Whole Genome Sequencing and Annotation of Naematelia aurantialba (Basidiomycota, Edible-Medicinal Fungi)

Adaptive laboratory evolution of Naematelia aurantialba under high temperature for efficient production of exopolysaccharide

Liquid fermentation could revolutionize mushroom polysaccharide production, but the low temperature constraint hampers the process. This study implemented adaptive laboratory evolution (ALE) to enhance the thermotolerance of Naematelia aurantialba strains and increase expolysaccharide production. After 75 ALE cycles at 30 °C, the adaptive strain surpassed the wild-type strain by 5 °C. In a 7.5 L fermentor at 30 °C, the ALE strain yielded 17 % more exopolysaccharide than the wild type strain at 25 °C. Although the exopolysaccharide synthesized by both strains shares a consistent monosaccharide composition, infrared spectrum, and glycosidic bond composition, the ALE strain's exopolysaccharide has a larger molecular weight. Furthermore, the ALE strain's exopolysaccharide exhibits superior cryoprotection performance compared to that produced by the original strain. The adapted strain demonstrated lower ROS levels and increased activity of antioxidant enzymes, indicating improved performance. Fatty acid profiling and transcriptomics revealed reconfiguration of carbohydrate metabolism, amino acid metabolism, and membrane lipid synthesis in thermophilic strains, maintaining cellular homeostasis and productivity. This study provides efficient strains and fermentation methods for high-temperature mushroom polysaccharide production, reducing energy consumption and costs.

In vitro digestion and fecal fermentation of basidiospore-derived exopolysaccharides from Naematelia aurantialba

Mushroom polysaccharides exhibit numerous health-enhancing attributes that are intricately linked to the breakdown, assimilation, and exploitation of polysaccharides within the organism. Naematelia aurantialba polysaccharides (NAPS-A), highly prized polysaccharides derived from mushrooms, remain shrouded in uncertainty regarding their characteristics pertaining to gastrointestinal digestion and gut microbial fermentation. The study aimed to understand the digestion and fecal fermentation patterns of NAPS-A. After simulated digestion, NAPS-A's physicochemical properties remained unchanged. However, during in vitro fecal fermentation, indigestible NAPS-A underwent significant changes in various properties, such as reducing sugar, chemical composition, constituent monosaccharides, Molecular weight, apparent viscosity, FT-IR spectra, and microscopic morphology. Notably, NAPS-A was effectively utilized by the gut microbiota, with unchanged properties after digestion but altered after fermentation. It influenced gut microbe composition by increasing beneficial bacteria (Lactobacillus, Faecalibacterium, and Roseburia), lowering pH, and producing short-chain fatty acids. NAPS-A fermentation enriches carbohydrate, fatty acid, and amino acid metabolic pathways through PICRUSt prediction analysis. Overall, these findings emphasize NAPS-A's role in regulating gut bacteria and their metabolic functions, despite its challenging digestibility.

Chromosome-level assembly of Dictyophora rubrovolvata genome using third-generation DNA sequencing and Hi-C analysis

Dictyophora rubrovolvata, a rare edible mushroom with both nutritional and medicinal values, was regarded as the "queen of the mushroom" for its attractive appearance. Dictyophora rubrovolvata has been widely cultivated in China in recent years, and many researchers were focusing on its nutrition, culture condition, and artificial cultivation. Due to a lack of genomic information, research on bioactive substances, cross breeding, lignocellulose degradation, and molecular biology is limited. In this study, we report a chromosome-level reference genome of D. rubrovolvata using the PacBio single-molecule real-time-sequencing technique and high-throughput chromosome conformation capture (Hi-C) technologies. A total of 1.83 Gb circular consensus sequencing reads representing ∼983.34 coverage of the D. rubrovolvata genome were generated. The final genome was assembled into 136 contigs with a total length of 32.89 Mb. The scaffold and contig N50 length were 2.71 and 2.48 Mb, respectively. After chromosome-level scaffolding, 11 chromosomes with a total length of 28.24 Mb were constructed. Genome annotation further revealed that 9.86% of the genome was composed of repetitive sequences, and a total of 508 noncoding RNA (rRNA: 329, tRNA: 150, ncRNA: 29) were annotated. In addition, 9,725 protein-coding genes were predicted, among which 8,830 (90.79%) genes were predicted using homology or RNA-seq. Benchmarking Universal Single-Copy Orthologs results further revealed that there were 80.34% complete single-copy fungal orthologs. In this study, a total of 360 genes were annotated as belonging to the carbohydrate-active enzymes family. Further analysis also predicted 425 cytochromes P450 genes, which can be classified into 41 families. This highly accurate, chromosome-level reference genome of D. rubrovolvata will provide essential genomic information for understanding the molecular mechanism in its fruiting body formation during morphological development and facilitate the exploitation of medicinal compounds produced by this mushroom.

The First Whole Genome Sequencing of Agaricus bitorquis and Its Metabolite Profiling

Agaricus bitorquis, an emerging wild mushroom with remarkable biological activities and a distinctive oversized mushroom shape, has gained increasing attention in recent years. Despite its status as an important resource of wild edible fungi, knowledge about this mushroom is still limited. In this study, we used the Illumina NovaSeq and Nanopore PromethION platforms to sequence, de novo assemble, and annotate the whole genome and mitochondrial genome (mitogenome) of the A. bitorquis strain BH01 isolated from Bosten Lake, Xinjiang Province, China. Using the genome-based biological information, we identified candidate genes associated with mating type and carbohydrate-active enzymes in A. bitorquis. Cluster analysis based on P450 of basidiomycetes revealed the types of P450 members of A. bitorquis. Comparative genomic, mitogenomic, and phylogenetic analyses were also performed, revealing interspecific differences and evolutionary features of A. bitorquis and A. bisporus. In addition, the molecular network of metabolites was investigated, highlighting differences in the chemical composition and content of the fruiting bodies of A. bitorquis and A. bisporus. The genome sequencing provides a comprehensive understanding and knowledge of A. bitorquis and the genus Agaricus mushrooms. This work provides valuable insights into the potential for artificial cultivation and molecular breeding of A. bitorquis, which will facilitate the development of A. bitorquis in the field of edible mushrooms and functional food manufacture.

