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Xie X, Zhao L, Song Y, Qiao Y, Wang ZX, Qi J. Genome-wide characterization and metabolite profiling of Cyathus olla: insights into the biosynthesis of medicinal compounds. BMC Genomics 2024; 25:618. [PMID: 38890562 PMCID: PMC11186289 DOI: 10.1186/s12864-024-10528-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 06/14/2024] [Indexed: 06/20/2024] Open
Abstract
Cyathus olla, belonging to the genus Cyathus within the order Agaricales, is renowned for its bird's nest-like fruiting bodies and has been utilized in folk medicine. However, its genome remains poorly understood. To investigate genomic diversity within the genus Cyathus and elucidate biosynthetic pathways for medicinal compounds, we generated a high-quality genome assembly of C. olla with fourteen chromosomes. The comparative genome analysis revealed variations in both genomes and specific functional genes within the genus Cyathus. Phylogenomic and gene family variation analyses provided insights into evolutionary divergence, as well as genome expansion and contraction in individual Cyathus species and 36 typical Basidiomycota. Furthermore, analysis of LTR-RT and Ka/Ks revealed apparent whole-genome duplication (WGD) events its genome. Through genome mining and metabolite profiling, we identified the biosynthetic gene cluster (BGC) for cyathane diterpenes from C. olla. Furthermore, we predicted 32 BGCs, containing 41 core genes, involved in other bioactive metabolites. These findings represent a valuable genomic resource that will enhance our understanding of Cyathus species genetic diversity. The genome analysis of C. olla provides insights into the biosynthesis of medicinal compounds and establishes a fundamental basis for future investigations into the genetic basis of chemodiversity in this significant medicinal fungus.
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Affiliation(s)
- Xiuchao Xie
- Shaanxi Province Key Laboratory of Bio-resources, Qinba State Key Laboratory of Biological Resources and Ecological Environment (Incubation), School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, 723000, China
| | - Ling Zhao
- Department of Pharmacy, School of Medicine, Xi'an International University, Xi'an 710077, China
| | - Yu Song
- Shaanxi Province Key Laboratory of Bio-resources, Qinba State Key Laboratory of Biological Resources and Ecological Environment (Incubation), School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, 723000, China
| | - Yanming Qiao
- Shaanxi Province Key Laboratory of Bio-resources, Qinba State Key Laboratory of Biological Resources and Ecological Environment (Incubation), School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, 723000, China
| | - Zhen-Xin Wang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, 712100, China
| | - Jianzhao Qi
- Shaanxi Province Key Laboratory of Bio-resources, Qinba State Key Laboratory of Biological Resources and Ecological Environment (Incubation), School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, 723000, China.
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, 712100, China.
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Kraisitudomsook N, Ahrendt S, Riley R, LaButti K, Lipzen A, Daum C, Barry K, Grigoriev IV, Rämä T, Martin F, Smith ME. On the origin of bird's nest fungi: Phylogenomic analyses of fungi in the Nidulariaceae (Agaricales, Basidiomycota). Mol Phylogenet Evol 2024; 193:108010. [PMID: 38195011 DOI: 10.1016/j.ympev.2024.108010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 11/15/2023] [Accepted: 01/06/2024] [Indexed: 01/11/2024]
Abstract
Nidulariaceae, also known as bird's nest fungi, is an understudied group of mushroom-forming fungi. The common name is derived from their nest-like morphology. Bird's nest fungi are ubiquitous wood decomposers or saprobes on dung. Recent studies showed that species in the Nidulariaceae form a monophyletic group with five sub-clades. However, phylogenetic relationships among genera and placement of Nidulariaceae are still unclear. We present phylogenomic analyses of bird's nest fungi and related Agaricales fungi to gain insight into the evolution of Nidulariaceae. A species tree with 17 newly generated genomes of bird's nest fungi and representatives from all major clades of Agaricales was constructed using 1044 single-copy genes to explore the intergeneric relationships and pinpoint the placement of Nidulariaceae within Agaricales. We corroborated the hypothesis that bird's nest fungi are sister to Squamanitaceae, which includes mushroom-shaped fungi with a stipe and pileus that are saprobes and mycoparasites. Lastly, stochastic character mapping of discrete traits on phylogenies (SIMMAP) suggests that the ancestor of bird's nest fungi likely possessed an evanescent, globose peridium without strings attaching to the spore packets (funiculi). This analysis suggests that the funiculus was gained twice and that the persistent, cupulate peridium form was gained at least four times and lost once. However, alternative coding schemes and datasets with a wider array of Agaricales produced conflicting results during ancestral state reconstruction, indicating that there is some uncertainty in the number of peridium transitions and that taxon sampling may significantly alter ancestral state reconstructions. Overall, our results suggest that several key morphological characters of Nidulariaceae have been subject to homoplasy.
