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Földi C, Merényi Z, Balázs B, Csernetics Á, Miklovics N, Wu H, Hegedüs B, Virágh M, Hou Z, Liu XB, Galgóczy L, Nagy LG. Snowball: a novel gene family required for developmental patterning of fruiting bodies of mushroom-forming fungi (Agaricomycetes). mSystems 2024; 9:e0120823. [PMID: 38334416 PMCID: PMC10949477 DOI: 10.1128/msystems.01208-23] [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: 11/10/2023] [Accepted: 01/10/2024] [Indexed: 02/10/2024] Open
Abstract
The morphogenesis of sexual fruiting bodies of fungi is a complex process determined by a genetically encoded program. Fruiting bodies reached the highest complexity levels in the Agaricomycetes; yet, the underlying genetics is currently poorly known. In this work, we functionally characterized a highly conserved gene termed snb1, whose expression level increases rapidly during fruiting body initiation. According to phylogenetic analyses, orthologs of snb1 are present in almost all agaricomycetes and may represent a novel conserved gene family that plays a substantial role in fruiting body development. We disrupted snb1 using CRISPR/Cas9 in the agaricomycete model organism Coprinopsis cinerea. snb1 deletion mutants formed unique, snowball-shaped, rudimentary fruiting bodies that could not differentiate caps, stipes, and lamellae. We took advantage of this phenotype to study fruiting body differentiation using RNA-Seq analyses. This revealed differentially regulated genes and gene families that, based on wild-type RNA-Seq data, were upregulated early during development and showed tissue-specific expression, suggesting a potential role in differentiation. Taken together, the novel gene family of snb1 and the differentially expressed genes in the snb1 mutants provide valuable insights into the complex mechanisms underlying developmental patterning in the Agaricomycetes. IMPORTANCE Fruiting bodies of mushroom-forming fungi (Agaricomycetes) are complex multicellular structures, with a spatially and temporally integrated developmental program that is, however, currently poorly known. In this study, we present a novel, conserved gene family, Snowball (snb), termed after the unique, differentiation-less fruiting body morphology of snb1 knockout strains in the model mushroom Coprinopsis cinerea. snb is a gene of unknown function that is highly conserved among agaricomycetes and encodes a protein of unknown function. A comparative transcriptomic analysis of the early developmental stages of differentiated wild-type and non-differentiated mutant fruiting bodies revealed conserved differentially expressed genes which may be related to tissue differentiation and developmental patterning fruiting body development.
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Affiliation(s)
- Csenge Földi
- Synthetic and Systems Biology Unit, Institute of Biochemistry, HUN-REN Biological Research Center, Szeged, Hungary
- Doctoral School of Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Zsolt Merényi
- Synthetic and Systems Biology Unit, Institute of Biochemistry, HUN-REN Biological Research Center, Szeged, Hungary
| | - Bálint Balázs
- Synthetic and Systems Biology Unit, Institute of Biochemistry, HUN-REN Biological Research Center, Szeged, Hungary
| | - Árpád Csernetics
- Synthetic and Systems Biology Unit, Institute of Biochemistry, HUN-REN Biological Research Center, Szeged, Hungary
| | - Nikolett Miklovics
- Synthetic and Systems Biology Unit, Institute of Biochemistry, HUN-REN Biological Research Center, Szeged, Hungary
| | - Hongli Wu
- Synthetic and Systems Biology Unit, Institute of Biochemistry, HUN-REN Biological Research Center, Szeged, Hungary
| | - Botond Hegedüs
- Synthetic and Systems Biology Unit, Institute of Biochemistry, HUN-REN Biological Research Center, Szeged, Hungary
| | - Máté Virágh
- Synthetic and Systems Biology Unit, Institute of Biochemistry, HUN-REN Biological Research Center, Szeged, Hungary
| | - Zhihao Hou
- Synthetic and Systems Biology Unit, Institute of Biochemistry, HUN-REN Biological Research Center, Szeged, Hungary
| | - Xiao-Bin Liu
- Synthetic and Systems Biology Unit, Institute of Biochemistry, HUN-REN Biological Research Center, Szeged, Hungary
| | - László Galgóczy
- Synthetic and Systems Biology Unit, Institute of Biochemistry, HUN-REN Biological Research Center, Szeged, Hungary
- Department of Biotechnology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - László G. Nagy
- Synthetic and Systems Biology Unit, Institute of Biochemistry, HUN-REN Biological Research Center, Szeged, Hungary
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Sagini JPN, Ligabue-Braun R. Fungal heat shock proteins: molecular phylogenetic insights into the host takeover. THE SCIENCE OF NATURE - NATURWISSENSCHAFTEN 2024; 111:16. [PMID: 38483597 DOI: 10.1007/s00114-024-01903-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 02/26/2024] [Accepted: 02/29/2024] [Indexed: 03/19/2024]
Abstract
Heat shock proteins are constitutively expressed chaperones induced by cellular stress, such as changes in temperature, pH, and osmolarity. These proteins, present in all organisms, are highly conserved and are recruited for the assembly of protein complexes, transport, and compartmentalization of molecules. In fungi, these proteins are related to their adaptation to the environment, their evolutionary success in acquiring new hosts, and regulation of virulence and resistance factors. These characteristics are interesting for assessment of the host adaptability and ecological transitions, given the emergence of infections by these microorganisms. Based on phylogenetic inferences, we compared the sequences of HSP9, HSP12, HSP30, HSP40, HSP70, HSP90, and HSP110 to elucidate the evolutionary relationships of different fungal organisms to suggest evolutionary patterns employing the maximum likelihood method. By the different reconstructions, our inference supports the hypothesis that these classes of proteins are associated with pathogenic gains against endothermic hosts, as well as adaptations for phytopathogenic fungi.
