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Marian IM, Valdes ID, Hayes RD, LaButti K, Duffy K, Chovatia M, Johnson J, Ng V, Lugones LG, Wösten HAB, Grigoriev IV, Ohm RA. High phenotypic and genotypic plasticity among strains of the mushroom-forming fungus Schizophyllum commune. Fungal Genet Biol 2024; 173:103913. [PMID: 39004162 DOI: 10.1016/j.fgb.2024.103913] [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: 02/22/2024] [Revised: 07/08/2024] [Accepted: 07/11/2024] [Indexed: 07/16/2024]
Abstract
Schizophyllum commune is a mushroom-forming fungus notable for its distinctive fruiting bodies with split gills. It is used as a model organism to study mushroom development, lignocellulose degradation and mating type loci. It is a hypervariable species with considerable genetic and phenotypic diversity between the strains. In this study, we systematically phenotyped 16 dikaryotic strains for aspects of mushroom development and 18 monokaryotic strains for lignocellulose degradation. There was considerable heterogeneity among the strains regarding these phenotypes. The majority of the strains developed mushrooms with varying morphologies, although some strains only grew vegetatively under the tested conditions. Growth on various carbon sources showed strain-specific profiles. The genomes of seven monokaryotic strains were sequenced and analyzed together with six previously published genome sequences. Moreover, the related species Schizophyllum fasciatum was sequenced. Although there was considerable genetic variation between the genome assemblies, the genes related to mushroom formation and lignocellulose degradation were well conserved. These sequenced genomes, in combination with the high phenotypic diversity, will provide a solid basis for functional genomics analyses of the strains of S. commune.
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Affiliation(s)
- Ioana M Marian
- Microbiology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Ivan D Valdes
- Microbiology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Richard D Hayes
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kurt LaButti
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kecia Duffy
- 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
| | - Jenifer Johnson
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Vivian Ng
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Luis G Lugones
- Microbiology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Han A B Wösten
- Microbiology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - 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
| | - Robin A Ohm
- Microbiology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
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2
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Olou BA, Hègbè ADMT, Piepenbring M, Yorou NS. Genetic diversity and population differentiation in Earliella scabrosa, a pantropical species of Polyporales. Sci Rep 2023; 13:23020. [PMID: 38155211 PMCID: PMC10754928 DOI: 10.1038/s41598-023-50398-5] [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: 07/05/2023] [Accepted: 12/19/2023] [Indexed: 12/30/2023] Open
Abstract
Earliella scabrosa is a pantropical species of Polyporales (Basidiomycota) and well-studied concerning its morphology and taxonomy. However, its pantropical intraspecific genetic diversity and population differentiation is unknown. We initiated this study to better understand the genetic variation within E. scabrosa and to test if cryptic species are present. Sequences of three DNA regions, the nuclear ribosomal internal transcribed spacer (ITS), the large subunit ribosomal DNA (LSU), and the translation elongation factor (EF1α) were analysed for 66 samples from 15 geographical locations. We found a high level of genetic diversity (haplotype diversity, Hd = 0.88) and low nucleotide diversity (π = 0.006) across the known geographical range of E. scabrosa based on ITS sequences. The analysis of molecular variance (AMOVA) indicates that the genetic variability is mainly found among geographical populations. The results of Mantel tests confirmed that the genetic distance among populations of E. scabrosa is positively correlated with the geographical distance, which indicates that geographical isolation is an important factor for the observed genetic differentiation. Based on phylogenetic analyses of combined dataset ITS-LSU-EF1α, the low intraspecific divergences (0-0.3%), and the Automated Barcode Gap Discovery (ABGD) analysis, E. scabrosa can be considered as a single species with five different geographical populations. Each population might be in the process of allopatric divergence and in the long-term they may evolve and become distinct species.
