Whole-genome sequence of Phellinus gilvus (mulberry Sanghuang) reveals its unique medicinal values

Immunomodulatory effects of Sanghuangporus flavonoids: Key insights into enhancing immunity and restoring immune function

The immune system is vital for maintaining homeostasis, defending against external threats, and regulating inflammation, forming the cornerstone of human health. Sanghuangporus, a natural medicinal mushroom, contains flavonoids that may increase immune cell activity, potentially improving human health. This study investigated the immunomodulatory effects of Sanghuangporus flavonoids (PBF) via network pharmacology and in vitro and in vivo experiments. Network pharmacology identified PBF compounds targeting 46 immunosuppression-related targets, with rutin emerging as a key component. Molecular docking confirmed the strong binding affinity of rutin for the core targets IL6, TNF, and IL1B. In vitro, PBF activated mouse macrophages, promoting their proliferation, phagocytic activity, NO production, and cytokine regulation. In vivo, PBF enhanced immune function in normal mice by promoting thymus and spleen growth, increasing cellular and humoral immunity, and restoring immune function in immunosuppressed mice. These findings highlight the potential of PBFs in increasing immunity and treating immunosuppressive diseases.

Comprehensive pharmacokinetic profiling of twelve compounds from Phellinus Igniarius extract in rats by UHPLC-MS/MS

The medicinal fungus Phellinus Igniarius (P. igniarius) has been demonstrated to possess a variety of pharmacological effects, including anti-oxidant, anti-tumor, blood circulation promotion, anti-diarrheal and sedative properties, etc. In order to gain a deeper understanding of the components in P. igniarius extract and its dynamic process in vivo, an ultra-performance liquid chromatography-triple quadrupole mass spectrometry method was developed and validated for the simultaneous determination of 12 major components (nobiletin tangeretin, narirutin, 3,4-dihydroxybenzaldehyde, hesperidin, hispidin, caffeic acid, hispolon, osmundacetone, amygdalin, salvianolic acid B and protocatechuic acid) of P. igniarius extract in rat plasma. The analyses were conducted using an ACQUITY UPLC BEH C18 column with acetonitrile and 0.1 % formic acid (v/v) in aqueous solution as the mobile phases. The intra-day and inter-day precision was less than 12.61 % for all 12 experiments, with a precision range of -11.28-12.25 %. Extraction recovery exhibited a range of 74.03-114.33 %, while the matrix effect demonstrated a range of 83.95-119.28 %. The stability tests demonstrated that the analytes remained stable, with relative standard deviations below 11.65 %. The pharmacokinetic parameters of the 12 compounds in rat plasma after oral administration of P. igniarius extract were successfully determined by the established UPLC-MS/MS method. The findings presented a pivotal foundation for advancing future research on the in vivo processes and mechanisms underlying the effects of P. igniarius extracts.

Enhancement hispolon production from Phellinus linteus via epigenetic-modified culture to inhibit human breast cancer cells

Phellinus linteus (PL) is a medicinal fungus known for producing hispolon, a bioactive compound with antioxidant, anti-inflammatory, and anticancer properties. However, the natural scarcity of PL and the unsuccessful cultivation of its fruiting bodies have led to the exploration of alternative methods for enhancing its bioactive compound production. In this study, static fermentation was employed, and Valproic acid (VPA), a histone deacetylase inhibitor (HDACi), was added to the culture medium to induce epigenetic modifications and enhance hispolon production. After 30 days of fermentation, the hispolon concentration was analyzed using high-performance liquid chromatography (HPLC), mycelial dry weight was measured, and the expression of hispolon synthesis-related enzymes was quantified using quantitative PCR (qPCR). Additionally, the anticancer potential of the fermented media was assessed in human breast adenocarcinoma HTB-26 cells using assays for cytotoxicity, reactive oxygen species (ROS) formation, apoptosis, antioxidant activity, and autophagy markers. The results revealed that the addition of 400 µM VPA increased hispolon production by 120% and mycelial dry weight by 41%, likely due to enhanced transcriptional accessibility. Furthermore, the PL fermentation media significantly inhibited HTB-26 cell growth through the induction of ROS formation, autophagy, and apoptosis. These findings suggest that VPA-enhanced static fermentation of PL offers a promising strategy for optimizing hispolon production and developing effective anticancer therapeutics.

Analysis of Gene Regulatory Network and Transcription Factors in Different Tissues of the Stropharia rugosoannulata Fruiting Body

Stropharia rugosoannulata is a mushroom that is rich in nutrients and has a pleasant flavor. Its cultivation area is expanding rapidly due to its simplicity and diversity. However, the developmental mechanism of the fruiting body, which constitutes the edible portion of S. rugosoannulata, remains to be elucidated. To address this knowledge gap, we conducted a comprehensive study. Our approach entailed the observation of sections through the fruiting body of S. rugosoannulata and the sequencing of the transcriptomes of various fruiting body tissues. The results demonstrated significant variations in the structure of the pileipellis, pileus, gill, veil, stipe, and trama of S. rugosoannulata. The predominant metabolic pathways included the amino acid metabolism of the pileus, sugar metabolism of the stipe, tryptophan metabolism, and wax production of the pileipellis, the DNA pathway of the gill, amino sugar metabolism of the veil, and the nitrogen metabolism of the trama. The promoter cis-element analysis revealed the roles of light response, methyl jasmonate, oxygen, and temperature on the differentiation of the veil, trama, and pileipellis, respectively. In summary, the present findings offer a molecular mechanism for the development of the fruiting body and provide directions for the enhancement of cultivation techniques of S. rugosoannulata.