Chromosome-Level Genome Sequences, Comparative Genomic Analyses, and Secondary-Metabolite Biosynthesis Evaluation of the Medicinal Edible Mushroom Laetiporus sulphureus

Laetiporus sulphureus mushroom is a complementary and alternative medicine that has anticancer, antioxidation, and analgesic effects and immunomodulatory activity; it is used as a treatment for cough and rheumatism and is a functional food that can improve physical fitness. Even though L. sulphureus has garnered considerable biotechnological and pharmacological interest due to its excellent cellulose-degrading ability and diverse biological activities, its biosynthetic potential regarding polysaccharides and secondary metabolites has not been thoroughly examined. In this study, we sequenced and assembled the whole genome of a wild L. sulphureus isolate, NWAFU-1, from the Qinling Mountains in China. Comparative genomes analysis revealed genomic differences between subspecies, and phylogenomic analysis revealed evolutionary divergence as well as genome expansion and contraction of individual Polyporaceae family species. Bioinformatics investigation identified candidate genes associated with mating type, polysaccharide synthesis, carbohydrate-active enzymes, and secondary-metabolite biosynthesis, which included multiple terpenoids, nonribosomal peptides, and polyketides. The locations of biosynthetic core genes were mapped and displayed on chromosomes and contigs. Totals of 143 proteins from 126 coding genes were identified and divided into 14 cytochrome P450 families. Furthermore, the biosynthetic network of tetracyclic triterpenoid active components was postulated by genome mining of related genes combined with the molecular network of metabolites. The genome analysis of L. sulphureus in this study improves the understanding of the biosynthesis of active compounds, which will lay a theoretical foundation for subsequent research on active-compound biosynthesis and promote the application of Laetiporus in the field of drug research and functional-food creation. IMPORTANCE L. sulphureus is a parasitic basidiomycete fungus that causes brown rot. The fruiting bodies of L. sulphureus are used as ancient medicines in China and Europe to cure cancer, analgesia, cough, and rheumatism and are considered a functional food that regulates the body and improves health. L. sulphureus was inferred to be a tetrapolar system based on a high-quality genome, which will aid molecular breeding and artificial farming. Screening polysaccharide synthesis candidate genes and comparing carbohydrate-associated genes in brown-rot basidiomycetes help understand their growth. Identifying core genes for secondary-metabolite biosynthesis, gene cluster family analysis, and comparative cluster analysis will guide heterologous-biosynthesis investigations of these genes and help elucidate the biosynthetic pathways for L. sulphureus bioactive natural components. The biosynthesis network of tetracyclic triterpenes was mapped using metabolite profiling and genome scanning. This work explores the biosynthetic capacity of L. sulphureus-derived natural products and lays the foundation for biosynthetic studies of them.

Antioxidant activity and cytotoxicity of exopolysaccharide from mushroom Hericium coralloides in submerged fermentation

Mushrooms of the genus Hericium spp. represent a series of delicious edible mushrooms with medicinal value. Here, for the first time, the species native to Iran, the mushroom Hericium coralloides, was collected in Mazandaran province, identified, and registered with the NCBI under accession number MW136052. The production of exopolysaccharides (EPS) in submerged culture was optimized using the response surface method. Among the physicochemical and culture medium conditions tested, rotation speed and concentration of maltose and peptone of soybean significantly affected the production of EPS. The proposed model predicts maximum EPS production (0.13 g/L) at 50 g/L maltose, 3 g/L soy peptone, and 1 g/L yeast extract, pH = 6.5, 200 rpm, inoculum at 5% v/v, and 22 °C. The molecular weight of the EPS chains was 413 and 1578 Da. EPS has antioxidant action (EC50 = 6.59 mg/mL) and cytotoxic activity against cancer cells. The viability of AGS and MKN-45 cancer cell lines declined to 20 and 30% after 48 h of the EPS treatment. H. coralloides EPS could be considered a natural dietary anti-cancer supplement. Further studies are necessary to understand the mechanism of the H. coralloides EPS activity on the cell cycle of cancer cells and to prove its action in vivo.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13399-022-03386-0.

Nutritional Function and Flavor Evaluation of a New Soybean Beverage Based on Naematelia aurantialba Fermentation

The soy beverage is a healthy product rich in plant protein; however, its unpleasant flavor affects consumer acceptance. The aim of this study was to determine the feasibility of using Naematelia aurantialba as a strain for the preparation of fermented soybean beverages (FSB). Increases in Zeta potential, particle size, and viscosity make soy beverages more stable. We found that nutrient composition was increased by fermenting N. aurantialba, and the antioxidant activity of soybean beverages significantly increased after 5 days of fermentation. By reducing the content of beany substances such as hexanal and increasing the content of 1-octen-3-ol, the aroma of soybean beverages fermented by N. aurantialba changed from “beany, green, and fatty” to “mushroom and aromatic”. The resulting FSB had reduced bitterness but considerably increased sourness while maintaining the fresh and sweet taste of unfermented soybean beverages (UFSB). This study not only provides a theoretical basis for the market promotion of FSB but also provides a reference for basidiomycetes-fermented beverages.