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Affiliation(s)
- João Pedro Nunes Sagini
- Graduate Program in Biological Sciences (PPGBio), Federal University of Health Sciences of Porto Alegre (UFCSPA), Sarmento Leite, 245, Porto Alegre, 90050-170, Brazil.
| | - Rodrigo Ligabue-Braun
- Graduate Program in Biological Sciences (PPGBio), Federal University of Health Sciences of Porto Alegre (UFCSPA), Sarmento Leite, 245, Porto Alegre, 90050-170, Brazil
- Department of Pharmacosciences, Federal University of Health Sciences of Porto Alegre (UFCSPA), Sarmento Leite, 245, Porto Alegre, 90050-170, Brazil
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3
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Merényi Z, Krizsán K, Sahu N, Liu XB, Bálint B, Stajich JE, Spatafora JW, Nagy LG. Genomes of fungi and relatives reveal delayed loss of ancestral gene families and evolution of key fungal traits. Nat Ecol Evol 2023; 7:1221-1231. [PMID: 37349567 PMCID: PMC10406608 DOI: 10.1038/s41559-023-02095-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 05/11/2023] [Indexed: 06/24/2023]
Abstract
Fungi are ecologically important heterotrophs that have radiated into most niches on Earth and fulfil key ecological services. Despite intense interest in their origins, major genomic trends of their evolutionary route from a unicellular opisthokont ancestor to derived multicellular fungi remain poorly known. Here we provide a highly resolved genome-wide catalogue of gene family changes across fungal evolution inferred from the genomes of 123 fungi and relatives. We show that a dominant trend in early fungal evolution has been the gradual shedding of protist genes and the punctuated emergence of innovation by two main gene duplication events. We find that the gene content of non-Dikarya fungi resembles that of unicellular opisthokonts in many respects, owing to the conservation of protist genes in their genomes. The most rapidly duplicating gene groups included extracellular proteins and transcription factors, as well as ones linked to the coordination of nutrient uptake with growth, highlighting the transition to a sessile osmotrophic feeding strategy and subsequent lifestyle evolution as important elements of early fungal history. These results suggest that the genomes of pre-fungal ancestors evolved into the typical filamentous fungal genome by a combination of gradual gene loss, turnover and several large duplication events rather than by abrupt changes. Consequently, the taxonomically defined Fungi represents a genomically non-uniform assemblage of species.
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Affiliation(s)
- Zsolt Merényi
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Krisztina Krizsán
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
- Institute of Forensic Genetics, Hungarian Institute for Forensic Sciences, Budapest, Hungary
| | - Neha Sahu
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Xiao-Bin Liu
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Balázs Bálint
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Jason E Stajich
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA, USA
| | - Joseph W Spatafora
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - László G Nagy
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Szeged, Hungary.
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4
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Liu S, Zhou JL, Song J, Sun YF, Dai YC, Cui BK. Climacocystaceae fam. nov. and Gloeoporellaceae fam. nov., two new families of Polyporales (Basidiomycota). Front Microbiol 2023; 14:1115761. [PMID: 36819032 PMCID: PMC9935835 DOI: 10.3389/fmicb.2023.1115761] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 01/11/2023] [Indexed: 02/05/2023] Open
Abstract
Polyporales is a diverse group of Agaricomycetes including more than 2,500 species belonging to 255 genera and 18 families. Recently, many studies focused on the classification of Polyporales, but the familial placements of some taxa remain uncertain. In this study, two new families, Climacocystaceae and Gloeoporellaceae of Polyporales, are proposed based on morphological characters and molecular data. Phylogenetic analyses of the two new families are inferred from the DNA sequences of the internal transcribed spacer regions (ITS), the large subunit of nuclear ribosomal RNA gene (nLSU), the largest subunit of RNA polymerase II gene (RPB1), the second largest subunit of RNA polymerase II gene (RPB2), and the translation elongation factor 1-α gene (TEF1). Furthermore, the divergence time of Polyporales was estimated as an additional taxonomic criterion based on the conserved regions of five DNA fragments (5.8S, nLSU, RPB1, RPB2, and TEF1). Bayesian evolutionary analysis revealed that the ancestor of Polyporales splits with a mean stem age of 136.53 Mya with a 95% highest posterior density (HPD) of 118.08-158.06 Mya. The mean stem ages of the families within Polyporales originated between 66.02 and 119.22 Mya, of which Climacocystaceae occurred in a mean stem age of 77.49 Mya with a 95% HPD of 61.45-93.16 Mya, and Gloeoporellaceae occurred in a mean stem age of 88.06 Mya with a 95% HPD of 67.15-107.76 Mya.