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Affiliation(s)
- Boris Armel Olou
- Research Unit Tropical Mycology and Plant-Soil Fungi Interactions (MyTIPS), Faculty of Agronomy, University of Parakou, BP 123, Parakou, Benin.
| | - Apollon D M T Hègbè
- Research Unit Tropical Mycology and Plant-Soil Fungi Interactions (MyTIPS), Faculty of Agronomy, University of Parakou, BP 123, Parakou, Benin
| | - Meike Piepenbring
- Mycology Research Group, Faculty of Biological Sciences, Goethe University Frankfurt am Main, Biologicum, Max-von-Laue-Str. 13, 60438, Frankfurt am Main, Germany
| | - Nourou Soulemane Yorou
- Research Unit Tropical Mycology and Plant-Soil Fungi Interactions (MyTIPS), Faculty of Agronomy, University of Parakou, BP 123, Parakou, Benin
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3
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James TY. Sex Without Sexes: Can the Cost of Finding a Mate Explain Diversity in Fungal Mating Systems? Integr Comp Biol 2023; 63:922-935. [PMID: 37218718 DOI: 10.1093/icb/icad037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/14/2023] [Accepted: 05/17/2023] [Indexed: 05/24/2023] Open
Abstract
Eukaryotes have evolved myriad ways of uniting gametes during sexual reproduction. A repeated pattern is the convergent evolution of a mating system with the fusion of larger gametes with smaller gametes (anisogamy) from that of fusion between morphologically identical gametes (isogamy). In anisogamous species, sexes are defined as individuals that produce only one gamete type. Although sexes abound throughout Eukarya, in fungi there are no biological sexes, because even in anisogamous species, individuals are hermaphroditic and produce both gamete types. For this reason, the term mating types is preferred over sexes, and, thus defined, only individuals of differing mating types can mate (homoallelic incompatibility). In anisogamous fungal species, there is scant evidence that there are more than two mating types, and this may be linked to genetic constraints, such as the use of mating types to determine the inheritance of cytoplasmic genomes. However, the mushroom fungi (Agaricomycetes) stand out as having both large numbers of mating types within a species, which will allow nearly all individuals to be compatible with each other, and reciprocal exchange of nuclei during mating, which will avoid cytoplasmic mixing and cyto-nuclear conflicts. Although the limitation of mating types to two in most fungi is consistent with the cyto-nuclear conflicts model, there are many facets of the Agaricomycete life cycle that also suggest they will demand a high outbreeding efficiency. Specifically, they are mostly obligately sexual and outcrossing, inhabit complex competitive niches, and display broadcast spore dispersal. Subsequently, the Agaricomycete individual pays a high cost to being choosy when encountering a mate. Here, I discuss the costs of mate finding and choice and demonstrate how most fungi have multiple ways of reducing these costs, which can explain why mating types are mostly limited to two per species. Nevertheless, it is perplexing that fungi have not evolved multiple mating types on more occasions nor evolved sexes. The few exceptions to these rules suggest that it is dictated by both molecular and evolutionary constraints.
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Affiliation(s)
- Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
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4
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Abstract
Within the next decade, the genomes of 1.8 million eukaryotic species will be sequenced. Identifying genes in these sequences is essential to understand the biology of the species. This is challenging due to the transcriptional complexity of eukaryotic genomes, which encode hundreds of thousands of transcripts of multiple types. Among these, a small set of protein-coding mRNAs play a disproportionately large role in defining phenotypes. Due to their sequence conservation, orthology can be established, making it possible to define the universal catalog of eukaryotic protein-coding genes. This catalog should substantially contribute to uncovering the genomic events underlying the emergence of eukaryotic phenotypes. This piece briefly reviews the basics of protein-coding gene prediction, discusses challenges in finalizing annotation of the human genome, and proposes strategies for producing annotations across the eukaryotic Tree of Life. This lays the groundwork for obtaining the catalog of all genes-the Earth's code of life.
