentially Expressed Genes in Flammulina velutipes

Light plays vital roles in fungal growth, development, reproduction, and pigmentation. In Flammulina velutipes, the color of the fruiting body exhibits distinct changes in response to light; however, the underlying molecular mechanisms remain unknown. Therefore, in this study, we aimed to analyze the F. velutipes transcriptome under red, green, and blue light-emitting diode (LED) lights to identify the key genes affecting the light response and fruiting body color in this fungus. Additionally, we conducted protein-protein interaction (PPI) network analysis of the previously reported fruiting body color-related gene, Fvpal1, to identify the hub genes. Phenotypic analysis revealed that fruiting bodies exposed to green and blue lights were darker than those untreated or exposed to red light, with the color intensifying more after 48 h of exposure to blue light compared to that after 24 h of exposure. Differentially expressed gene (DEG) analyses of all light treatments for 24 h revealed that the numbers of DEGs were 17, 74, and 257 under red, green, and blue lights, respectively. Subsequently, functional enrichment analysis was conducted of the DEGs identified under green and blue lights, which influenced the color of F. velutipes. In total, 103 of 168 downregulated DEGs under blue and green lights were included in the enrichment analysis. Among the DEGs enriched under both green and blue light treatments, four genes were related to monooxygenases, with three genes annotated as cytochrome P450s that are crucial for various metabolic processes in fungi. PPI network analysis of Fvpal1 revealed associations with 11 genes, among which the expression of one gene, pyridoxal-dependent decarboxylase, was upregulated in F. velutipes exposed to blue light. These findings contribute to our understanding of the molecular mechanisms involved in the fruiting body color changes in response to light and offer potential molecular markers for further exploration of light-mediated regulatory pathways.

Comparative Proteomic Analysis Reveals Candidate Pathways Related to the Effect of Different Light Qualities on the Development of Mycelium and Fruiting Body of Pleurotus ostreatus

Light affects the morphology and physiology of Pleurotus ostreatus. However, the underlying molecular mechanism of this effect remains unclear. In this study, a label-free comparative proteomic analysis was conducted to investigate the global protein expression profile of the mycelia and fruiting bodies of P. ostreatus PH11 growing under four different light quality treatments. Among all the 2234 P. ostreatus proteins, 1349 were quantifiable under all tested conditions. A total of 1100 differentially expressed proteins were identified by comparing the light group data with those of the darkness group. GO and KEGG enrichment analyses indicated that the oxidative phosphorylation, proteasome, and mRNA surveillance pathways were the most related pathways under the light condition. qRT-PCR verified that the expression of the white collar 1 protein was significantly enhanced under white light. Additionally, glutamine synthetase and aldehyde dehydrogenase played important roles during light exposure. This study provides valuable insight into the P. ostreatus light response mechanism, which will lay the foundation for improved cultivation.

The Tissue Browning and Concomitant Toughening of Yellow Flammulina filiformis Stipes Is Caused by Oxidative Damage-Mediated Metabolic Disorder and Cell Wall Glycan Remodeling

The browning and associated toughening of fruiting body stipes are the main causes of declines in the commercial production of yellow Flammulina filiformis. The dynamic metabolic changes from the top to bottom stipe sections of yellow F. filiformis fruiting bodies were investigated by integrating physiological, transcriptomic, and metabolomic analyses. The results indicated that oxidative stress levels gradually increased accompanying the degree of tissue browning and toughening from the top to bottom sections of F. filiformis stipes. In-depth analysis showed that there were remarkable changes in the expression of genes, and the content of metabolites correlated with the primary and secondary metabolism of F. filiformis stipes. Interestingly, the expression levels of genes participating in chitosan biosynthesis and the degree of deacetylation of chitosan increased from top to bottom in F. filiformis stipes, implying that cell wall glycan remodeling may contribute to concomitant toughening of the browning of F. filiformis stipes.