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Affiliation(s)
- Shun Liu
- School of Ecology and Nature Conservation, Institute of Microbiology, Beijing Forestry University, Beijing, China
| | - Jun-Liang Zhou
- International Exchange and Cooperation Department, Kunming University, Kunming, Yunnan, China
| | - Jie Song
- Department of Horticulture and Food, Guangdong Eco-Engineering Polytechnic, Guangzhou, China
| | - Yi-Fei Sun
- School of Ecology and Nature Conservation, Institute of Microbiology, Beijing Forestry University, Beijing, China
| | - Yu-Cheng Dai
- School of Ecology and Nature Conservation, Institute of Microbiology, Beijing Forestry University, Beijing, China
| | - Bao-Kai Cui
- School of Ecology and Nature Conservation, Institute of Microbiology, Beijing Forestry University, Beijing, China,*Correspondence: Bao-Kai Cui,
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5
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Roik A, Reverter M, Pogoreutz C. A roadmap to understanding diversity and function of coral reef-associated fungi. FEMS Microbiol Rev 2022; 46:6615459. [PMID: 35746877 PMCID: PMC9629503 DOI: 10.1093/femsre/fuac028] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/01/2022] [Accepted: 06/14/2022] [Indexed: 01/09/2023] Open
Abstract
Tropical coral reefs are hotspots of marine productivity, owing to the association of reef-building corals with endosymbiotic algae and metabolically diverse bacterial communities. However, the functional importance of fungi, well-known for their contribution to shaping terrestrial ecosystems and global nutrient cycles, remains underexplored on coral reefs. We here conceptualize how fungal functional traits may have facilitated the spread, diversification, and ecological adaptation of marine fungi on coral reefs. We propose that functions of reef-associated fungi may be diverse and go beyond their hitherto described roles of pathogens and bioeroders, including but not limited to reef-scale biogeochemical cycles and the structuring of coral-associated and environmental microbiomes via chemical mediation. Recent technological and conceptual advances will allow the elucidation of the physiological, ecological, and chemical contributions of understudied marine fungi to coral holobiont and reef ecosystem functioning and health and may help provide an outlook for reef management actions.
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Affiliation(s)
- Anna Roik
- Corresponding author: Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Ammerländer Heerstrasse 231, D-26129 Oldenburg, Germany. E-mail:
| | - Miriam Reverter
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Wilhelmshaven, 26046, Germany,School of Biological and Marine Sciences, University of Plymouth, Plymouth PL4 8AA, United Kingdom
| | - Claudia Pogoreutz
- Corresponding author: Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Federale de Lausanne (EPFL), 1015 Lausanne, Switzerland.,
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6
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Liu S, Song CG, Xu TM, Ji X, Wu DM, Cui BK. Species Diversity, Molecular Phylogeny, and Ecological Habits of Fomitopsis (Polyporales, Basidiomycota). Front Microbiol 2022; 13:859411. [PMID: 35464982 PMCID: PMC9019680 DOI: 10.3389/fmicb.2022.859411] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 02/21/2022] [Indexed: 11/30/2022] Open
Abstract
Fomitopsis is a worldwide brown-rot fungal genus of Polyporales, which grows on different gymnosperm and angiosperm trees and has important ecological functions and economic values. In this study, species diversity, phylogenetic relationships, and ecological habits of Fomitopsis were investigated. A total of 195 specimens from 24 countries representing 29 species of Fomitopsis were studied. Based on the morphological characters and phylogenetic evidence of DNA sequences including the internal transcribed spacer (ITS) regions, the large subunit of nuclear ribosomal RNA gene (nLSU), the small subunit of nuclear ribosomal RNA gene (nSSU), the small subunit of mitochondrial rRNA gene (mtSSU), the translation elongation factor 1-α gene (TEF), and the second subunit of RNA polymerase II (RPB2), 30 species are accepted in Fomitopsis, including four new species: F. resupinata, F. srilankensis, F. submeliae and F. yimengensis. Illustrated descriptions of the novel species and the geographical locations of the Fomitopsis species are provided.
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Affiliation(s)
- Shun Liu
- School of Ecology and Nature Conservation, Institute of Microbiology, Beijing Forestry University, Beijing, China
| | - Chang-Ge Song
- School of Ecology and Nature Conservation, Institute of Microbiology, Beijing Forestry University, Beijing, China
| | - Tai-Min Xu
- School of Ecology and Nature Conservation, Institute of Microbiology, Beijing Forestry University, Beijing, China
| | - Xing Ji
- School of Ecology and Nature Conservation, Institute of Microbiology, Beijing Forestry University, Beijing, China
| | - Dong-Mei Wu
- Xinjiang Production and Construction Group Key Laboratory of Crop Germplasm Enhancement and Gene Resources Utilization, Biotechnology Research Institute, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Bao-Kai Cui
- School of Ecology and Nature Conservation, Institute of Microbiology, Beijing Forestry University, Beijing, China
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7
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Kuhar F, Terzzoli L, Nouhra E, Robledo G, Mercker M. Pattern formation features might explain homoplasy: fertile surfaces in higher fungi as an example. Theory Biosci 2022; 141:1-11. [PMID: 35174438 DOI: 10.1007/s12064-022-00363-z] [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: 03/20/2021] [Accepted: 01/20/2022] [Indexed: 11/25/2022]
Abstract
Fungi show a high degree of morphological convergence. Regarded for a long time as an obstacle for phylogenetic studies, homoplasy has also been proposed as a source of information about underlying morphogenetic patterning mechanisms. The "local-activation and long-range inhibition principle" (LALIP), underlying the famous reaction-diffusion model proposed by Alan Turing in 1952, appears to be one of the universal phenomena that can explain the ontogenetic origin of seriate patterns in living organisms. Reproductive structures of fungi in the class Agaricomycetes show a highly periodic structure resulting in, for example, poroid, odontoid, lamellate or labyrinthic hymenophores. In this paper, we claim that self-organized patterns might underlie the basic ontogenetic processes of these structures. Simulations based on LALIP-driven models and covering a wide range of parameters show an absolute mutual correspondence with the morphospace explored by extant agaricomycetes. This could not only explain geometric particularities but could also account for the limited possibilities displayed by hymenial configurations, thus making homoplasy a direct consequence of the limited morphospace resulting from the proposed patterning dynamics.