Comparison of antioxidant and antimicrobial activities of submerged culture mycelium and basidioma extracts of Tropicoporus linteus

This research aimed to assess the biological characteristics of both submerged culture mycelium and artificial basidioma of Tropicoporus linteus NTH-PL4. The extraction yield from the basidioma surpassed that of the mycelium. The use of hot water extract resulted in the highest total carbohydrate content, predominantly found in the basidioma. Conversely, the 75% methanol extract exhibited higher levels of total phenolics and total flavonoids, predominantly in the mycelium. Tests on antioxidant capacity indicated that 75% methanol yielded the best results among the tested solvents, with the basidioma extract displaying superior DPPH scavenging, ferrous ion chelation, and reduction power compared to the mycelium extract. Moreover, ethyl acetate emerged as an effective solvent, yielding a stronger extract from the basidioma. Compound analysis revealed higher concentrations of gallic acid, salicylic acid, caffeic acid, and ellagic acid in the mycelium for the solvents used, while hispidin and beta-glucan exhibited an opposite trend.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10068-024-01612-1.

Isolation and Antioxidant Mechanism of Polyphenols from Sanghuangporous vaninii

Sanghuangporous vaninii, as an edible and medicinal macrofungus, represents a high source of polyphenols with considerable antioxidant activities. However, due to the significant differences in polyphenol content and bioactivity caused by different cultivation substrates, its antioxidant mechanism has not been fully determined. In this paper, five groups of S. vaninii fruiting bodies were collected from cultivation substrates from different areas. The ethanol extracts of mulberry sawdust from Haining City (HNMS) had the highest polyphenol content, as well as excellent antioxidant activity. HNMS3, a polyphenol component with promising antioxidant capacity, was further isolated through optimization with different extractants, silica gel column chromatography, and thin layer chromatography analysis. UPLC-Q-TOF-MS analysis showed that HNMS3 was composed of 33 compounds, corresponding to 257 targets of oxidative stress by network pharmacology analysis, which were strongly associated with mental health and neurodegenerative diseases. Protein-protein interaction and molecular docking analysis indicated that eight hub genes (PPARG, IL-6, STAT3, PTGS2, SRC, MTOR, ERS1, and EGFR) are attributed to the regulation of the key compounds hispidin, inoscavin A, inoscavin_C, and phellibaumin B. Consequently, this study obtains S. vaninii polyphenolic component HNMS3 with excellent antioxidant capacity, simultaneously revealing its potential antioxidant mechanisms, providing new insights into the application of S. vaninii.

Chromosome-Scale Genome and Transcriptomic Analyses Reveal Differential Regulation of Terpenoid Secondary Metabolites in Hericium coralloides

Construction of the genome of Hericium coralloides, a species of edible mushroom, and identification of the genes involved in terpenoid biosynthesis can determine the biology and genetics of terpenoids. The present study describes the assembly of a high-quality chromosome-scale genome of H. coralloides using Pacbio HiFi sequencing and Hi-C technology. This genome consisted of 13 chromosomes, a total size of 43.6 Mb, contigs of N50 3.6 Mb, GC content at 54%, and BUSCOs integrity of 96.9%. Genes associated with terpenoid biosynthesis were predicted by KEGG enrichment analysis and homologous alignment. The Her011461 and Her008335 genes, encoding proteins in the terpenoid backbone synthesis pathway, were found to encode geranylgeranyl pyrophosphate and farnesyl diphosphate synthases, key enzymes in the biosynthesis of geranylgeranyl diphosphate, a precursor of several diterpenoids. Her011463 was found to be involved in regulating diterpene cyclase. The Her005433, Her006724, Her010605, and Her010608 genes were found to encode sesquiterpene synthesis. Most of these genes were more highly expressed in dikaryotic mycelia than in the primordium and fruiting bodies, indicating that terpenoids may be more abundant in dikaryotic mycelia. To our knowledge, this study is the first to assemble the H. coralloides genome at the chromosome scale and to identify the genes involved in terpenoid biosynthesis.

Distinguishing Sanghuangporus from sanghuang-related fungi: a comparative and phylogenetic analysis based on mitogenomes

The Chinese medicinal fungi "Sanghuang" have been long recognized for their significant and valued medicinal properties, as documented in ancient medical literature. However, in traditional folk medicine, various macrofungi sharing similar appearance, habitat, and therapeutic effects with Sanghuang were erroneously used. These Sanghuang-like fungi mainly belong to the Porodaedalea, Phellinus, and Inonotus genera within the Hymenochaetaceae family. Despite the establishment of the Sanghuangporus genus and the identification of multiple species, the emerging taxonomic references based on morphological, ITS, and mycelial structural features have been inadequate to differentiate Sanghuangporus and Sanghuang-like fungi. To address this limitation, this study presents the first comparative and phylogenetic analysis of Sanghuang-related fungi based on mitogenomes. Our results show that Sanghuangporus species show marked convergence in mitochondrial genomic features and form a distinct monophyletic group based on phylogenetic analyses of five datasets. These results not only deepen our understanding of Sanghuang-like fungi but also offer novel insights into their mitochondrial composition and phylogeny, thereby providing new research tools for distinguishing members of the Sanghuangporus genus. KEY POINTS: • Sanghuangporus, Inonotus, and Porodaedalea are monophyly in sanghuang-like species. • Mitogenome-based analysis exhibits high resolution in sanghuang-like genus. • The mitogenomes provide strong evidence for reclassifying Phellinus gilvus S12 as Sanghuangporus vaninii.