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Affiliation(s)
- Nattapol Kraisitudomsook
- Plant Pathology Department, Institute of Food and Agricultural Sciences (UF-IFAS), University of Florida, Gainesville, FL 32607, USA; Department of Biology, Faculty of Science and Technology, Muban Chombueng Rajabhat University, Ratchaburi 70150, Thailand.
| | - Steven Ahrendt
- U.S Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Robert Riley
- U.S Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Kurt LaButti
- U.S Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Anna Lipzen
- U.S Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Chris Daum
- U.S Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Kerrie Barry
- U.S Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Igor V Grigoriev
- U.S Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA; Department of Plant and Microbial Biology, University of California Berkeley, 110 Koshland Hall, Berkeley, CA 94720, USA
| | - Teppo Rämä
- The Norwegian College of Fishery Science, UiT the Arctic University of Norway, Tromsø N-9037, Norway
| | - Francis Martin
- University of Lorraine, National Research Institute for Agriculture, Food, and Environment (INRAE), Tree-Microbe Interactions Department, Champenoux 54280, France.
| | - Matthew E Smith
- Plant Pathology Department, Institute of Food and Agricultural Sciences (UF-IFAS), University of Florida, Gainesville, FL 32607, USA.
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Li ZC, Xie TC, Feng XL, Wang ZX, Lin C, Li GM, Li XZ, Qi J. The First Five Mitochondrial Genomes for the Family Nidulariaceae Reveal Novel Gene Rearrangements, Intron Dynamics, and Phylogeny of Agaricales. Int J Mol Sci 2023; 24:12599. [PMID: 37628782 PMCID: PMC10454537 DOI: 10.3390/ijms241612599] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/04/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
The family Nidulariaceae, consisting of five genera including Cyathus, is a unique group of mushrooms commonly referred to as bird's nest fungi due to their striking resemblance to bird's nests. These mushrooms are considered medicinal mushrooms in Chinese medicine and have received attention in recent years for their anti-neurodegenerative properties. However, despite the interest in these mushrooms, very little is known about their mitochondrial genomes (mitogenomes). This study is the first comprehensive investigation of the mitogenomes of five Nidulariaceae species with circular genome structures ranging in size from 114,236 bp to 129,263 bp. Comparative analyses based on gene content, gene length, tRNA, and codon usage indicate convergence within the family Nidulariaceae and heterogeneity within the order Agaricales. Phylogenetic analysis based on a combined mitochondrial conserved protein dataset provides a well-supported phylogenetic tree for the Basidiomycetes, which clearly demonstrates the evolutionary relationships between Nidulariaceae and other members of Agaricales. Furthermore, phylogenetic inferences based on four different gene sets reveal the stability and proximity of evolutionary relationships within Agaricales. These results reveal the uniqueness of the family Nidulariaceae and its similarity to other members of Agaricales; provide valuable insights into the origin, evolution, and genetics of Nidulariaceae species; and enrich the fungal mitogenome resource. This study will help to expand the knowledge and understanding of the mitogenomes in mushrooms.
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Affiliation(s)
- Zhao-chen Li
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Tian-chen Xie
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Xi-long Feng
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Zhen-xin Wang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Chao Lin
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Guo-ming Li
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Xiu-Zhang Li
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai Academy of Animal and Veterinary Sciences, Qinghai University, Xining 810016, China
| | - Jianzhao Qi
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Xianyang 712100, China
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da Cruz RHSF, Dos Santos Góis J, Marinho P, Baseia IG, Hosaka K. Rearranging the Bird's Nest Fungi: molecular review of internal clades in Cyathus (Nidulariaceae, Basidiomycota). IMA Fungus 2023; 14:8. [PMID: 37029439 PMCID: PMC10082518 DOI: 10.1186/s43008-023-00111-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 03/21/2023] [Indexed: 04/09/2023] Open
Abstract
The genus Cyathus was established in 1768, but more in-depth taxonomic studies with the group only occurred after 1844. In the following years, changes in the infrageneric classification of Cyathus were proposed based mainly on morphology. With advances in phylogenetic studies, the morphological classifications were tested and a new subdivision into three groups was proposed in 2007. Based on the last two classifications, this work aims to expand and understand the internal phylogenetic relationships among the fungi of the genus Cyathus and examine how these relationships are reflected in the taxonomic classification, through molecular analyses covering most of the species in the group, based on materials obtained from type specimens deposited in major fungal collections worldwide, besides expanding sampling with tropical species. Molecular analyses followed the protocols available in the literature, including the design of specific primers for Cyathus. In the phylogenetic analysis, using Maximum Parsimony and Bayesian methods, sequences of ITS and LSU regions from 41 samples of 39 species of Cyathus, 26 were placed with some nomenclatural types. The monophyly of Cyathus was confirmed with maximum support in both tests, and the infrageneric groups of the most recent classification were unchanged, but the clade striatum showed segregation into four groups and three subgroups. The phylogenetic organization is supported morphological characters, and diagnoses are presented for each group, as well as a dichotomous key for the infrageneric separation.