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Affiliation(s)
- Francisco Kuhar
- Instituto Multidisciplinario de Biología Vegetal (CONICET-UNC), Universidad Nacional de Córdoba, Av. Vélez Sársfield 1611 CC. 4955000, Córdoba, Argentina.
| | - Leticia Terzzoli
- Instituto Multidisciplinario de Biología Vegetal (CONICET-UNC), Universidad Nacional de Córdoba, Av. Vélez Sársfield 1611 CC. 4955000, Córdoba, Argentina
| | - Eduardo Nouhra
- Instituto Multidisciplinario de Biología Vegetal (CONICET-UNC), Universidad Nacional de Córdoba, Av. Vélez Sársfield 1611 CC. 4955000, Córdoba, Argentina
| | - Gerardo Robledo
- Facultad de Ciencias Agropecuarias BioTecA3 - Centro de Biotecnología Aplicada Al Agro Y Alimentos, Universidad Nacionel de Córdoba, Ing. Agr. Félix Aldo Marrone 746, CC509 - CP 5000, Córdoba, Argentina.,CONICET, Consejo Nacional de Investigaciones Científicas Y Técnicas, Godoy Cruz 2290, (C1425FQB), CABA, Argentina
| | - Moritz Mercker
- Institute of Applied Mathematics (IAM), Heidelberg University, Im Neuenheimer Feld 205, 69120, Heidelberg, Germany
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8
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Krah FS, Hagge J, Schreiber J, Brandl R, Müller J, Bässler C. Fungal fruit body assemblages are tougher in harsh microclimates. Sci Rep 2022; 12:1633. [PMID: 35102234 PMCID: PMC8803873 DOI: 10.1038/s41598-022-05715-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 01/13/2022] [Indexed: 11/16/2022] Open
Abstract
Forest species are affected by macroclimate, however, the microclimatic variability can be more extreme and change through climate change. Fungal fruiting community composition was affected by microclimatic differences. Here we ask whether differences in the fruiting community can be explained by morphological traits of the fruit body, which may help endure harsh conditions. We used a dead wood experiment and macrofungal fruit body size, color, and toughness. We exposed logs of two host tree species under closed and experimentally opened forest canopies in a random-block design for four years and identified all visible fruit bodies of two fungal lineages (Basidio- and Ascomycota). We found a consistently higher proportion of tough-fleshed species in harsher microclimates under open canopies. Although significant, responses of community fruit body size and color lightness were inconsistent across lineages. We suggest the toughness-protection hypothesis, stating that tough-fleshed fruit bodies protect from microclimatic extremes by reducing dehydration. Our study suggests that the predicted increase of microclimatic harshness with climate change will likely decrease the presence of soft-fleshed fruit bodies. Whether harsh microclimates also affect the mycelium of macrofungi with different fruit body morphology would complement our findings and increase predictability under climate change.
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Affiliation(s)
- Franz-Sebastian Krah
- Faculty of Biological Sciences, Institute for Ecology, Evolution and Diversity, Conservation Biology, Goethe University Frankfurt, Frankfurt am Main, Germany.
| | - Jonas Hagge
- Forest Nature Conservation, Northwest German Forest Research Institute, Hann. Münden, Germany
- Forest Nature Conservation, Georg-August-University Göttingen, Göttingen, Germany
| | - Jasper Schreiber
- Faculty of Biological Sciences, Institute for Ecology, Evolution and Diversity, Conservation Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Roland Brandl
- Department of Ecology, Philips University of Marburg, Marburg, Germany
| | - Jörg Müller
- Department of Animal Ecology and Tropical Biology, University of Würzburg, Würzburg, Germany
- Bavarian Forest National Park, Grafenau, Germany
| | - Claus Bässler
- Faculty of Biological Sciences, Institute for Ecology, Evolution and Diversity, Conservation Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Bavarian Forest National Park, Grafenau, Germany
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9
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Wang XW, May TW, Liu SL, Zhou LW. Towards a Natural Classification of Hyphodontia Sensu Lato and the Trait Evolution of Basidiocarps within Hymenochaetales ( Basidiomycota). J Fungi (Basel) 2021; 7:jof7060478. [PMID: 34204800 PMCID: PMC8231612 DOI: 10.3390/jof7060478] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/08/2021] [Accepted: 06/09/2021] [Indexed: 11/16/2022] Open
Abstract
Hyphodontia sensu lato, belonging to Hymenochaetales, accommodates corticioid wood-inhabiting basidiomycetous fungi with resupinate basidiocarps and diverse hymenophoral characters. Species diversity of Hyphodontia sensu lato has been extensively explored worldwide, but in previous studies the six accepted genera in Hyphodontia sensu lato, viz. Fasciodontia, Hastodontia, Hyphodontia, Kneiffiella, Lyomyces and Xylodon were not all strongly supported from a phylogenetic perspective. Moreover, the relationships among these six genera in Hyphodontia sensu lato and other lineages within Hymenochaetales are not clear. In this study, we performed comprehensive phylogenetic analyses on the basis of multiple loci. For the first time, the independence of each of the six genera receives strong phylogenetic support. The six genera are separated in four clades within Hymenochaetales: Fasciodontia, Lyomyces and Xylodon are accepted as members of a previously known family Schizoporaceae, Kneiffiella and Hyphodontia are, respectively, placed in two monotypic families, viz. a previous name Chaetoporellaceae and a newly introduced name Hyphodontiaceae, and Hastodontia is considered to be a genus with an uncertain taxonomic position at the family rank within Hymenochaetales. The three families emerged between 61.51 and 195.87 million years ago. Compared to other families in the Hymenochaetales, these ages are more or less similar to those of Coltriciaceae, Hymenochaetaceae and Oxyporaceae, but much older than those of the two families Neoantrodiellaceae and Nigrofomitaceae. In regard to species, two, one, three and 10 species are newly described from Hyphodontia, Kneiffiella, Lyomyces and Xylodon, respectively. The taxonomic status of additional 30 species names from these four genera is briefly discussed; an epitype is designated for X. australis. The resupinate habit and poroid hymenophoral configuration were evaluated as the ancestral state of basidiocarps within Hymenochaetales. The resupinate habit mainly remains, while the hymenophoral configuration mainly evolves to the grandinioid-odontioid state and also back to the poroid state at the family level. Generally, a taxonomic framework for Hymenochaetales with an emphasis on members belonging to Hyphodontia sensu lato is constructed, and trait evolution of basidiocarps within Hymenochaetales is revealed accordingly.
