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

Whole-Genome Characterization of Inonotus hispidus from Ulmus macrocarpa and Its Comparative Genomics with Strains from Morus alba and Acer truncatum

Inonotus hispidus growing on Morus alba is traditionally regarded as the authentic source of the medicinal fungus. However, this species is also found on other host trees, such as Ulmus macrocarpa and Acer truncatum; yet, whether these strains share comparable genomic and functional traits with Morus-derived strains remains unknown. Here, we performed whole-genome sequencing of a strain isolated from U. macrocarpa (UMI) using Illumina and PacBio platforms and conducted comparative genomic analysis with strains from M. alba (MAI) and A. truncatum (AMI). Antagonistic interactions were also evaluated via dual-culture confrontation assays. The UMI genome was 36.44 Mb in size, comprising 9097 predicted genes, of which 6991 and 1672 were annotated in the KEGG and COG databases, respectively. SNP analysis revealed 623,498 and 335,343 variants in AMI and MAI, with AMI showing greater genomic variation. Core-pan genome analysis identified 2651 core genes and 1046, 1424, and 1217 strain-specific genes in UMI, AMI, and MAI, respectively. Phenotypic assays demonstrated distinct mycelial growth dynamics and antagonistic behaviors, which likely reflect host-related environmental adaptation. Overall, I. hispidus strains from non-Morus hosts exhibit unique genomic and phenotypic features, providing a valuable basis for resource evaluation, artificial domestication, and the medicinal development of wild Sanghuang strains beyond traditional sources.

Structural characterization of polysaccharide isolated from Inonotus hispidus and its anti-obesity effect based on regulation of the interleukin-17-mediated inflammatory response

A heteropolysaccharide (IHP3) with a molecular weight of 22.0 kDa was isolated from Inonotus hispidus (Bull.: Fr.) P. Karst using column chromatography purification from water extraction. Its backbone was predominantly composed of →6)-α-D-Galp-(1→, →2,6)-α-D-Galp-(1→,→6)-α-D-O-Me-Galp-(1→, →3)-α-D-Manp-(1→, and →3,4,6) -β-D-Galp-(1→ residues, branched at C2 of partial α-D-Galp, or C3 and C4 of β-D-Galp, and terminated by α-D-Manp, and α-L-Fucp. In high-fat diet (HFD)-fed obese mice, IHP3 effectively suppressed body weight and plasma glucose gain, decreased fat accumulation, ameliorated lipid metabolism, and protected liver function from HFD-induced damage. Combining the analysis of gut microbiota metabolomics, hepatic proteomics and biochemical detection revealed, IHP3 significantly altered cecum fecal metabolite abundances, inhibited the phosphorylation of peroxisome proliferator-activated receptor gamma, and promoted the browning of white adipose tissue and the activation of brown adipose tissue. These changes collectively contributed to alleviating obesity symptoms by suppressing the interleukin (IL)-17-mediated inflammatory response in obese mice. Therefore, these findings suggest that IHP3 could be a potential candidate for the development of anti-obesity drugs.

Polypeptide of Inonotus hispidus extracts alleviates periodontitis through suppressing inflammatory bone loss

This study aimed to characterize and evaluate the effects of a novel polypeptide isolated from Inonotus hispidus (IH) against periodontitis. The polypeptides extracted and purified from the fruiting body of IH had a uniform molar mass, including 23 types of peptides. IH polypeptide (IHP) exerted antimicrobial activity against Porphyromonas gingivalis (P. gingivalis) by damaging the cell walls and membranes of microorganisms, disturbing energy metabolism, and regulating the expression of virulence factors. IHP significantly inhibited inflammation in lipopolysaccharides (LPS)-stimulated Raw264.7 cells evidenced by the regulation of inflammatory cytokine levels. In rats with ligature-induced periodontitis, IHP treatment ameliorated alveolar bone destruction and preserved the balance between oral flora and gut microbes. The interaction between oral and intestinal flora possibly affected the relevant metabolites. Proteomics combined with confirmation experiment revealed that the β-catenin/ nuclear factor-kappa B (NF-κB) signaling may be involved in IHP-mediated anti-periodontitis in rats, which helps reduce the secretion of pro-inflammatory factors and inhibit inflammatory osteoclastic response in the periodontal tissue. Additionally, IHP improved clinical parameters, including the plaque index (PLI), pocket depth (PD), bleeding on probing (BOP), and average probing depth in individuals with periodontitis. These findings augment the understanding of the potential role of IHP in treating periodontitis.