Development of RP HPLC-PDA method for simultaneous quantitative analysis of Inoscavin A and Meshimakobnol A and application on some Phellinus mushroom species

Phellinus igniarius, a medicinal mushroom containing many active ingredients with health benefits, can be applied in functional food. At present, the quantification of the main active ingredients from higher fungi (Ganoderma, Phellinus…) materials from different growing sources is a mandatory requirement to standardize the input resources of pharmaceutical and food production. Our study's aims are to perfect the RP HPLC-PDA method for quantitative analysis of Inoscavin A and Meshimakobnol A which are two main active ingredients present in Phellinus mushroom. In this analytical method, a C18-HPLC column and the mixture of methanol and formic acid solutions (pH = 2.2) are used to analyze and elute the active substances with the column activity parameters being the concentration gradient. This perfect method was tested for system suitability, repeatability, intermediate precision, recovery, and linear curve calibration to validate the method. After validation, the perfected RP HPLC-PDA method was applied to analyze eight samples of Phellinus and three samples of Ganoderma mushroom category. This method can be the basis for classifying between Phellinus and some other medicinal mushrooms.

The gut microbiota-aromatic hydrocarbon receptor (AhR) axis mediates the anticolitic effect of polyphenol-rich extracts from Sanghuangporus

Inflammatory bowel disease (IBD) is a significant global health concern. The gut microbiota plays an essential role in the onset and development of IBD. Sanghuangporus (SH), a traditional Chinese medicinal mushroom, has excellent anti-inflammatory effects and is effective at modulating the gut microbiota. Despite these attributes, the specific anticolitic effects of SH and the mechanisms through which the gut microbiota mediates its benefits remain unclear. Herein, we demonstrated that polyphenol-rich extract from SH effectively alleviated the pathological symptoms of dextran sodium sulfate (DSS)-induced colitis in mice by modulating the gut microbiota. Treatment with SH distinctly enriched Alistipes, especially Alistipes onderdonkii, and its metabolite 5-hydroxyindole-3-acetic acid (5HIAA). Oral gavage of live A. onderdonkii or 5HIAA potently mitigated DSS-induced colitis in mice. Moreover, both 5HIAA and SH significantly activated the aromatic hydrocarbon receptor (AhR), and the administration of an AhR antagonist abrogated their protective effects against colitis. These results underscore the potent efficacy of SH in diminishing DSS-induced colitis through the promotion of A. onderdonkii and 5HIAA, ultimately activating AhR signaling. This study unveils potential avenues for developing therapeutic strategies for colitis based on the interplay between SH and the gut microbiota.

Bacillus amyloliquefaciens A-1 inhibiting fungal spoilage in agricultural products is improved by metabolic engineering of enhancing surfactin yield

Fungi and subsequent mycotoxins contamination in agricultural products have caused enormous losses and great harm to human and animal health. Biological control has attracted the attention of researchers due to its advantages, including mild conditions, low cost, high efficiency and low nutrient loss. In this study, a newly isolated strain Bacillus amyloliquefaciens A-1 (A-1), was screened for its ability to inhibit the growth and Aflatoxin B1 (AFB1) production of Aspergillus flavus NRRL 3357. Electron microscopy results revealed that mycelium and conidia of A. flavus were destroyed by A-1, affecting hyphae, cell walls, cell membranes and organelles. RNA-seq analysis indicated disturbance in gene expression profiles of A. flavus, including amino acid degradation and starch and sucrose metabolism pathways. Importantly, the biosynthesis of AFB1 was significantly inhibited by the down-regulation of key regulatory genes, aflR and aflS, and the simultaneous down-regulation of most structural genes. Genome analysis predicted six secondary metabolites biosynthetic gene clusters. Then, four surfactin synthesized by cluster C were identified as the main active substance of A-1 using HPLC-Q-TOF-MS. The addition of alanine, threonine, Fe2+ increased surfactin production. Notably, the overexpression of comX also improved surfactin production. The vivo test results indicated that A-1 could significantly inhibit the decay of pear by Aspergillus westerdijkiae, and the mildew of maize and peanuts. Especially, the overexpression of comX in A-1 could enhance the inhibitory activity. In conclusion, the inhibition mechanism of A-1 was revealed, and comX was found can improve the production of surfactin and subsequent activities, which provides the scientific basis for the development of biocontrol agents to reduce spoilage in agricultural products.

Comparative Genomic Analysis and Metabolic Potential Profiling of a Novel Culinary-Medicinal Mushroom, Hericium rajendrae (Basidiomycota)

Hericium rajendrae is an emerging species in the genus Hericium with few members. Despite being highly regarded due to its rarity, knowledge about H. rajendrae remains limited. In this study, we sequenced, de novo assembled, and annotated the complete genome of H. rajendrae NPCB A08, isolated from the Qinling Mountains in Shaanxi, China, using the Illumina NovaSeq and Nanopore PromethION technologies. Comparative genomic analysis revealed similarities and differences among the genomes of H. rajendrae, H. erinaceus, and H. coralloides. Phylogenomic analysis revealed the divergence time of the Hericium genus, while transposon analysis revealed evolutionary characteristics of the genus. Gene family variation reflected the expansion and contraction of orthologous genes among Hericium species. Based on genomic bioinformation, we identified the candidate genes associated with the mating system, carbohydrate-active enzymes, and secondary metabolite biosynthesis. Furthermore, metabolite profiling and comparative gene clusters analysis provided strong evidence for the biosynthetic pathway of erinacines in H. rajendrae. This work provides the genome of H. rajendrae for the first time, and enriches the genomic content of the genus Hericium. These findings also facilitate the application of H. rajendrae in complementary drug research and functional food manufacturing, advancing the field of pharmaceutical and functional food production involving H. rajendrae.