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Affiliation(s)
- Xue-Wei Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (X.-W.W.); (S.-L.L.)
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tom W. May
- Royal Botanic Gardens Victoria, Birdwood Avenue, Melbourne 3004, Australia;
| | - Shi-Liang Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (X.-W.W.); (S.-L.L.)
| | - Li-Wei Zhou
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (X.-W.W.); (S.-L.L.)
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
- Correspondence:
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10
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Blackstone NW, Gutterman JU. Can natural selection and druggable targets synergize? Of nutrient scarcity, cancer, and the evolution of cooperation. Bioessays 2020; 43:e2000160. [PMID: 33165962 DOI: 10.1002/bies.202000160] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 10/03/2020] [Accepted: 10/06/2020] [Indexed: 01/21/2023]
Abstract
Since the dawn of molecular biology, cancer therapy has focused on druggable targets. Despite some remarkable successes, cell-level evolution remains a potent antagonist to this approach. We suggest that a deeper understanding of the breakdown of cooperation can synergize the evolutionary and druggable-targets approaches. Complexity requires cooperation, whether between cells of different species (symbiosis) or between cells of the same organism (multicellularity). Both forms of cooperation may be associated with nutrient scarcity, which in turn may be associated with a chemiosmotic metabolism. A variety of examples from modern organisms supports these generalities. Indeed, mammalian cancers-unicellular, glycolytic, and fast-replicating-parallel these examples. Nutrient scarcity, chemiosmosis, and associated signaling may favor cooperation, while under conditions of nutrient abundance a fermentative metabolism may signal the breakdown of cooperation. Manipulating this metabolic milieu may potentiate the effects of targeted therapeutics. Specific opportunities are discussed in this regard, including avicins, a novel plant product.
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Affiliation(s)
- Neil W Blackstone
- Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois, USA
| | - Jordan U Gutterman
- Department of Leukemia, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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11
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Lücking R, Aime MC, Robbertse B, Miller AN, Ariyawansa HA, Aoki T, Cardinali G, Crous PW, Druzhinina IS, Geiser DM, Hawksworth DL, Hyde KD, Irinyi L, Jeewon R, Johnston PR, Kirk PM, Malosso E, May TW, Meyer W, Öpik M, Robert V, Stadler M, Thines M, Vu D, Yurkov AM, Zhang N, Schoch CL. Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding? IMA Fungus 2020; 11:14. [PMID: 32714773 PMCID: PMC7353689 DOI: 10.1186/s43008-020-00033-z] [Citation(s) in RCA: 182] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
True fungi (Fungi) and fungus-like organisms (e.g. Mycetozoa, Oomycota) constitute the second largest group of organisms based on global richness estimates, with around 3 million predicted species. Compared to plants and animals, fungi have simple body plans with often morphologically and ecologically obscure structures. This poses challenges for accurate and precise identifications. Here we provide a conceptual framework for the identification of fungi, encouraging the approach of integrative (polyphasic) taxonomy for species delimitation, i.e. the combination of genealogy (phylogeny), phenotype (including autecology), and reproductive biology (when feasible). This allows objective evaluation of diagnostic characters, either phenotypic or molecular or both. Verification of identifications is crucial but often neglected. Because of clade-specific evolutionary histories, there is currently no single tool for the identification of fungi, although DNA barcoding using the internal transcribed spacer (ITS) remains a first diagnosis, particularly in metabarcoding studies. Secondary DNA barcodes are increasingly implemented for groups where ITS does not provide sufficient precision. Issues of pairwise sequence similarity-based identifications and OTU clustering are discussed, and multiple sequence alignment-based phylogenetic approaches with subsequent verification are recommended as more accurate alternatives. In metabarcoding approaches, the trade-off between speed and accuracy and precision of molecular identifications must be carefully considered. Intragenomic variation of the ITS and other barcoding markers should be properly documented, as phylotype diversity is not necessarily a proxy of species richness. Important strategies to improve molecular identification of fungi are: (1) broadly document intraspecific and intragenomic variation of barcoding markers; (2) substantially expand sequence repositories, focusing on undersampled clades and missing taxa; (3) improve curation of sequence labels in primary repositories and substantially increase the number of sequences based on verified material; (4) link sequence data to digital information of voucher specimens including imagery. In parallel, technological improvements to genome sequencing offer promising alternatives to DNA barcoding in the future. Despite the prevalence of DNA-based fungal taxonomy, phenotype-based approaches remain an important strategy to catalog the global diversity of fungi and establish initial species hypotheses.