Influence of Mycobiota in the Nasopharyngeal Tract of COVID-19 Patients

The nasopharyngeal tract contains a complex microbial community essential to maintaining host homeostasis. Recent studies have shown that SARS-CoV-2 infection changes the microbial composition of the nasopharynx. Still, little is known about how it affects the fungal microbiome, which could provide valuable insights into disease pathogenesis. Nasopharyngeal swabs were collected from 55 patients, during three distinct COVID-19 waves that occurred in the Campania Region (southern Italy). An RNA-seq-based analysis was performed to evaluate changes in mycobiota diversity, showing variations depending on the disease's severity and the sample collection wave. The phyla Basidiomycota and Ascomycota were shown to have higher abundance in patients with severe symptoms. Furthermore, the diversity of the fungal population was greater in the second wave. Conclusion: According to our research, COVID-19 induces significant dysbiosis of the fungal microbiome, which may contribute to disease pathogenesis, and understanding its underlying mechanisms could contribute to developing effective treatments.

Structural characterization, chain conformation and immunomodulatory activity of a heteropolysaccharide from Inonotus hispidus

A new polysaccharide (IHP-1aa) was isolated from the fruiting body of Inonotus hispidus by hot water extraction, ethanol precipitation and column chromatography. The molecular weight of IHP-1aa was 26.9 kDa. Structural analysis showed that IHP-1aa consisted of glucose (Glc), galactose (Gal), fucose (Fuc), mannose (Man) and contained a certain amount of 3-O-methylgalactose (3-O-Me-Gal). The structure was mainly composed of →6)-α/β-D-Glcp-(1→, →6)-α-D-Galp-(1→, →6)-(3-O-Me)-α-D-Galp-(1→, →6)-α-D-Manp-(1 → and →2, 6)-α-D-Galp-(1 → as the main chain. Branched at O-2 with single β-L-Fucp-(1 → 6)-α-D-Galp-(1 → 6)-α-D-Glcp-(1 → as major the side chain. The results of SEM, XRD and AFM combined with Congo red indicated that IHP-1aa may be amorphous granular chain conformation. In addition, IHP-1aa stimulated macrophage function and improved phagocytic ability of RAW264.7, as well as promoted the secretion of NO, TNF-α and IL-6. IHP-1aa, a 3-O-methylgalactose-containing heteropolysaccharide, was isolated for the first time from the I. hispidus, which may be used as a potential immunomodulator in functional foods.

Genomic comparison between two Inonotus hispidus strains isolated from growing in different tree species

Inonotus hispidus mainly growing in broad-leaved trees, including Morus alba, Fraxinus mandshurica, and Ulmus macrocarpa etc. The fruiting body of I. hispidus growing in M. alba (hereafter as MA) is used as a traditional Chinese medicine "Sanghuang". However, differences between the genetic material basis of I. hispidus growing in other tree species have not been reported. Therefore, in this paper, the genomic comparison between MA and I. hispidus growing in F. mandshurica (hereafter as FM) were studied. The whole genome of MA monokaryon was sequenced by Illumina combined with Pac Bio platform. Next, genome assembly, genome component prediction and genome functional annotation were performed. Comparative genomics analysis was performed between FM monokaryon and MA monokaryon, using MA as the reference. The results showed that, MA had 24 contigs with a N50 length of 2.6 Mb. Specifically, 5,342, 6,564, 1,595, 383 and 123 genes were annotated from GO, KEGG, KOG, CAZymes and CYP450, respectively. Moreover, comparative genomics showed that, the coding genes and total number of genes annotated in different databases of FM were higher than that of MA. This study provides a foundation for the medicinal application of FM as MA from the perspective of genetic composition.

Whole Genome Sequence of an Edible Mushroom Oudemansiella raphanipes (Changgengu)

Oudemansiella raphanipes, considered as a well-known culinary edible mushroom with a high content of natural bioactive substances, is widely cultivated in China with the commercial name Changgengu. However, due to the lack of genomic data, molecular and genetic study on O. raphanipes is rare. To obtain a comprehensive overview of genetic characteristics and enhance the value of O. raphanipes, two mating-compatible monokaryons isolated from the dikaryon were applied for de novo genome sequencing and assembly using Nanopore and /or Illumina sequencing platforms. One of the monokaryons, O. raphanipes CGG-A-s1, was annotated with 21,308 protein-coding genes, of which 56 were predicted to be involved in the biosynthesis of secondary metabolites such as terpene, type I PKS, NRPS, and siderophore. Phylogenetic and comparative analysis of multiple fungi genomes revealed a close evolutionary relationship between O. raphanipes and Mucidula mucid based on single-copy orthologous protein genes. Significant collinearity was detected between O. raphanipes and Flammulina velutipes on the synteny of inter-species genomes. 664 CAZyme genes in CGG-A-s1 were identified with GHs and AAs families significantly elevated when compared with the other 25 sequenced fungi, indicating a strong wood degradation ability. Furthermore, the mating type locus analysis revealed that CGG-A-s1 and CGG-A-s2 were conserved in the gene organization of the mating A locus but various in that of the mating B locus. The genome resource of O. raphanipes will provide new insights into its development of genetic studies and commercial production of high-quality varieties.