Transcriptome Analysis Reveals the Putative Polyketide Synthase Gene Involved in Hispidin Biosynthesis in Sanghuangporus sanghuang

Hispidin is an important styrylpyrone produced by Sanghuangporus sanghuang. To analyze hispidin biosynthesis in S. sanghuang, the transcriptomes of hispidin-producing and non-producing S. sanghuang were determined by Illumina sequencing. Five PKSs were identified using genome annotation. Comparative analysis with the reference transcriptome showed that two PKSs (ShPKS3 and ShPKS4) had low expression levels in four types of media. The gene expression pattern of only ShPKS1 was consistent with the yield variation of hispidin. The combined analyses of gene expression with qPCR and hispidin detection by liquid chromatography-mass spectrometry coupled with ion-trap and time-of-flight technologies (LCMS-IT-TOF) showed that ShPKS1 was involved in hispidin biosynthesis in S. sanghuang. ShPKS1 is a partially reducing PKS gene with extra AMP and ACP domains before the KS domain. The domain architecture of ShPKS1 was AMP-ACP-KS-AT-DH-KR-ACP-ACP. Phylogenetic analysis shows that ShPKS1 and other PKS genes from Hymenochaetaceae form a unique monophyletic clade closely related to the clade containing Agaricales hispidin synthase. Taken together, our data indicate that ShPKS1 is a novel PKS of S. sanghuang involved in hispidin biosynthesis.

A chromosome-scale genome and proteome draft of Tremella fuciformis

In this study, we first reported a high-quality chromosome-scale genome of Tremella fuciformis using Pacbio HiFi sequencing combining Hi-C technology. According to 21.6 Gb PacBio HiFi reads and 18.1 Gb Hi-C valid reads, we drafted a T. fuciformis genome of 27.38 Mb assigned to 10 chromosomes, with the contig N50 of 2.28 Mb, GC content of 56.51 %, BUSCOs completeness of 93.1 % and consensus quality value of 33.7. The following annotation of genomic components predicted 5,171 repeat sequences, 283 RNAs, and 10,150 protein-coding genes. Next, the intracellular proteins at three differential life stages of T. fuciformis (conidium, hyphal and fruiting body) were identified by the shot-gun proteomics. 6,823 canonical proteins (68.1 % of predicted proteome) have been identified with protein FDR cut-off of 0.01, establishing the first proteome draft of predicted protein-coding genes of T. fuciformis. Finally, 24 T. fuciformis polysaccharides (TPS) biosynthesis-related genes in mycelia were identified by comparative transcriptomics and proteomics, which may be more active than in conidium and revealed the TPS biosynthesis process in mycelia. This present study elucidated T. fuciformis genome composition and organization, drafted its associated proteome, and provided a genome-view of TPS biosynthesis, which will be a powerful platform for biological and genetic studies in T. fuciformis.

Uncovering pharmacological mechanisms of Phellinus linteus on focal segmental glomeruloscleosis rats through tandem mass tag-based quantitative proteomic analysis, network pharmacology analysis and experimental validation

OBJECTIVE

To explore the underlying molecular mechanism of ().

METHODS

We used a tandem mass tag-based quantitative proteomic method to determine the differentially expressed proteins. Network pharmacology analysis was used to analysis the main components of and construct the compound-target network. Western blotting and quantitative real-time polymerase chain reaction (qRT-PCR) were used to validate the analyses results.

RESULTS

The expression levels of thrombospondin-1 (TSP-1) and transforming growth factor (TGF)-β1/Smad3 signaling pathway proteins were significantly upregulated in focal segmental glomeruloscleosis (FSGS) rats. The reduced the expression levels of TSP-1 and TGF-β1 signaling pathway proteins. Network pharmacology analysis revealed that protocatechualdehyde was the main active component. Subsequent and experiments validated the results of proteomic and network pharmacology analyses.

CONCLUSIONS

Our results suggested that may inhibit renal sclerosis by inhibiting TSP-1-activated TGF-β1 signaling and may have potential applications in the treatment of FSGS.

Identifying Bioactive Ingredients and Antioxidant Activities of Wild Sanghuangporus Species of Medicinal Fungi

Sanghuangporus refers to a group of rare medicinal fungi with remarkable therapeutic properties. However, current knowledge on the bioactive ingredients and antioxidant activities of different species of this genus is limited. In this study, a total of 15 wild strains from 8 species of Sanghuangporus were selected as the experimental materials for identification of the bioactive components (polysaccharide, polyphenol, flavonoid, triterpenoid, and ascorbic acid) and antioxidant activities (scavenging activities against hydroxyl, superoxide, DPPH, and ABTS radicals; superoxide dismutase activity; and ferric reducing ability of plasma). Notably, individual strains contained different levels of various indicators, among which Sanghuangporus baumii Cui 3573, S. sanghuang Cui 14419 and Cui 14441, S. vaninii Dai 9061, and S. zonatus Dai 10841 displayed the strongest activities. The correlation analysis of bioactive ingredients and antioxidant activities revealed that the antioxidant capacity of Sanghuangporus is mainly associated with the contents of flavonoid and ascorbic acid, followed by polyphenol and triterpenoid, and finally, polysaccharide. Together, the results obtained from the comprehensive and systematic comparative analyses contribute further potential resources and critical guidance for the separation, purification, and further development and utilization of bioactive agents from wild Sanghuangporus species, as well as the optimization of their artificial cultivation conditions.

