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Dirks AC, Methven AS, Miller AN, Orozco-Quime M, Maurice S, Bonito G, Van Wyk J, Ahrendt S, Kuo A, Andreopoulos W, Riley R, Lipzen A, Chovatia M, Savage E, Barry K, Grigoriev IV, Bradshaw AJ, Martin FM, Elizabeth Arnold A, James TY. Phylogenomic insights into the taxonomy, ecology, and mating systems of the lorchel family Discinaceae (Pezizales, Ascomycota). Mol Phylogenet Evol 2025:108286. [PMID: 39788220 DOI: 10.1016/j.ympev.2025.108286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 11/21/2024] [Accepted: 01/05/2025] [Indexed: 01/12/2025]
Abstract
Lorchels, also known as false morels (Gyromitra sensu lato), are iconic due to their brain-shaped mushrooms and production of gyromitrin, a deadly mycotoxin. Molecular phylogenetic studies have hitherto failed to resolve deep-branching relationships in the lorchel family, Discinaceae, hampering our ability to settle longstanding taxonomic debates and to reconstruct the evolution of toxin production. We generated 75 draft genomes from cultures and ascomata (some collected as early as 1960), conducted phylogenomic analyses using 1542 single-copy orthologs to infer the early evolutionary history of lorchels, and identified genomic signatures of trophic mode and mating-type loci to better understand lorchel ecology and reproductive biology. Our phylogenomic tree was supported by high gene tree concordance, facilitating taxonomic revisions in Discinaceae. We recognized 10 genera across two tribes: tribe Discineae (Discina, Maublancomyces, Neogyromitra, Piscidiscina, and Pseudodiscina) and tribe Gyromitreae (Gyromitra, Hydnotrya, Paragyromitra, Pseudorhizina, and Pseudoverpa); Piscidiscina was newly erected and 26 new combinations were formalized. Paradiscina melaleuca and Marcelleina donadinii formed their own family-level clade sister to Morchellaceae, which merits further taxonomic study. Genome size and CAZyme content were consistent with a mycorrhizal lifestyle for the truffle species (Hydnotrya spp.), whereas the other Discinaceae genera possessed genomic properties of a saprotrophic habit. Lorchels were found to be predominantly heterothallic-either MAT1-1 or MAT1-2-but a single occurrence of colocalized mating-type idiomorphs indicative of homothallism was observed in Gyromitra esculenta strain CBS101906 and requires additional confirmation and follow-up study. Lastly, we confirmed that gyromitrin has a phylogenetically discontinuous distribution, having been detected exclusively in two distantly related genera (Gyromitra and Piscidiscina) belonging to separate tribes. Our genomic dataset will facilitate further investigations into the gyromitrin biosynthesis genes and their evolutionary history. With additional sampling of Geomoriaceae and Helvellaceae-two closely related families with no publicly available genomes-these data will enable comprehensive studies on the independent evolution of truffles and ecological diversification in an economically important group of pezizalean fungi.
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Affiliation(s)
- Alden C Dirks
- Department of Ecology and Evolutionary Biology and University of Michigan Herbarium, University of Michigan, Ann Arbor, MI 48109, USA.
