Yingce Duan

Armillaria is a genus of macrofungi with high ecological, biological, medicinal, and edible value. As facultative plant pathogens and nutritional symbionts, Armillaria species support the growth of valuable medicinal plants including Gastrodia elata and Polyporus umbellatus. They also exhibit unique traits such as exceptional longevity, widespread clonal expansion, rhizomorph formation, and bioluminescence, making them a valuable model for studying fungal ecology, symbiosis, specialized metabolism, and applied research. This review summarizes recent progress in Armillaria research, covering biological characteristics, nutritional components, bioactive constituents, species identification, genomic resources, and biosynthetic pathways. We discuss advances in artificial cultivation and the regulatory roles of exogenous phytohormones in mycelial and rhizomorph development. The nutritional value of fruiting bodies is highlighted, with a focus on key pharmacologically active metabolites such as protoilludane-type sesquiterpenes and polysaccharides. We also review multilocus phylogenetic analysis, comparative genomics, and the biosynthetic gene clusters of melleolides and bioluminescence, which have improved understanding of Armillaria evolution and functional differentiation.

Irpex lacteus is an edible and medicinal macrofungus with significant biological activity and broad pharmaceutical prospects that has received increasing attention in recent years. Although it is an important resource for macrofungi, knowledge of it remains limited. In this study, we sequenced, de novo assembled, and annotated the whole genome of I. lacteus using a PacBio Sequel II sequencer. The assembled 41.83 Mb genome contains 13,135 predicted protein-coding genes, 83.44% of which have searchable sequence similarity to other genes available in public databases. Using genome-based bioinformatics analysis, we identified 556 enzymes involved in carbohydrate metabolism and 103 cytochrome P450 proteins. Genome annotation revealed genes for key enzymes responsible for the biosynthesis of secondary metabolites, such as terpenoids and polyketides. Among them, we identified 14 terpene synthases, 8 NRPS-like enzymes, and 4 polyketide synthases (PKS), as well as 2 clusters of biosynthetic genes presumably related to terpene synthesis in I. lacteus. Gene family analysis revealed that the MYB transcription factor gene family plays an important role in the growth and development of I. lacteus. This study further enriches the genomic content of I. lacteus, provides genomic information for further research on the molecular mechanism of I. lacteus, and promotes the development of I. lacteus in the fields of drug research and functional food production.

Fomitopsis betulina, as a macrofungus with both medicinal and dietary applications, is renowned for its rich content of bioactive substances. The recent advancements in research have significantly enhanced our understanding of its polysaccharides, cellulose-degrading enzymes, and wide range of secondary metabolites. This paper provides a comprehensive review of the artificial cultivation techniques and the chemical profiling of over 100 secondary metabolites identified in F. betulina, including terpenoids, phenols, and various other classes. These compounds exhibit notable pharmacological activities, such as anti-cancer, anti-inflammatory, antimicrobial, antiviral, and anti-malarial effects. Moreover, this review delves into the genomic analysis of F. betulina, focusing on the prediction and classification of terpene synthases, which play a crucial role in the biosynthesis of these bioactive compounds. This insight is instrumental for potentially facilitating future biochemical studies and pharmaceutical applications. Through this review, we aim to solidify the foundation for future in-depth studies and the development of new drugs derived from this promising natural resource.

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.

Sesterterpenes are 25-carbon terpenoids formed by the cyclization of dimethyl allyl diphosphate (DMAPP) and isopentenyl diphosphate (IPP) as structural units by sesterterpenes synthases. Some (not all) sesterterpenoids are modified by cytochrome P450s (CYP450s), resulting in more intricate structures. These compounds have significant physiological activities and pharmacological effects in anti-inflammatory, antibacterial, antitumour, and hypolipidemic communities. Despite being a rare class of terpenoids, sesterterpenoids derived from fungi show a wide range of structural variations. The discovered fungal sesterterpenoid synthases are composed of C-terminal prenyltransferase (PT) and N-terminal terpene synthase (TS) domains, which were given the name PTTSs. PTTSs have the capacities to catalyze chain lengthening and cyclization concurrently. This review summarizes all 52 fungal PTTSs synthases and their biosynthetic pathways involving 100 sesterterpenoids since the discovery of the first PTTSs synthase from fungi in 2013.

Sesquiterpenes are common small-molecule natural products with a wide range of promising applications and are biosynthesized by sesquiterpene synthase (STS). Basidiomycetes are valuable and important biological resources. To date, hundreds of related sesquiterpenoids have been discovered in basidiomycetes, and the biosynthetic pathways of some of these compounds have been elucidated. This review summarizes 122 STSs and 2 fusion enzymes STSs identified from 26 species of basidiomycetes over the past 20 years. The biological functions of enzymes and compound structures are described, and related research is discussed.