Increasing the production of the bioactive compounds in medicinal mushrooms: an omics perspective

Macroscopic fungi, mainly higher basidiomycetes and some ascomycetes, are considered medicinal mushrooms and have long been used in different areas due to their pharmaceutically/nutritionally valuable bioactive compounds. However, the low production of these bioactive metabolites considerably limits the utilization of medicinal mushrooms both in commerce and clinical trials. As a result, many attempts, ranging from conventional methods to novel approaches, have been made to improve their production. The novel strategies include conducting omics investigations, constructing genome-scale metabolic models, and metabolic engineering. So far, genomics and the combined use of different omics studies are the most utilized omics analyses in medicinal mushroom research (both with 31% contribution), while metabolomics (with 4% contribution) is the least. This article is the first attempt for reviewing omics investigations in medicinal mushrooms with the ultimate aim of bioactive compound overproduction. In this regard, the role of these studies and systems biology in elucidating biosynthetic pathways of bioactive compounds and their contribution to metabolic engineering will be highlighted. Also, limitations of omics investigations and strategies for overcoming them will be provided in order to facilitate the overproduction of valuable bioactive metabolites in these valuable organisms.

MicroRNA-like RNA Functions Are Required for the Biosynthesis of Active Compounds in the Medicinal Fungus Sanghuangporus vaninii

miRNA-like RNAs (milRNAs) have been recognized as sequence-specific regulators of posttranscriptional regulation of gene expression in eukaryotes. However, the functions of hundreds of fungal milRNAs in the biosynthesis of metabolic components are obscure. Sanghuangporus produces diverse bioactive compounds and is widely used in Asian countries. Here, genes encoding two Dicers, four Argonautes, and four RdRPs were identified and characterized in Sanghuangporus vanini. Due to the lack of an efficient gene manipulation system, the efficacy of spray-induced gene silencing (SIGS) was determined in S. vanini, which showed efficient double-stranded RNA (dsRNA) uptake and gene silencing efficiency. SIGS-mediated gene knockdown showed that SVRDRP-3, SVRDRP-4, SVDICER-1, and SVDICER-2 were critical for mycelial biomass, flavonoid, triterpenoid, and polysaccharide production. Illumina deep sequencing was performed to characterize the milRNAs from S. vanini mycelium and fruiting body. A total of 31 milRNAs were identified, out of which, SvmilR10, SvmilR17, and SvmilR33 were Svrdrp-4- and Svdicer-1-dependent milRNAs. Importantly, SIGS-mediated overexpression of SvmilR10 and SvmilR33 resulted in significant changes in the yields of flavonoids, triterpenoids, and polysaccharides. Further analysis showed that these milRNA target genes encoding the retrotransposon-derived protein PEG1 and histone-lysine N-methyltransferase were potentially downregulated in the milRNA overexpressing strain. Our results revealed that S. vanini has high external dsRNA and small RNA uptake efficiency and that milRNAs may play crucial regulatory roles in the biosynthesis of bioactive compounds. IMPORTANCE Fungi can take up environmental RNA that can silence fungal genes with RNA interference, which prompts the development of SIGS. Efficient dsRNA and milRNA uptake in S. vanini, successful dsRNA-targeted gene block, and the increase in intracellular miRNA abundance showed that SIGS technology is an effective and powerful tool for the functional dissection of fungal genes and millRNAs. We found that the RdRP, Dicer, and Argonaute genes are critical for mycelial biomass and bioactive compound production. Our study also demonstrated that overexpressed SVRDRP-4- and SVDICER-1-dependent milRNAs (SvmilR10 and SvmilR33) led to significant changes in the yields of the three active compounds. This study not only provides the first report on SIGS-based gene and milRNA function exploration, but also provides a theoretical platform for exploration of the functions of milRNAs involved in biosynthesis of metabolic compounds in fungi.

Genomic and Metabolomic Analyses of the Medicinal Fungus Inonotus hispidus for Its Metabolite's Biosynthesis and Medicinal Application

Inonotus hispidus mushroom is a traditional medicinal fungus with anti-cancer, antioxidation, and immunomodulatory activities, and it is used in folk medicine as a treatment for indigestion, cancer, diabetes, and gastric illnesses. Although I. hispidus is recognized as a rare edible medicinal macrofungi, its genomic sequence and biosynthesis potential of secondary metabolites have not been investigated. In this study, using Illumina NovaSeq combined with the PacBio platform, we sequenced and de novo assembled the whole genome of NPCB_001, a wild I. hispidus isolate from the Aksu area of Xinjiang Province, China. Comparative genomic and phylogenomic analyses reveal interspecific differences and evolutionary traits in the genus Inonotus. Bioinformatics analysis identified candidate genes associated with mating type, polysaccharide synthesis, carbohydrate-active enzymes, and secondary metabolite biosynthesis. Additionally, molecular networks of metabolites exhibit differences in chemical composition and content between fruiting bodies and mycelium, as well as association clusters of related compounds. The deciphering of the genome of I. hispidus will deepen the understanding of the biosynthesis of bioactive components, open the path for future biosynthesis research, and promote the application of Inonotus in the fields of drug research and functional food manufacturing.

Edible and medicinal fungi breeding techniques, a review: Current status and future prospects

Mushrooms of the edible and medicinal which are highly nutritious and environmentally friendly crops carry numerous medicinal benefits. For the abundant and high diversity of bioactive metabolites they possess, which are considered to be an important pool of bioresources. The efficient breeding technique is always a challenging task in mushrooms for obtaining better character strains, which are essential for developing healthy products and even consumption. This review comprehensively summarizes the breeding techniques applied to the edible and medicinal mushrooms. Including the traditional mutagenesis method, and even modern gene-editing breeding techniques, the effects of each method, and the comparison of each breeding technique are systematic illustrations. Strategies for mushroom breeding techniques in the future are also discussed in this review paper. With the ongoing sequencing of the mushroom genome, knowledge of the gene background of the strains and functions can be available for developing better markers for gene-editing breeding as CRISPR/Cas9 systems. Combine the metabolism engineering and in-silico tools analysis was the rational design of the novel strains. Modern physical mutagenesis techniques such as the ARTP and the combination of the other physical, and chemical breeding mutagens with cross-breeding techniques or the protoplasts fusion will also lead to superior strains for cultivation and pave the way for higher quality and yield.