| | | | - Andrew N Miller
- Illinois Natural History Survey, University of Illinois Urbana-Champaign, Champaign, IL 61820, USA
| | - Michelle Orozco-Quime
- Department of Ecology and Evolutionary Biology and University of Michigan Herbarium, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sundy Maurice
- Department of Biosciences, University of Oslo, Blindernveien 31 0316, Oslo, Norway
| | - Gregory Bonito
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
| | - Judson Van Wyk
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
| | - Steven Ahrendt
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Alan Kuo
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - William Andreopoulos
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Robert Riley
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Anna Lipzen
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Mansi Chovatia
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Emily Savage
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kerrie Barry
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Alexander J Bradshaw
- Natural History Museum of Utah and School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Francis M Martin
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE-GrandEst-Nancy, Champenoux, France
| | - A Elizabeth Arnold
- Department of Ecology and Evolutionary Biology, Bio5 Institute, and Gilbertson Mycological Herbarium, University of Arizona, Tucson, AZ 85719, USA
| | - Timothy Y James
- Department of Ecology and Evolutionary Biology and University of Michigan Herbarium, University of Michigan, Ann Arbor, MI 48109, USA
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Steindorff AS, Aguilar-Pontes MV, Robinson AJ, Andreopoulos B, LaButti K, Kuo A, Mondo S, Riley R, Otillar R, Haridas S, Lipzen A, Grimwood J, Schmutz J, Clum A, Reid ID, Moisan MC, Butler G, Nguyen TTM, Dewar K, Conant G, Drula E, Henrissat B, Hansel C, Singer S, Hutchinson MI, de Vries RP, Natvig DO, Powell AJ, Tsang A, Grigoriev IV. Comparative genomic analysis of thermophilic fungi reveals convergent evolutionary adaptations and gene losses. Commun Biol 2024; 7:1124. [PMID: 39266695 PMCID: PMC11393059 DOI: 10.1038/s42003-024-06681-w] [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: 04/11/2024] [Accepted: 08/05/2024] [Indexed: 09/14/2024] Open
Abstract
Thermophily is a trait scattered across the fungal tree of life, with its highest prevalence within three fungal families (Chaetomiaceae, Thermoascaceae, and Trichocomaceae), as well as some members of the phylum Mucoromycota. We examined 37 thermophilic and thermotolerant species and 42 mesophilic species for this study and identified thermophily as the ancestral state of all three prominent families of thermophilic fungi. Thermophilic fungal genomes were found to encode various thermostable enzymes, including carbohydrate-active enzymes such as endoxylanases, which are useful for many industrial applications. At the same time, the overall gene counts, especially in gene families responsible for microbial defense such as secondary metabolism, are reduced in thermophiles compared to mesophiles. We also found a reduction in the core genome size of thermophiles in both the Chaetomiaceae family and the Eurotiomycetes class. The Gene Ontology terms lost in thermophilic fungi include primary metabolism, transporters, UV response, and O-methyltransferases. Comparative genomics analysis also revealed higher GC content in the third base of codons (GC3) and a lower effective number of codons in fungal thermophiles than in both thermotolerant and mesophilic fungi. Furthermore, using the Support Vector Machine classifier, we identified several Pfam domains capable of discriminating between genomes of thermophiles and mesophiles with 94% accuracy. Using AlphaFold2 to predict protein structures of endoxylanases (GH10), we built a similarity network based on the structures. We found that the number of disulfide bonds appears important for protein structure, and the network clusters based on protein structures correlate with the optimal activity temperature. Thus, comparative genomics offers new insights into the biology, adaptation, and evolutionary history of thermophilic fungi while providing a parts list for bioengineering applications.
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Affiliation(s)
- Andrei S Steindorff
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Maria Victoria Aguilar-Pontes
- Centre for Structural and Functional Genomics, Concordia University, Montreal, QC, Canada
- Departamento de Genética, University of Córdoba, 14071, Córdoba, Spain
| | | | - Bill Andreopoulos
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Kurt LaButti
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Alan Kuo
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Stephen Mondo
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Robert Riley
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Robert Otillar
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Sajeet Haridas
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jane Grimwood
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Jeremy Schmutz
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Alicia Clum
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- National Microbiome Data Collaborative, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ian D Reid
- Centre for Structural and Functional Genomics, Concordia University, Montreal, QC, Canada
| | - Marie-Claude Moisan
- Centre for Structural and Functional Genomics, Concordia University, Montreal, QC, Canada
| | - Gregory Butler
- Centre for Structural and Functional Genomics, Concordia University, Montreal, QC, Canada
| | - Thi Truc Minh Nguyen
- Centre for Structural and Functional Genomics, Concordia University, Montreal, QC, Canada
| | - Ken Dewar
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Gavin Conant
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Elodie Drula
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix Marseille Université, Marseille, France
| | - Bernard Henrissat
- DTU Bioengineering, Technical University of Denmark, 2800 Kgs, Lyngby, Denmark
| | | | - Steven Singer
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, the Netherlands
| | - Donald O Natvig
- Department of Biology, The University of New Mexico, Albuquerque, NM, USA
| | - Amy J Powell
- Systems Design and Architecture, Sandia National Laboratories, Albuquerque, NM, 87123, USA
| | - Adrian Tsang
- Centre for Structural and Functional Genomics, Concordia University, Montreal, QC, Canada
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA.