Low temperature, mechanical wound, and exogenous salicylic acid (SA) can stimulate the SA signaling molecule as well as its downstream pathway and the formation of fruiting bodies in Flammulina filiformis

Low temperature (LT) and mechanical wound (MW), as two common physics methods, have been empirically used in production to stimulate the primordia formation of Flammulina filiformis, which is typically produced using the industrial production mode. However, the detailed effect on the fruiting body formation and important endogenous hormones and signaling pathways in this process is poorly understood. In this study, LT, MW, their combination, i.e., MW + LT, and low concentration of SA (0.1 mM SA) treatments were applied to the physiologically mature mycelia of F. filiformis. The results showed that the primordia under the four treatments began to appear on the 5th-6th days compared with the 12th day in the control (no treatment). The MW + LT treatment produced the largest number of primordia (1,859 per bottle), followed by MW (757), SA (141), and LT (22), compared with 47 per bottle in the control. The HPLC results showed that the average contents of endogenous SA were significantly increased by 1.3 to 2.6 times under four treatments. A total of 11 SA signaling genes were identified in the F. filiformis genome, including 4 NPR genes (FfNpr1-4), 5 TGA genes (FfTga1-5), and 2 PR genes (FfPr1-2). FfNpr3 with complete conserved domains (ANK and BTB/POZ) showed significantly upregulated expression under all four above treatments, while FfNpr1/2/4 with one domain showed significantly upregulated response expression under the partial treatment of all four treatments. FfTga1-5 and FfPr1-2 showed 1.6-fold to 8.5-fold significant upregulation with varying degrees in response to four treatments. The results suggested that there was a correlation between "low temperature/mechanical wound-SA signal-fruiting body formation", and it will help researchers to understand the role of SA hormone and SA signaling pathway genes in the formation of fruiting bodies in fungi.

Application progress of CRISPR/Cas9 genome-editing technology in edible fungi

Edible fungi are not only delicious but are also rich in nutritional and medicinal value, which is highly sought after by consumers. As the edible fungi industry continues to rapidly advance worldwide, particularly in China, the cultivation of superior and innovative edible fungi strains has become increasingly pivotal. Nevertheless, conventional breeding techniques for edible fungi can be arduous and time-consuming. CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR-associated nuclease 9) is a powerful tool for molecular breeding due to its ability to mediate high-efficiency and high-precision genome modification, which has been successfully applied to many kinds of edible fungi. In this review, we briefly summarized the working mechanism of the CRISPR/Cas9 system and highlighted the application progress of CRISPR/Cas9-mediated genome-editing technology in edible fungi, including Agaricus bisporus, Ganoderma lucidum, Flammulina filiformis, Ustilago maydis, Pleurotus eryngii, Pleurotus ostreatus, Coprinopsis cinerea, Schizophyllum commune, Cordyceps militaris, and Shiraia bambusicola. Additionally, we discussed the limitations and challenges encountered using CRISPR/Cas9 technology in edible fungi and provided potential solutions. Finally, the applications of CRISPR/Cas9 system for molecular breeding of edible fungi in the future are explored.

Optimization of the Solid-State Culture Conditions and Chemical Component Analysis of Poria cocos (Agaricomycetes)

The optimal cultivation conditions and chemical components of Poria cocos fruiting bodies were examined by employing the single factor and response surface methods to screen for optimal conditions for artificial cultivation. The differences in chemical composition among the fruiting bodies, fermented mycelium, and sclerotia of P. cocos were compared using UV spectrophotometry and high-performance liquid chromatography (HPLC). The optimal growth conditions for P. cocos fruiting bodies were 28.5°C temperature, 60% light intensity, and 2.5 g pine sawdust, which resulted in the production of numerous basidiocarps and basidiospores under microscopic examination. Polysaccharides, triterpenoids, and other main active components of P. cocos were found in the fruiting bodies, sclerotia, and fermented mycelium. The triterpenoid components of the fruiting bodies were consistent with those of the sclerotia. The content of pachymic acid in the fruiting bodies was significantly higher than that in the sclerotia, with a value of 33.37 ± 0.1902 mg/g. These findings provide novel insights into the sexual breeding and comprehensive development and utilization of P. cocos.