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Affiliation(s)
- Robert Lücking
- Botanischer Garten und Botanisches Museum, Freie Universität Berlin, Königin-Luise-Straße 6–8, 14195 Berlin, Germany
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
| | - M. Catherine Aime
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907 USA
| | - Barbara Robbertse
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD 20892 USA
| | - Andrew N. Miller
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Illinois Natural History Survey, University of Illinois, 1816 South Oak Street, Champaign, IL 61820-6970 USA
| | - Hiran A. Ariyawansa
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Department of Plant Pathology and Microbiology, College of Bio-Resources and Agriculture, National Taiwan University, Taipe City, Taiwan
| | - Takayuki Aoki
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- National Agriculture and Food Research Organization, Genetic Resources Center, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan
| | - Gianluigi Cardinali
- Department Pharmaceutical Sciences, University of Perugia, Via Borgo 20 Giugno, 74, Perugia, Italy
| | - Pedro W. Crous
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Wageningen University and Research Centre (WUR), Laboratory of Phytopathology, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Irina S. Druzhinina
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Microbiology and Applied Genomics Group, Research Area Biochemical Technology, Institute of Chemical, Environmental & Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - David M. Geiser
- Department of Plant Pathology & Environmental Microbiology, The Pennsylvania State University, University Park, PA 16802 USA
| | - David L. Hawksworth
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD UK
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Surrey, TW9 3DS UK
- Geography and Environment, University of Southampton, Southampton, SO17 1BJ UK
- Jilin Agricultural University, Changchun, 130118 Jilin Province China
| | - Kevin D. Hyde
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, 650201 Yunnan China
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100 Thailand
- World Agroforestry Centre, East and Central Asia, Kunming, 650201 Yunnan China
- Mushroom Research Foundation, 128 M.3 Ban Pa Deng T. Pa Pae, A. Mae Taeng, Chiang Rai, 50150 Thailand
| | - Laszlo Irinyi
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Hospital (Research and Education Network), Westmead Institute for Medical Research, Sydney, NSW Australia
| | - Rajesh Jeewon
- Department of Health Sciences, Faculty of Science, University of Mauritius, Reduit, Mauritius
| | - Peter R. Johnston
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Manaaki Whenua – Landcare Research, Private Bag 92170, Auckland, 1142 New Zealand
| | | | - Elaine Malosso
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Universidade Federal de Pernambuco, Centro de Biociências, Departamento de Micologia, Laboratório de Hifomicetos de Folhedo, Avenida da Engenharia, s/n Cidade Universitária, Recife, PE 50.740-600 Brazil
| | - Tom W. May
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Royal Botanic Gardens Victoria, Birdwood Avenue, Melbourne, Victoria 3004 Australia
| | - Wieland Meyer
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Hospital (Research and Education Network), Westmead Institute for Medical Research, Sydney, NSW Australia
| | - Maarja Öpik
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- University of Tartu, 40 Lai Street, 51 005 Tartu, Estonia
| | - Vincent Robert
- Department Pharmaceutical Sciences, University of Perugia, Via Borgo 20 Giugno, 74, Perugia, Italy
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Marc Stadler
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Department Microbial Drugs, Helmholtz Centre for Infection Research, and German Centre for Infection Research (DZIF), partner site Hannover-Braunschweig, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Marco Thines
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Straße 9, 60439 Frankfurt (Main); Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt (Main), Germany
| | - Duong Vu
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Andrey M. Yurkov
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Ning Zhang
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901 USA
| | - Conrad L. Schoch
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD 20892 USA
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12
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Zanne AE, Abarenkov K, Afkhami ME, Aguilar-Trigueros CA, Bates S, Bhatnagar JM, Busby PE, Christian N, Cornwell WK, Crowther TW, Flores-Moreno H, Floudas D, Gazis R, Hibbett D, Kennedy P, Lindner DL, Maynard DS, Milo AM, Nilsson RH, Powell J, Schildhauer M, Schilling J, Treseder KK. Fungal functional ecology: bringing a trait-based approach to plant-associated fungi. Biol Rev Camb Philos Soc 2019; 95:409-433. [PMID: 31763752 DOI: 10.1111/brv.12570] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 10/27/2019] [Accepted: 10/31/2019] [Indexed: 12/21/2022]
Abstract
Fungi play many essential roles in ecosystems. They facilitate plant access to nutrients and water, serve as decay agents that cycle carbon and nutrients through the soil, water and atmosphere, and are major regulators of macro-organismal populations. Although technological advances are improving the detection and identification of fungi, there still exist key gaps in our ecological knowledge of this kingdom, especially related to function. Trait-based approaches have been instrumental in strengthening our understanding of plant functional ecology and, as such, provide excellent models for deepening our understanding of fungal functional ecology in ways that complement insights gained from traditional and -omics-based techniques. In this review, we synthesize current knowledge of fungal functional ecology, taxonomy and systematics and introduce a novel database of fungal functional traits (FunFun ). FunFun is built to interface with other databases to explore and predict how fungal functional diversity varies by taxonomy, guild, and other evolutionary or ecological grouping variables. To highlight how a quantitative trait-based approach can provide new insights, we describe multiple targeted examples and end by suggesting next steps in the rapidly growing field of fungal functional ecology.