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Affiliation(s)
- Roderic Guigó
- Bioinformatics and Genomics, Center for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Dr. Aiguader 88, 08003 Barcelona, Catalonia
- Universitat Pompeu Fabra (UPF), Barcelona, Catalonia
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5
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Liang J, Li Y, Dodds PN, Figueroa M, Sperschneider J, Han S, Tsui CKM, Zhang K, Li L, Ma Z, Cai L. Haplotype-phased and chromosome-level genome assembly of Puccinia polysora, a giga-scale fungal pathogen causing southern corn rust. Mol Ecol Resour 2023; 23:601-620. [PMID: 36403246 DOI: 10.1111/1755-0998.13739] [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: 05/30/2022] [Revised: 11/16/2022] [Accepted: 11/17/2022] [Indexed: 11/21/2022]
Abstract
Rust fungi are characterized by large genomes with high repeat content and have two haploid nuclei in most life stages, which makes achieving high-quality genome assemblies challenging. Here, we described a pipeline using HiFi reads and Hi-C data to assemble a gigabase-sized fungal pathogen, Puccinia polysora f.sp. zeae, to haplotype-phased and chromosome-scale. The final assembled genome is 1.71 Gbp, with ~850 Mbp and 18 chromosomes in each haplotype, being currently one of the two giga-scale fungi assembled to chromosome level. Transcript-based annotation identified 47,512 genes for the dikaryotic genome with a similar number for each haplotype. A high level of interhaplotype variation was found with 10% haplotype-specific BUSCO genes, 5.8 SNPs/kbp, and structural variation accounting for 3% of the genome size. The P. polysora genome displayed over 85% repeat contents, with genome-size expansion and copy number increasing of species-specific orthogroups. Interestingly, these features did not affect overall synteny with other Puccinia species having smaller genomes. Fine-time-point transcriptomics revealed seven clusters of coexpressed secreted proteins that are conserved between two haplotypes. The fact that candidate effectors interspersed with all genes indicated the absence of a "two-speed genome" evolution in P. polysora. Genome resequencing of 79 additional isolates revealed a clonal population structure of P. polysora in China with low geographic differentiation. Nevertheless, a minor population differentiated from the major population by having mutations on secreted proteins including AvrRppC, indicating the ongoing virulence to evade recognition by RppC, a major resistance gene in Chinese corn cultivars. The high-quality assembly provides valuable genomic resources for future studies on disease management and the evolution of P. polysora.
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Affiliation(s)
- Junmin Liang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yuanjie Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Peter N Dodds
- Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Melania Figueroa
- Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Jana Sperschneider
- Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Shiling Han
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Clement K M Tsui
- Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,National Centre for Infectious Diseases, Tan Tock Seng Hospital, Singapore City, Singapore.,LKC School of Medicine, Nanyang Technological University, Singapore City, Singapore
| | - Keyu Zhang
- Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Leifu Li
- Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Zhanhong Ma
- Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Lei Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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Zhu Q, Lin Y, Lyu X, Qu Z, Lu Z, Fu Y, Cheng J, Xie J, Chen T, Li B, Cheng H, Chen W, Jiang D. Fungal Strains with Identical Genomes Were Found at a Distance of 2000 Kilometers after 40 Years. J Fungi (Basel) 2022; 8:1212. [PMID: 36422033 PMCID: PMC9697809 DOI: 10.3390/jof8111212] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 10/26/2022] [Accepted: 11/11/2022] [Indexed: 11/26/2023] Open
Abstract
Heredity and variation are inherent characteristics of species and are mainly reflected in the stability and variation of the genome; the former is relative, while the latter is continuous. However, whether life has both stable genomes and extremely diverse genomes at the same time is unknown. In this study, we isolated Sclerotinia sclerotiorum strains from sclerotium samples in Quincy, Washington State, USA, and found that four single-sclerotium-isolation strains (PB4, PB273, PB615, and PB623) had almost identical genomes to the reference strain 1980 isolated in the west of Nebraska 40 years ago. The genome of strain PB4 sequenced by the next-generation sequencing (NGS) and Pacific Biosciences (PacBio) sequencing carried only 135 single nucleotide polymorphisms (SNPs) and 18 structural variations (SVs) compared with the genome of strain 1980 and 48 SNPs were distributed on Contig_20. Based on data generated by NGS, three other strains, PB273, PB615, and PB623, had 256, 275, and 262 SNPs, respectively, against strain 1980, which were much less than in strain PB4 (532 SNPs) and none of them occurred on Contig_20, suggesting much closer genomes to strain 1980 than to strain PB4. All other strains from America and China are rich in SNPs with a range of 34,391-77,618 when compared with strain 1980. We also found that there were 39-79 SNPs between strain PB4 and its sexual offspring, 53.1% of which also occurred on Contig_20. Our discoveries show that there are two types of genomes in S. sclerotiorum, one is very stable and the other tends to change constantly. Investigating the mechanism of such genome stability will enhance our understanding of heredity and variation.