Evolutionary Morphogenesis of Sexual Fruiting Bodies in Basidiomycota: Toward a New Evo-Devo Synthesis

The development of sexual fruiting bodies is one of the most complex morphogenetic processes in fungi. Mycologists have long been fascinated by the morphological and developmental diversity of fruiting bodies; however, evolutionary developmental biology of fungi still lags significantly behind that of animals or plants. Here, we summarize the current state of knowledge on fruiting bodies of mushroom-forming Basidiomycota, focusing on phylogenetic and developmental biology. Phylogenetic approaches have revealed a complex history of morphological transformations and convergence in fruiting body morphologies. Frequent transformations and convergence is characteristic of fruiting bodies in contrast to animals or plants, where main body plans are highly conserved. At the same time, insights into the genetic bases of fruiting body development have been achieved using forward and reverse genetic approaches in selected model systems. Phylogenetic and developmental studies of fruiting bodies have each yielded major advances, but they have produced largely disjunct bodies of knowledge. An integrative approach, combining phylogenetic, developmental, and functional biology, is needed to achieve a true fungal evolutionary developmental biology (evo-devo) synthesis for fungal fruiting bodies.

The Fvclp1 gene regulates mycelial growth and fruiting body development in edible mushroom Flammulina velutipes

Fruiting body development in Agaricomycetes represents the most complex and unclear process in the fungi. Mating type pathways (A and B) and transcription factors are important regulators in the sexual development of mushrooms. It is known that clampless1 (clp1) is an additional gene that participate under the homeodomain (HD) genes in the matA pathway and clp1 inactivation blocks clamps formation in Coprinopsis cinerea. In this study we identified and analyzed a homologous Fvclp1 gene in the edible mushroom Flammulina velutipes. The coding sequence of the Fvclp1 was 1011 bp without intron interruption, encoding a protein of 336 amino acids. To exhibit the role of Fvclp1 in clamp development and fruiting body formation, knockdown and overexpression mutants were prepared. No significant difference was observed in the monokaryotic hyphal morphology of overexpression and knockdown transformants. In the dikaryotic hyphae from the compatible crossings between the wild-type L22 strain and Fvclp1 knockdown or overexpression mutants, clamp connections developed. However, knockdown mutants could generate fewer fruiting bodies than the wild-type strain. On the contrary, reduced mycelial growth rate but improved fruiting ability was observed in the dikaryotic Fvclp1 overexpression mutants as compared to the wild-type strain. These results indicate that Fvclp1 is necessary and actively involved in fruiting body development in F. velutipes. Overall, these findings suggest that further studies on the function of Fvclp1 would advance our understanding of sexual reproduction and fruiting body development in edible mushrooms.

Transcriptome analysis of the edible mushroom Lentinula edodes in response to blue light

Lentinula edodes is one of the most popular edible mushrooms worldwide and contains important medicinal components such as lentinan, ergosterol, and eritadenine. Mushroom metabolism is regulated by the mycelia and fruit body using light; however, in mushrooms, the underlying molecular mechanisms controlling this process as well as light-induced gene expression remain unclear. Therefore, in this study, we compared morphological changes and gene expression in the fruit bodies of L. edodes cultivated under blue light and continuous darkness. Our results showed that blue light primarily induced pileus growth (diameter and thickness) compared to dark cultivation. Alternatively, stipe length development was promoted by dark cultivation. We also performed RNAseq on L. edodes under the blue light/dark cultivation conditions. A total of 12,051 genes were used for aligning the Illumina raw reads and 762 genes that showed fold change cut-offs of >|2| and significance p-values of <0.05 were selected under blue light condition. Among the genes which showed two-fold changed genes, 221 were upregulated and 541 were downregulated. In order to identify blue light induced candidate genes, differentially expressed genes (DEGs) were selected according to 4-fold changes and validated by RT-PCR. We identified 8 upregulated genes under blue light condition, such as DDR48-heat shock protein, Fasciclin-domain-containing protein and carbohydrate esterase family 4 protein, FAD NAD-binding domain-containing protein that are involved in morphological development of primordium and embryonic muscle development, cell adhesion and affect the structure of cellulosic and non-cellulosic cell walls of fruit body development, and photoreceptor of blue light signaling for fruit body and pigment development, respectively. This study provides valuable insights into the molecular mechanisms underlying the role of blue light in mushroom growth and development and can thus contribute to breeding programs to improve mushroom cultivation.