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Affiliation(s)
- Amy E Zanne
- Department of Biological Sciences, George Washington University, Washington, DC, 20052, U.S.A
| | - Kessy Abarenkov
- Natural History Museum, University of Tartu, Vanemuise 46, Tartu, 51014, Estonia
| | - Michelle E Afkhami
- Department of Biology, University of Miami, Coral Gables, FL, 33146, U.S.A
| | - Carlos A Aguilar-Trigueros
- Freie Universität-Berlin, Berlin-Brandenburg Institute of Advanced Biodiversity Research, 14195, Berlin, Germany
| | - Scott Bates
- Department of Biological Sciences, Purdue University Northwest, Westville, IN, 46391, U.S.A
| | | | - Posy E Busby
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97330, U.S.A
| | - Natalie Christian
- Department of Plant Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, U.S.A.,Department of Biology, University of Louisville, Louisville, KY 40208, U.S.A
| | - William K Cornwell
- Evolution & Ecology Research Centre, School of Biological Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - Thomas W Crowther
- Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zürich, 8092, Zürich, Switzerland
| | - Habacuc Flores-Moreno
- Department of Ecology, Evolution, and Behavior, and Department of Forest Resources, University of Minnesota, St. Paul, MN, 55108, U.S.A
| | - Dimitrios Floudas
- Microbial Ecology Group, Department of Biology, Lund University, Lund, Sweden
| | - Romina Gazis
- Department of Plant Pathology, Tropical Research & Education Center, University of Florida, Homestead, FL, 33031, U.S.A
| | - David Hibbett
- Biology Department, Clark University, Worcester, MA, 01610, U.S.A
| | - Peter Kennedy
- Plant & Microbial Biology, University of Minnesota, St. Paul, MN, 55108, U.S.A
| | - Daniel L Lindner
- US Forest Service, Northern Research Station, Center for Forest Mycology Research, Madison, Wisconsin, WI, 53726, U.S.A
| | - Daniel S Maynard
- Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zürich, 8092, Zürich, Switzerland
| | - Amy M Milo
- Department of Biological Sciences, George Washington University, Washington, DC, 20052, U.S.A
| | - Rolf Henrik Nilsson
- University of Gothenburg, Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, Box 461, 405 30, Göteborg, Sweden
| | - Jeff Powell
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, 2751, Australia
| | - Mark Schildhauer
- National Center for Ecological Analysis and Synthesis, 735 State Street, Suite 300, Santa Barbara, CA, 93101, U.S.A
| | - Jonathan Schilling
- Plant & Microbial Biology, University of Minnesota, St. Paul, MN, 55108, U.S.A
| | - Kathleen K Treseder
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, 92697, U.S.A
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13
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Comparative genomics reveals the origin of fungal hyphae and multicellularity. Nat Commun 2019; 10:4080. [PMID: 31501435 PMCID: PMC6733946 DOI: 10.1038/s41467-019-12085-w] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 08/20/2019] [Indexed: 02/01/2023] Open
Abstract
Hyphae represent a hallmark structure of multicellular fungi. The evolutionary origins of hyphae and of the underlying genes are, however, hardly known. By systematically analyzing 72 complete genomes, we here show that hyphae evolved early in fungal evolution probably via diverse genetic changes, including co-option and exaptation of ancient eukaryotic (e.g. phagocytosis-related) genes, the origin of new gene families, gene duplications and alterations of gene structure, among others. Contrary to most multicellular lineages, the origin of filamentous fungi did not correlate with expansions of kinases, receptors or adhesive proteins. Co-option was probably the dominant mechanism for recruiting genes for hypha morphogenesis, while gene duplication was apparently less prevalent, except in transcriptional regulators and cell wall - related genes. We identified 414 novel gene families that show correlated evolution with hyphae and that may have contributed to its evolution. Our results suggest that hyphae represent a unique multicellular organization that evolved by limited fungal-specific innovations and gene duplication but pervasive co-option and modification of ancient eukaryotic functions.
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14
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Krah FS, Büntgen U, Schaefer H, Müller J, Andrew C, Boddy L, Diez J, Egli S, Freckleton R, Gange AC, Halvorsen R, Heegaard E, Heideroth A, Heibl C, Heilmann-Clausen J, Høiland K, Kar R, Kauserud H, Kirk PM, Kuyper TW, Krisai-Greilhuber I, Norden J, Papastefanou P, Senn-Irlet B, Bässler C. European mushroom assemblages are darker in cold climates. Nat Commun 2019; 10:2890. [PMID: 31253790 PMCID: PMC6599080 DOI: 10.1038/s41467-019-10767-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 05/30/2019] [Indexed: 12/22/2022] Open
Abstract
Thermal melanism theory states that dark-colored ectotherm organisms are at an advantage at low temperature due to increased warming. This theory is generally supported for ectotherm animals, however, the function of colors in the fungal kingdom is largely unknown. Here, we test whether the color lightness of mushroom assemblages is related to climate using a dataset of 3.2 million observations of 3,054 species across Europe. Consistent with the thermal melanism theory, mushroom assemblages are significantly darker in areas with cold climates. We further show differences in color phenotype between fungal lifestyles and a lifestyle differentiated response to seasonality. These results indicate a more complex ecological role of mushroom colors and suggest functions beyond thermal adaption. Because fungi play a crucial role in terrestrial carbon and nutrient cycles, understanding the links between the thermal environment, functional coloration and species' geographical distributions will be critical in predicting ecosystem responses to global warming.
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Affiliation(s)
- Franz-Sebastian Krah
- Plant Biodiversity Research Group, Department of Ecology & Ecosystem Management, Technische Universität München, 85354, Freising, Germany.