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Charria-Girón E, Zeng H, Gorelik TE, Pahl A, Truong KN, Schrey H, Surup F, Marin-Felix Y. Arcopilins: A New Family of Staphylococcus aureus Biofilm Disruptors from the Soil Fungus Arcopilus navicularis. J Med Chem 2024; 67:15029-15040. [PMID: 39141525 PMCID: PMC11403616 DOI: 10.1021/acs.jmedchem.4c00585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2024]
Abstract
Biofilms represent a key challenge in the treatment of microbial infections; for instance, Staphylococcus aureus causes chronic or fatal infections by forming biofilms on medical devices. Herein, the fungus Arcopilus navicularis was found to produce a novel family of PKS-NRPS metabolites that are able to disrupt preformed biofilms of S. aureus. Arcopilins A-F (1-6), tetramic acids, and arcopilin G (7), a 2-pyridone, were elucidated using HR-ESI-MS and one-dimensional (1D) and two-dimensional (2D) nuclear magnetic resonance (NMR) spectroscopy. Their absolute configuration was established by the synthesis of MPTA-esters for 2, analysis of 1H-1H coupling constants, and ROESY correlations, along with comparison with the crystal structure of 7. Arcopilin A (1) not only effectively disrupts preformed biofilms of S. aureus but also potentiates the activity of gentamicin and vancomycin up to 115- and 31-fold times, respectively. Our findings demonstrate the potential application of arcopilins for the conjugated treatment of infections caused by S. aureus with antibiotics unable to disrupt preformed biofilms.
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Affiliation(s)
- Esteban Charria-Girón
- Department Microbial Drugs, Helmholtz Centre for Infection Research (HZI), German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Inhoffenstrasse 7, 38124 Braunschweig, Germany
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Haoxuan Zeng
- Department Microbial Drugs, Helmholtz Centre for Infection Research (HZI), German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Inhoffenstrasse 7, 38124 Braunschweig, Germany
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Tatiana E Gorelik
- Department Structure and Function of Proteins, Helmholtz Centre for Infection Research (HZI), Inhoffenstrasse 7, 38124 Braunschweig, Germany
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Campus E8.1, 66123 Saarbrücken, Germany
| | - Alexandra Pahl
- Department Microbial Drugs, Helmholtz Centre for Infection Research (HZI), German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Khai-Nghi Truong
- Rigaku Europe SE, Hugenottenallee 167, 63263 Neu-Isenburg, Germany
| | - Hedda Schrey
- Department Microbial Drugs, Helmholtz Centre for Infection Research (HZI), German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Inhoffenstrasse 7, 38124 Braunschweig, Germany
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Frank Surup
- Department Microbial Drugs, Helmholtz Centre for Infection Research (HZI), German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Inhoffenstrasse 7, 38124 Braunschweig, Germany
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Yasmina Marin-Felix
- Department Microbial Drugs, Helmholtz Centre for Infection Research (HZI), German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Inhoffenstrasse 7, 38124 Braunschweig, Germany
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Braunschweig, Germany
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Luo J, Walsh E, Faulborn A, Gao K, White J, Zhang N. Pinibarreniales, a new order of Sordariomycetes from pine barrens ecosystem. Mycologia 2024; 116:835-847. [PMID: 38959129 DOI: 10.1080/00275514.2024.2363084] [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: 02/22/2024] [Accepted: 05/30/2024] [Indexed: 07/05/2024]
Abstract
Pinibarrenia chlamydospora, sp. nov. isolated from the roots of highbush blueberry in the New Jersey Pine Barrens, is described and illustrated. Based on multigene phylogenetic analysis, as well as morphological and ecological characteristics, Pinibarreniales and Pinibarreniaceae are established to accommodate this novel lineage in Sordariomycetidae, Sordariomycetes. Pinibarreniales, Tracyllalales, and Vermiculariopsiellales are proposed to be included in the subclass Sordariomycetidae. Pinibarreniales likely have a wide distribution and forms association with Ericaceae plants that live in acidic and oligotrophic environments because its DNA barcode matches with environmental sequences from other independent ecological studies. The plant-fungal interaction experiment revealed negative impacts on Arabidopsis, indicating its pathogenicity. This uncovered new fungal lineage will contribute to a better understanding of the diversity and systematics of Sordariomycetes.