Non-targeted metabonomics and transcriptomics revealed the mechanism of mulberry branch extracts promoting the growth of Sanghuangporus vaninii mycelium

Sanghuangprous vaninii is a wood-inhabiting fungus, and its mycelium and fruiting body show excellent medicinal values. Mulberry is one of the major hosts of S. vaninii, however, the mechanism of mulberry affecting the growth of S. vaninii has not been reported. In the present study, a mulberry-inhabiting strain of S. vaninii was selected to explore the effects of mulberry branch extracts (MBE) on the growth of the strain. Results showed that MBE could significantly promote the growth of S. vaninii mycelium at the concentration of 0.2 g/l. After 16 days of liquid culture, the dry weight of mycelium in 0.2 g/l MBE medium was higher by three times compared with that in the control. The non-targeted metabonomic analysis of the culture medium at different culture times and concentrations was conducted to find the key components in MBE that promoted the growth of S. vaninii mycelium. Under the different concentrations of MBE culture for 10 and 16 days, 22 shared differential metabolites were identified. Next, in accordance with the peak value trend of these metabolites, HPLC–MS and liquid culture validation, four components derived from MBE (i.e., scopoletin, kynurenic acid, 3,5-dihydroxybenzoic acid and 2,4-dihydroxybenzoic acid) could significantly increase the growth rate of mycelium at the concentration of 2 mg/l. Transcriptomic and qRT-PCR analyzes showed that MBE could upregulate hydrolase-related genes, such as serine–glycine–asparaginate–histidine (SGNH) hydrolase, alpha-amylase, poly-beta-hydroxybutyrate (PHB) depolymerase, glycosyl hydrolase family 61, cerato-platanin protein and Fet3, which might enhance the nutrient absorption ability of S. vaninii. Importantly, MBE could significantly increase the content of harmine, androstenedione and vesamicol, which have been reported to possess various medicinal effects. Results suggested that MBE could be an excellent additive for liquid culture of S. vaninii mycelium, and these hydrolase-related genes also provided candidate genes for improving the nutrient absorption capacity of S. vaninii.

Whole-genome assembly and analysis of a medicinal fungus: Inonotus hispidus

Inonotus hispidus (I. hispidus) is a medicinal macrofungus that plays a key role in anti-tumor and antioxidant functions. To further understand and enhance the value of I. hispidus, we performed whole-genome sequencing and an analysis of its strain for the first time. I. hispidus was sequenced using the Illumina NovaSeq high-throughput sequencing platform. The genome length was 35,688,031 bp and 30 contigs, with an average length of 1,189,601.03 bp. Moreover, database alignment annotated 402 CAZyme genes and 93 functional genes involved in regulating secondary metabolites in the I. hispidus genome to find the greatest number of genes involved in terpenes in that genome, thus providing a theoretical basis for its medicinal value. Finally, the phylogenetic analysis and comparative genomic analysis of single-copy orthologous protein genes from other fungi in the same family were conducted; it was found that I. hispidus and Sanghuangporus baumii have high homology. Our results can be used to screen candidate genes for the nutritional utilization of I. hispidus and the development of high-yielding and high-quality I. hispidus via genetic means.

Whole-genome sequence of a high-temperature edible mushroom Pleurotus giganteus (zhudugu)

Most of the sequenced wood-rotting edible mushroom produce fruiting body at relatively low temperatures. Little information has been known about the high-temperature wood-rotting mushroom. Here, we performed de novo sequencing and assembly of the genome of a high-temperature edible mushroom Pleurotus giganteus from a monokaryotic strain zhudugu2 using the Illumina and Pac-Bio CLR sequencing technologies. P. giganteus, also known as Zhudugu in China, is a well-known culinary edible mushroom that has been widely distributed and cultivated in China, Southeast Asia, and South Asia. The genome consists of 40.00 Mb in 27 contigs with a contig N50 of 4.384 Mb. Phylogenetic analysis reveals that P. giganteus and other strains in Pleurotus clustered in one clade. Phylogenetic analysis and average nucleotide identity analysis indicated that the P. giganteus genome showed a closer relationship with other Pleurotus species. Chromosome collinearity analysis revealed a high level of collinearity between P. ostreatus and P. giganteus. There are 12,628 protein-coding genes annotated in this monoploid genome. A total of 481 enzymes accounting for 514 carbohydrate-active enzymes (CAZymes) terms were identified in the P. giganteus genome, including 15 laccases and 10 class II peroxidases predicted in the genome, which revealed the robustness of lignocellulose degradation capacity of P. giganteus. The mating-A type locus of P. giganteus consisted of a pair of homeodomain mating-type genes HD1 and HD2. The mating-B type locus of P. giganteus consisted of at least four pheromone receptor genes and three pheromone genes. The genome is not only beneficial for the genome-assisted breeding of this mushroom but also helps us to understand the high-temperature tolerance of the edible mushroom.