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Affiliation(s)
- Rhudson Henrique Santos Ferreira da Cruz
- Centro das Ciências Biológicas e da Saúde, Universidade Federal do Oeste da Bahia, Barreiras, Bahia, Brazil.
- Departamento de Botânica e Zoologia, Programa de Pós-Graduação em Sistemática e Evolução, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil.
| | - Jefferson Dos Santos Góis
- Departamento de Botânica e Zoologia, Programa de Pós-Graduação em Sistemática e Evolução, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Paulo Marinho
- Departamento de Biologia Celular e Genética, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Iuri Goulart Baseia
- Departamento de Botânica e Zoologia, Programa de Pós-Graduação em Sistemática e Evolução, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Kentaro Hosaka
- Department of Botany, National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba, Ibakari, Japan
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Sum WC, Mitschke N, Schrey H, Wittstein K, Kellner H, Stadler M, Matasyoh JC. Antimicrobial and Cytotoxic Cyathane-Xylosides from Cultures of the Basidiomycete Dentipellis fragilis. Antibiotics (Basel) 2022; 11:antibiotics11081072. [PMID: 36009941 PMCID: PMC9405216 DOI: 10.3390/antibiotics11081072] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/04/2022] [Accepted: 08/06/2022] [Indexed: 11/16/2022] Open
Abstract
In our continued search for biologically active metabolites from cultures of rare Basidiomycota species, we found eight previously undescribed cyathane-xylosides from submerged cultures of Dentipellis fragilis, which were named dentifragilins A–H. In addition, the known cyathane derivatives striatal D and laxitextine A were isolated. All compounds were characterized by high-resolution electrospray ionization mass spectrometry (HR-ESIMS) as well as by 1D and 2D nuclear magnetic resonance (NMR) spectroscopy. Several of the compounds exhibited significant activities in standardized cell-based assays for the determination of antimicrobial and cytotoxic effects. The discovery of cyathanes in the genus Dentipellis has chemotaxonomic implications, as this class of diterpenoids has already been shown to be characteristic for mycelial cultures of the related genera Hericium and Laxitextum, which are classified as Dentipellis in the family Hericiaceae.
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Affiliation(s)
- Winnie Chemutai Sum
- Department Microbial Drugs, Helmholtz Centre for Infection Research GmbH (HZI), Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Nico Mitschke
- Department Microbial Drugs, Helmholtz Centre for Infection Research GmbH (HZI), Inhoffenstraße 7, 38124 Braunschweig, Germany
- Research Group for Marine Geochemistry (ICBM-MPI Bridging Group), Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky Universität Oldenburg, Carl-von-Ossietzky-Str. 9-11, 26129 Oldenburg, Germany
| | - Hedda Schrey
- Department Microbial Drugs, Helmholtz Centre for Infection Research GmbH (HZI), Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Kathrin Wittstein
- Department Microbial Drugs, Helmholtz Centre for Infection Research GmbH (HZI), Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Harald Kellner
- Department of Bio- and Environmental Sciences, Technische Universität Dresden—International Institute Zittau, Markt 23, 02763 Zittau, Germany
| | - Marc Stadler
- Department Microbial Drugs, Helmholtz Centre for Infection Research GmbH (HZI), Inhoffenstraße 7, 38124 Braunschweig, Germany
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
- Correspondence: (M.S.); (J.C.M.); Tel.: +49-531-6181-4240 (M.S.); +254-722871521 (J.C.M.)
| | - Josphat Clement Matasyoh
- Department of Chemistry, Egerton University, P.O. Box 536, Njoro 20115, Kenya
- Correspondence: (M.S.); (J.C.M.); Tel.: +49-531-6181-4240 (M.S.); +254-722871521 (J.C.M.)
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Hidden in the tropics: Retiperidiolia gen. nov., a new genus of bird’s nest fungi (Nidulariaceae), and a systematic study of the genus Mycocalia. Mycol Prog 2022. [DOI: 10.1007/s11557-022-01807-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Duan ZY, Yu J, Zhao CL. Molecular phylogeny and morphology reveal a new wood-rotting fungal species, <i>Cyathus wenshanensis</i> sp. nov. from the Yunnan-Guizhou Plateau. STUDIES IN FUNGI 2022. [DOI: 10.48130/sif-2022-0008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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