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Affiliation(s)
- Jing Luo
- Department of Plant Biology, Rutgers University, 59 Dudley Road, New Brunswick, New Jersey 08901
| | - Emily Walsh
- Department of Plant Biology, Rutgers University, 59 Dudley Road, New Brunswick, New Jersey 08901
| | - Alexis Faulborn
- Department of Plant Biology, Rutgers University, 59 Dudley Road, New Brunswick, New Jersey 08901
| | - Kevin Gao
- Department of Plant Biology, Rutgers University, 59 Dudley Road, New Brunswick, New Jersey 08901
| | - James White
- Department of Plant Biology, Rutgers University, 59 Dudley Road, New Brunswick, New Jersey 08901
| | - Ning Zhang
- Department of Plant Biology, Rutgers University, 59 Dudley Road, New Brunswick, New Jersey 08901
- Department of Biochemistry and Microbiology, Rutgers University, 76 Lipman Drive, New Brunswick, New Jersey 08901
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Clavé C, Dheur S, Ament-Velásquez SL, Granger-Farbos A, Saupe SJ. het-B allorecognition in Podospora anserina is determined by pseudo-allelic interaction of genes encoding a HET and lectin fold domain protein and a PII-like protein. PLoS Genet 2024; 20:e1011114. [PMID: 38346076 PMCID: PMC10890737 DOI: 10.1371/journal.pgen.1011114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/23/2024] [Accepted: 01/29/2024] [Indexed: 02/25/2024] Open
Abstract
Filamentous fungi display allorecognition genes that trigger regulated cell death (RCD) when strains of unlike genotype fuse. Podospora anserina is one of several model species for the study of this allorecognition process termed heterokaryon or vegetative incompatibility. Incompatibility restricts transmission of mycoviruses between isolates. In P. anserina, genetic analyses have identified nine incompatibility loci, termed het loci. Here we set out to clone the genes controlling het-B incompatibility. het-B displays two incompatible alleles, het-B1 and het-B2. We find that the het-B locus encompasses two adjacent genes, Bh and Bp that exist as highly divergent allelic variants (Bh1/Bh2 and Bp1/Bp2) in the incompatible haplotypes. Bh encodes a protein with an N-terminal HET domain, a cell death inducing domain bearing homology to Toll/interleukin-1 receptor (TIR) domains and a C-terminal domain with a predicted lectin fold. The Bp product is homologous to PII-like proteins, a family of small trimeric proteins acting as sensors of adenine nucleotides in bacteria. We show that although the het-B system appears genetically allelic, incompatibility is in fact determined by the non-allelic Bh1/Bp2 interaction while the reciprocal Bh2/Bp1 interaction plays no role in incompatibility. The highly divergent C-terminal lectin fold domain of BH determines recognition specificity. Population studies and genome analyses indicate that het-B is under balancing selection with trans-species polymorphism, highlighting the evolutionary significance of the two incompatible haplotypes. In addition to emphasizing anew the central role of TIR-like HET domains in fungal RCD, this study identifies novel players in fungal allorecognition and completes the characterization of the entire het gene set in that species.
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Affiliation(s)
- Corinne Clavé
- IBGC, UMR 5095, CNRS-Université de Bordeaux, Bordeaux, France
| | - Sonia Dheur
- IBGC, UMR 5095, CNRS-Université de Bordeaux, Bordeaux, France
| | | | | | - Sven J. Saupe
- IBGC, UMR 5095, CNRS-Université de Bordeaux, Bordeaux, France
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