Diverse Metabolites and Pharmacological Effects from the Basidiomycetes Inonotus hispidus

Inonotus hispidus mushroom is a popular edible and medicinal mushroom with a long history of use. It is well known as a medicinal fungus with various health benefits for its significant anticancer and immunomodulatory activities. Over the last 60 years, secondary metabolites derived from I. hispidus and their biological activities have been discovered and investigated. Structurally, these compounds are mainly polyphenols and triterpenoids, which have anticancer, anti-inflammatory, antioxidant, antimicrobial, and enzyme inhibitor activities. Here, the secondary metabolites derived from I. hispidus and their activities were systematically and comprehensively classified and summarized, and the biosynthetic pathway of stylylpyrones was deduced and analyzed further. This review contributes to our understanding of I. hispidus and will help with research into natural product chemistry, pharmacology, and the biosynthesis of I. hispidus metabolites. According to this review, I. hispidus could be a promising source of bioactive compounds for health promotion and the development of functional foods.

The First Whole Genome Sequence Discovery of the Devastating Fungus Arthrinium rasikravindrae

Devastating fungi are one of the most important biotic factors associated with numerous infectious diseases not only in plants but in animals and humans too. Arthrinium rasikravindrae a devastating fungus is responsible for severe infections in a large number of host plants all over the world. In the present study, we analyzed the whole genome sequence of devastating fungus A. rasikravindrae strain AQZ-20, using Illumina Technology from the Novogene Bio-informatics Co., Ltd. Beijing, China. To identify associated annotation results, various corresponding functional annotations databases were utilized. The genome size was 48.24 MB with an N90 (scaffolds) length of 2,184,859 bp and encoded putative genes were 11,101, respectively. In addition, we evaluated the comparative genomic analyses with 4 fungal strains of Ascomycetes. Two related species showed a strong correlation while others exhibited a weak correlation with the A. rasikravindrae AQZ-20 fungus. This study is a discovery of the genome-scale assembly, as well as annotation for A. rasikravindrae. The results obtained from the whole genome sequencing and genomic resources developed in this study will contribute significantly to genetic improvement applications against diseases caused by A. rasikravindrae. In addition, the phylogenetic tree, followed by genomic RNA, transcriptomic, proteomic, metabolic, as well as pathogenic data reported in current research will provide deep insight for further studies in the future.

Inoscavin A, a pyrone compound isolated from a Sanghuangporus vaninii extract, inhibits colon cancer cell growth and induces cell apoptosis via the hedgehog signaling pathway

BACKGROUND

Sanghuangporus vaninii, a large precious medicinal fungus called Sanghuang in China, has significant antitumor activity. We previously reported that a Sanghuangporus vaninii extract could lead to apoptosis in HT-29 cells through the intrinsic apoptotic pathway. We further found that Inoscavin A exhibited anti-colon cancer activity, but its specific mechanisms have not been fully elucidated.

METHODS

Inoscavin A was obtained from Sanghuangporus vaninii by the classic phytochemical separation technology. The male BALB/c nude mice were injected with HT-29 colon cancer cells as animal model. In order to observe the pathological changes of tumor section, the hematoxylin-eosin(H&E) staining was applied in the histological analysis. Metabolomics was utilized for the investigation of the overall changes of serum metabolites in animal model, and the potential targets of Inoscavin A were analyzed by Ingenuity Pathway Analysis (IPA). We further employed a molecular docking approach to predict the degree of combination of Inoscavin A and Smo. Then we further performed Western blotting and immunofluorescence analysis to investigate the expression of proteins involved in Hh-related pathways in tumor tissues. In addition, the colony formation assay, scratch-wound assay and transwell migration and invasion assay were conducted to evaluate the anti-colon-cancer activity of Inoscavin A. Concurrently, the mitochondrial membrane potential assay and TUNEL apoptosis assay were detected to demonstrate the effect of Inoscavin A on promoting HT-29 cells apoptosis. Western blot experiments verified the anti-tumor effects of Inoscavin A were modulated the protein expression of Shh, Ptch1, Smo and Gli1 in HT-29 cells.

RESULTS

We showed that Inoscavin A, a pyrone compound isolated from the Sanghuangporus vaninii extract, exerted its antitumor activity in an HT-29 colon cancer cell xenograft mouse model. Subsequently, we first time prove that the antitumor effects of Inoscavin A were related to the hedgehog (Hh) signaling pathway. Furthermore, we demonstrated that Smo, the core receptor of the Hh pathway, was critical for the induction of apoptosis of Inoscavin A and that overexpression of this target could significantly rescue cell apoptosis induced by Inoscavin A treatment.

CONCLUSION

Thus, our studies first propose that the natural outgrowth Inoscavin A exerted its anti-cancer effects by inhibiting Smo to suppress the activity of the Hh pathway though inhibiting cell proliferation and promoting apoptosis. These findings further indicate that Inoscavin A will be expected to be a prospective remedical compound for the treatment of colon cancer.

Application of High-Throughput Sequencing on the Chinese Herbal Medicine for the Data-Mining of the Bioactive Compounds

The Chinese Herbal Medicine (CHM) has been used worldwide in clinic to treat the vast majority of human diseases, and the healing effect is remarkable. However, the functional components and the corresponding pharmacological mechanism of the herbs are unclear. As one of the main means, the high-throughput sequencing (HTS) technologies have been employed to discover and parse the active ingredients of CHM. Moreover, a tremendous amount of effort is made to uncover the pharmacodynamic genes associated with the synthesis of active substances. Here, based on the genome-assembly and the downstream bioinformatics analysis, we present a comprehensive summary of the application of HTS on CHM for the synthesis pathways of active ingredients from two aspects: active ingredient properties and disease classification, which are important for pharmacological, herb molecular breeding, and synthetic biology studies.