- Bavarian Forest National Park, 94481, Grafenau, Germany.
| | - Ulf Büntgen
- Department of Geography, University of Cambridge, Cambridge, CB2 3EN, UK
- Research Unit Biodiversity & Conservation Biology, Swiss Federal Research Institute WSL, 8903, Birmensdorf, Switzerland
- Global Change Research Centre and Masaryk University, 61300, Brno, Czech Republic
| | - Hanno Schaefer
- Plant Biodiversity Research Group, Department of Ecology & Ecosystem Management, Technische Universität München, 85354, Freising, Germany
| | - Jörg Müller
- Bavarian Forest National Park, 94481, Grafenau, Germany
- Field Station Fabrikschleichach, Department of Animal Ecology and Tropical Biology, Biocenter University of Würzburg, 96181, Rauhenebrach, Germany
| | - Carrie Andrew
- Norwegian Institute for Nature Research, Gaustadalléen 21, NO-0349, Oslo, Norway
| | - Lynne Boddy
- School of Biosciences, Cardiff University, Cardiff, CF10 3AX, UK
| | - Jeffrey Diez
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Simon Egli
- Research Unit Biodiversity & Conservation Biology, Swiss Federal Research Institute WSL, 8903, Birmensdorf, Switzerland
| | - Robert Freckleton
- Department of Animal & Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Alan C Gange
- School of Biological Sciences, Royal Holloway, University of London, Egham, Surrey, TW20 0EX, UK
| | - Rune Halvorsen
- Natural History Museum, University of Oslo, Blindern, 0318, Oslo, Norway
| | - Einar Heegaard
- Norwegian Institute of Bioeconomy Research, 5244, Fana, Norway
| | - Antje Heideroth
- Bavarian Forest National Park, 94481, Grafenau, Germany
- Ecology Research Group, Department of Biology, Philipps Uuniversity Marburg, 35043, Marburg, Germany
| | | | - Jacob Heilmann-Clausen
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Klaus Høiland
- Norwegian Institute for Nature Research, Gaustadalléen 21, NO-0349, Oslo, Norway
| | - Ritwika Kar
- Centre for Plant Molecular Biology, Developmental Genetics, University of Tübingen, 72076, Tuebingen, Germany
| | - Håvard Kauserud
- Norwegian Institute for Nature Research, Gaustadalléen 21, NO-0349, Oslo, Norway
| | - Paul M Kirk
- Mycology Section, Jodrell Laboratory, Royal Botanic Gardens Kew, Surrey, TW9 3DS, UK
| | - Thomas W Kuyper
- Department of Soil Quality, Wageningen University, 6700 AA, Wageningen, The Netherlands
| | - Irmgard Krisai-Greilhuber
- Division of Systematic and Evolutionary Botany, Department of Botany and Biodiversity Research, University of Vienna, 1030, Vienna, Austria
| | - Jenni Norden
- Norwegian Institute for Nature Research, Gaustadalléen 21, NO-0349, Oslo, Norway
| | - Phillip Papastefanou
- TUM School of Life Sciences Weihenstephan, Land Surface-Atmosphere Interactions, Technical University of Munich, 85354, Freising, Germany
| | - Beatrice Senn-Irlet
- Research Unit Biodiversity & Conservation Biology, Swiss Federal Research Institute WSL, 8903, Birmensdorf, Switzerland
| | - Claus Bässler
- Bavarian Forest National Park, 94481, Grafenau, Germany.
- Technical University of Munich, Chair for Terrestrial Ecology, 85354, Freising, Germany.
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15
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Abstract
Ubiquitin ligases (E3s) are basic components of the eukaryotic ubiquitination system. In this work, the emergence and diversification of fungal HECT ubiquitin ligases is described. Phylogenetic and structural data indicate that six HECT subfamilies (RSP5, TOM1, UFD4, HUL4, HUL4A and HUL5) existed in the common ancestor of all fungi. These six subfamilies have evolved very conservatively, with only occasional losses and duplications in particular fungal lineages. However, an early, drastic reduction in the number of HECT genes occurred in microsporidians, in parallel to the reduction of their genomes. A significant correlation between the total number of genes and the number of HECT-encoding genes present in fungi has been observed. However, transitions from unicellularity to multicellularity or vice versa apparently had no effect on the evolution of this family. Likely orthologs or co-orthologs of all fungal HECT genes have been detected in animals. Four genes are deduced to be present in the common ancestor of fungi, animals and plants. Protein-protein interactions detected in both the yeast Saccharomyces cerevisiae and humans suggest that some ancient functions of HECT proteins have been conserved since the animals/fungi split.
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16
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McGee CF. Microbial ecology of the Agaricus bisporus mushroom cropping process. Appl Microbiol Biotechnol 2017; 102:1075-1083. [PMID: 29222576 DOI: 10.1007/s00253-017-8683-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 11/28/2017] [Accepted: 11/29/2017] [Indexed: 10/18/2022]
Abstract
Agaricus bisporus is the most widely cultivated mushroom species in the world. Cultivation is commenced by inoculating beds of semi-pasteurised composted organic substrate with a pure spawn of A. bisporus. The A. bisporus mycelium subsequently colonises the composted substrate by degrading the organic material to release nutrients. A layer of peat, often called "casing soil", is laid upon the surface of the composted substrate to induce the development of the mushroom crop and maintain compost environmental conditions. Extensive research has been conducted investigating the biochemistry and genetics of A. bisporus throughout the cultivation process; however, little is currently known about the wider microbial ecology that co-inhabits the composted substrate and casing layers. The compost and casing microbial communities are known to play important roles in the mushroom production process. Microbial species present in the compost and casing are known for (1) being an important source of nitrogen for the A. bisporus mycelium, (2) releasing sugar residues through the degradation of the wheat straw in the composted substrate, (3) playing a critical role in inducing development of the A. bisporus fruiting bodies and (4) acting as pathogens by parasitising the mushroom mycelium/crop. Despite a long history of research into the mushroom cropping process, an extensive review of the microbial communities present in the compost and casing has not as of yet been undertaken. The aim of this review is to provide a comprehensive summary of the literature investigating the compost and casing microbial communities throughout cultivation of the A. bisporus mushroom crop.
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Affiliation(s)
- Conor F McGee
- Department of Agriculture, Food and the Marine, Celbridge, Co. Kildare, Ireland.
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