Comparative transcriptomic analysis reveals molecular processes involved in pileus morphogenesis in Pleurotus eryngii under different light conditions

Light plays an important role in pileus differentiation in Pleurotus eryngii cultivation, and pileus morphology is influenced by light quality. To understand the effects of light quality on pileus morphology at the transcriptional level, we performed a comparative transcriptomic analysis of pilei grown under blue and red light irradiation. We identified 3959 differentially expressed genes (DEGs) between the blue and red light-treated pilei, which included 1664 up-regulated and 2295 down-regulated genes. These DEGs were significantly associated with light sensing, signal transduction, cell wall degradation and melanogenesis, suggesting that these processes are involved in pileus morphogenesis. Multiple DEGs related to respiratory functions were differentially expressed, suggesting that respiratory activity increased during pileus development regardless of light quality. These results provide a valuable view of the transcriptional changes and molecular processes involved in pileus morphogenesis under different light conditions and provide a foundation for yield improvement and quality control of P. eryngii.

A Comparative Proteome Approach Reveals Metabolic Changes Associated with Flammulina velutipes Mycelia in Response to Cold and Light Stress

In some industrial processes, cold and light stresses are recognized as two important environmental triggers for the transformation of mycelia into fruit-bodies via intermediate primordia in Flammulina velutipes cultivation. To gain insights into the mechanism of regulation of F. velutipes mycelia in response to cold and light stress, proteins expressed abundantly and characteristically at particular stress states were investigated by using the isobaric tags for the relative and absolute quantitation labeling technique. Among the 1046 nonredundant proteins identified with a high degree of confidence, 264 proteins, which were detected as differentially expressed proteins, were associated with 176 specific KEGG pathways. In-depth data analysis revealed that the regulatory network underlying the cold and light response mechanisms of F. velutipes mycelia was complex and multifaceted, as it included varied functions such as rapid energy supply, the biosynthesis of lysine, phenylalanine, tyrosine, and γ-aminobutyric acid, the calcium signal transduction process, dynein-dependent actin and microtubule cytoskeleton formation, autolysis, oxidative stress adaptation, pigment secretion, tissue and organ morphogenesis, and other interesting stress-related processes. Insights into the proteins might shed light on an intuitive understanding of the cold and light stress response mechanism underlying the fruiting processes of F. velutipes. Furthermore, the data might also provide further insights into the stress response mechanism of macro-fungi and valuable information for scientific improvement of some mushroom cultivation techniques in practice.

Influencia de la luz azul sobre la productividad del cultivo sólido de Ganoderma lucidum

Ganoderma lucidum es un hongo macromiceto reconocido por sus propiedades medicinales y su contenido de compuestos bioactivos que incluyen polisacáridos, triterpenoides, proteínas inmunomoduladoras, entre otros, lo que ha generado un incremento notable en su producción. La mayoría de especies de hongos responden y se adaptan a diversas señales ambientales incluida la luz, que favorece su productividad, tanto en calidad como en cantidad al estar estrechamente relacionada con la formación de cuerpos fructíferos. Por tal razón, el objetivo de este estudio fue evaluar la eficiencia biológica (EB) y la tasa de producción (TP) como parámetros de productividad del cultivo sólido de Ganoderma lucidum bajo irradiación de los sustratos con luz emitida por diodos azules (LED) con dos periodos de foto-estímulo de 12 y 24 h durante todas las fases de cultivo para inducir el crecimiento micelial y la formación de los cuerpos fructíferos. Se aplicaron parámetros convencionales para el crecimiento y desarrollo del hongo en las etapas de producción. Para la formulación de los sustratos, se emplearon residuos agroindustriales y materiales lignocelulósicos. El diámetro de los cuerpos fructíferos sometidos a tratamientos con luz azul fue mayor que los exhibidos a luz blanca fluorescente (Testigo). Los resultados muestran que el cultivo de Ganoderma lucidum con exposición a la luz azul es útil para la inducción de cuerpos fructíferos de alta calidad, logrando una disminución del periodo de fermentación en 16 días para el foto-estímulo de 24 h con EB de 28,04% y TP de 0,64.