The First Whole Genome Sequencing of Sanghuangporus sanghuang Provides Insights into Its Medicinal Application and Evolution

Sanghuangporus is a medicinal macrofungal genus typified by S. sanghuang, the very species utilized in traditional Chinese medicines by Chinese ancient people. To facilitate the medicinal application of S. sanghuang, we, for the first time, perform its genome sequencing and analyses from a monokaryon strain. A 33.34 Mb genome sequence was assembled to 26 contigs, which lead to the prediction of 8278 protein-coding genes. From these genes, the potential biosynthesis pathway of sesquiterpenoids was, for the first time, identified from Sanghuangporus, besides that of triterpenoids. While polysaccharides are the main medicinal metabolites in S. sanghuang, flavonoids are especially abundant medicinal metabolites comparing with other medicinal macrofungal groups. From the genomic perspective, S. sanghuang has a tetrapolar heterothallic mating system, and has its special nutritional strategy and advantageous medicinal properties compared with S. baumii and S. vaninii. A phylogenomics analysis indicates that Sanghuangporus emerged 15.39 million years ago and S. sanghuang has a closer phylogenetic relationship with S. baumii than S. vaninii. However, S. sanghuang shares a higher region of synteny and more orthologous genes, including carbohydrate-active enzymes with S. vaninii than S. baumii. A comparative genomics analysis with S. baumii and S. vaninii indicates that species diversification within Sanghuangporus may be driven by the translocation and translocation plus inversion of genome sequences, while the expansion and contraction of gene families may contribute to the host specificity of Sanghuangporus species. In general, the genome sequence of S. sanghuang provides insights into its medicinal application and evolution.

Aqueous extracts of Sanghuangporus vaninii induce S-phase arrest and apoptosis in human melanoma A375 cells

Sanghuangporus vaninii, also called 'Sanghuang' mushroom in Chinese, has various medicinal uses, but its effects on human melanoma cells have not been reported. The present study investigated the inhibitory ability and potential anticancer mechanism of the aqueous extracts of S. vaninii (SH). The results revealed that SH inhibited the proliferation of A375 human melanoma cells in a dose-dependent manner, and flow cytometry analysis suggested that SH induced A375 cell cycle arrest at S phase and apoptosis. Reverse transcription-quantitative PCR, western blotting and immunofluorescence analyses indicated that SH induced S-phase arrest by upregulating p21 expression, and p21 inhibited the expression of cyclin-cyclin-dependent kinases complexes at both the RNA and protein levels. In addition, SH induced apoptosis of A375 cells by inhibiting the expression levels of the anti-apoptosis gene Bcl-2. Therefore, the results suggested that SH may be a potential candidate for the treatment of human melanoma, thus providing new ideas for developing drugs that target melanoma.

Addressing widespread misidentifications of traditional medicinal mushrooms in Sanghuangporus (Basidiomycota) through ITS barcoding and designation of reference sequences

"Sanghuang" refers to a group of important traditionally-used medicinal mushrooms belonging to the genus Sanghuangporus. In practice, species of Sanghuangporus referred to in medicinal studies and industry are now differentiated mainly by a BLAST search of GenBank with the ITS barcoding region as a query. However, inappropriately labeled ITS sequences of "Sanghuang" in GenBank restrict accurate species identification and, to some extent, the utilization of these species as medicinal resources. We examined all available 271 ITS sequences related to "Sanghuang" in GenBank including 31 newly submitted sequences from this study. Of these sequences, more than half were mislabeled so we have now corrected the corresponding species names. The mislabeled sequences mainly came from strains utilized by non-taxonomists. Based on the analyses of ITS sequences submitted by taxonomists as well as morphological characters, we separate the newly described Sanghuangporus subbaumii from S. baumii and treat S. toxicodendri as a later synonym of S. quercicola. Fourteen species of Sanghuangporus are accepted, with intraspecific distances up to 1.30% (except in S. vaninii, S. weirianus and S. zonatus) and interspecific distances above 1.30% (except between S. alpinus and S. lonicerinus, and S. baumii and S. subbaumii). To stabilize the concept of these 14 species of Sanghuangporus, their taxonomic information and reliable ITS reference sequences are provided. Moreover, ten potential diagnostic sequences are provided for Hyperbranched Rolling Circle Amplification to rapidly confirm three common commercial species, viz. S. baumii, S. sanghuang, and S. vaninii. Our results provide a practical method for ITS barcoding-based species identification of Sanghuangporus and will promote medicinal studies and commercial development from taxonomically correct material.

Safety evaluation of aqueous extracts of Sanghuangporus vaninii fruiting body in Sprague-Dawley rats

Sanghuangporus vaninii, called "Sanghuang," is orally used for health care, tumor, and inflammation treatment in Asia. However, the safety of S. vaninii has not been evaluated. The major compounds analysis showed that aqueous extracts of S. vaninii fruiting body were rich in polysaccharides, nucleotides, and polyphenols. Then, the aqueous was given orally to Sprague-Dawley rats for toxical test. In acute toxicity study, the maximum tolerated dose was 21 g/kg. In 17-week repeated dose toxicity experiment, all rats had no abnormal reaction among control group, low dose group (0.15 g/kg) and middle dose group (1.00 g/kg). At high dose group (6.00 g/kg), the feces began to darken on 16th day (D16), and turned to drug stained stool on D21, all rats recovered on the 3rd day (D92) of recovery period. During the whole experiment, there were no animal death and no treatment-related changes in any of the parameters under the all doses. These results indicated the No-Observed Adverse Effect Level of aqueous extract of S. vaninii fruiting body was 1.0 g/kg.