Identification and physiological properties of a Nigerian strain of Volvariella sp. isolated from oil palm waste

Over the years several species of edible mushrooms have been collected for consumption from different agro-wastes in Nigeria. Identification of most of these mushrooms was often by morphological descriptive methods. This study reports the morphological study, physiological study and identification of a Nigerian wild strain of Volvariella sp. (VNW) isolated from discarded oil palm waste and three Indian commercial strains V11, V245 and V247 of V. volvacea. Effect of incubation temperatures and medium pH was investigated. Molecular characterization of the strains was carried out using ITS-1 and ITS-4 primers. Results obtained showed close similarities of the Nigerian strain to the Indian strains with few morphological variations in colour, shape and appearance. Growth was observed at temperature range of 20-40 °C and pH range of 4.0-8.0 for all strains with optimum mycelia extension at 35 °C and pH 6.0. VNW recorded a significantly higher (p ≤ 0.05) mycelia extension rate at 35 °C (25.20 ± 1.80 mm/day) and pH 6.0 (40.20 ± 0.34 mm/day). Highest biomass yield was observed at pH 6.0 with V11 recording a significantly (p ≤ 0.05) higher yield (1.74 ± 0.07 g/100 mL). Increasing percentage (w/v) of CaSO₄·H₂O increased biomass yield of all the strains. NJ phylogenetic tree showed the Nigerian and Indian strains in the same cluster indicating evolutionary closeness than with other species of Volvariella from GenBank in a separate cluster even though they share a common ancestor. This successfully proves the identity of a Nigerian strain of Volvariella sp. VNW from oil palm waste as V. volvacea with GenBank accession number KC894923.

iTRAQ-based quantitative proteome revealed metabolic changes of Flammulina velutipes mycelia in response to cold stress

Temperature is one of the pivotal factors influencing mycelium growth and fruit-body formation of Flammulina velutipes. To gain insights into hyphae growth and fruit-body formation events and facilitate the identification of potential stage-specific biomarker candidates, we investigated the proteome response of F. velutipes mycelia to cold stresses using iTRAQ-coupled two-dimensional liquid chromatography tandem mass spectrometry (2D LC-MS/MS) technique. Among 1198 proteins identified with high confidence, a total of 63 displayed altered expression level after cold stress treatments. In-depth data analysis reveals that differentially expressed proteins were involved in a variety of cellular processes, particularly metabolic processes. Among the 31 up-regulated proteins, 24 (77.42%) were associated with 22 specific KEGG pathways. These up-regulated proteins could possibly serve as potential biomarkers to study the molecular mechanisms of F. velutipes mycelia response to cold stresses. These data of the proteins might provide valuable evidences to better understand the molecular mechanisms of mycelium resistance to cold stress and fruit-body formation in fungi.

BIOLOGICAL SIGNIFICANCE

Low-temperature is one of the pivotal factors in some Flammulina velutipes industrial processes influencing mycelium growth, inducing primordia and controlling fruit-body development. Preliminary study has indicated that effectively regulating cultivation could augment the yield by controlling optimal cold stress level on mycelia. However, we are still far from understanding the molecular and physiological mechanisms of adaptation of these fungi at cold stress. In the present study, the experiments reported above were undertaken to investigate chronological changes of protein expression during F. velutipes mycelia in response to cold stress by using iTRAQ-coupled 2D LC-MS/MS technique. This result would provide new insights to the underlying mycelium growth and fruit-body formation mechanisms of basidiomycetes under cold stress.

Pileus differentiation and pileus-specific protein expression in Flammulina velutipes

Fruiting bodies of Flammulina velutipes formed under complete darkness had a poorly developed pileus on top (pinhead fruiting body), and lacked a hymenium. Upon light stimulation, the pileus immediately began to develop on the apical region of the pinhead fruiting body. Swelling of the apical region caused by cell division was observed 2 days after light treatment; at day 4, the junction fracture between the pileus and stipe, and formation of the hymenium primordia were observed; at 6 days, gills were observed. We identified a cell wall-associated protein (PSH) that was specifically induced in the pileus, but not in the stipe, following light treatment of the pinhead fruiting body. Cloning and sequence analysis of the gene encoding PSH (psh) revealed a motif in the C-terminal region of the predicted amino acid sequence that was similar to hydrophobin. The level of transcription of psh was low in the stipe, but it was expressed at a high level in the pileus of the normal fruiting body. Transcription was also low in pinhead fruiting bodies, but increased after light treatment. These results indicate that psh is specifically expressed during pileus differentiation induced by light stimulation.