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Affiliation(s)
- Qili Zhu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yang Lin
- Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xueliang Lyu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Zheng Qu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ziyang Lu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yanping Fu
- Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiasen Cheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiatao Xie
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Tao Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Bo Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Hui Cheng
- Xinyang Academy of Agricultural Sciences, Xinyang 464000, China
| | - Weidong Chen
- United States Department of Agriculture, Agricultural Research Service, Washington State University, Pullman, WA 99164, USA
| | - Daohong Jiang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
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7
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Abstract
We discuss the genetic, demographic, and selective forces that are likely to be at play in restricting observed levels of DNA sequence variation in natural populations to a much smaller range of values than would be expected from the distribution of census population sizes alone-Lewontin's Paradox. While several processes that have previously been strongly emphasized must be involved, including the effects of direct selection and genetic hitchhiking, it seems unlikely that they are sufficient to explain this observation without contributions from other factors. We highlight a potentially important role for the less-appreciated contribution of population size change; specifically, the likelihood that many species and populations may be quite far from reaching the relatively high equilibrium diversity values that would be expected given their current census sizes.
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Affiliation(s)
- Brian Charlesworth
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Jeffrey D Jensen
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
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8
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Liu X, Huang X, Chu C, Xu H, Wang L, Xue Y, Arifeen Muhammad ZU, Inagaki F, Liu C. Genome, genetic evolution, and environmental adaptation mechanisms of Schizophyllum commune in deep subseafloor coal-bearing sediments. iScience 2022; 25:104417. [PMID: 35663011 PMCID: PMC9156946 DOI: 10.1016/j.isci.2022.104417] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 01/30/2022] [Accepted: 05/12/2022] [Indexed: 12/15/2022] Open
Abstract
To understand the genomic evolution and adaptation strategies of fungi to subseafloor sedimentary environments, we de novo assembled the genome of Schizophyllum commune strain 20R-7-F01 isolated from ∼2.0 km-deep, ∼20-millionyearsago (Mya) coal-bearing sediments. Phylogenomics study revealed a differentiation time of 28-73 Mya between this strain and the terrestrial type-strain H4-8, in line with sediment age records. Comparative genome analyses showed that FunK1 protein kinase, NmrA family, and transposons in this strain are significantly expanded, possibly linking to the environmental adaptation and persistence in sediment for over millions of years. Re-sequencing study of 14 S. commune strains sampled from different habitats revealed that subseafloor strains have much lower nucleotide diversity, substitution rate, and homologous recombination rate than other strains, reflecting that the growth and/or reproduction of subseafloor strains are extremely slow. Our data provide new insights into the adaptation and long-term survival of the fungi in the subseafloor sedimentary biosphere.
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Affiliation(s)
- Xuan Liu
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210023, China
| | - Xin Huang
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210023, China
| | - Chen Chu
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210023, China
| | - Hui Xu
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210023, China
| | - Long Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210023, China
| | - Yarong Xue
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210023, China
| | | | - Fumio Inagaki
- Mantle Drilling Promotion Office, Institute for Marine-Earth Exploration and Engineering (MarE3), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokohama 236-0001, Japan
- Department of Earth Sciences, Graduate School of Science, Tohoku University, Sendai 980-8574, Japan
| | - Changhong Liu
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210023, China
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The Transcription Factor Roc1 Is a Key Regulator of Cellulose Degradation in the Wood-Decaying Mushroom
Schizophyllum commune. mBio 2022; 13:e0062822. [PMID: 35604096 PMCID: PMC9239231 DOI: 10.1128/mbio.00628-22] [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] [Indexed: 11/20/2022] Open
Abstract
Wood-degrading fungi in the phylum Basidiomycota play a crucial role in nutrient recycling by breaking down all components of wood. Fungi have evolved transcriptional networks that regulate expression of wood-degrading enzymes, allowing them to prioritize one nutrient source over another.
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10
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Stolyarova AV, Neretina TV, Zvyagina EA, Fedotova AV, Kondrashov A, Bazykin GA. Complex fitness landscape shapes variation in a hyperpolymorphic species. eLife 2022; 11:76073. [PMID: 35532122 PMCID: PMC9187340 DOI: 10.7554/elife.76073] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 05/09/2022] [Indexed: 11/13/2022] Open
Abstract
It is natural to assume that patterns of genetic variation in hyperpolymorphic species can reveal large-scale properties of the fitness landscape that are hard to detect by studying species with ordinary levels of genetic variation. Here, we study such patterns in a fungus Schizophyllum commune, the most polymorphic species known. Throughout the genome, short-range linkage disequilibrium (LD) caused by attraction of minor alleles is higher between pairs of nonsynonymous than of synonymous variants. This effect is especially pronounced for pairs of sites that are located within the same gene, especially if a large fraction of the gene is covered by haploblocks, genome segments where the gene pool consists of two highly divergent haplotypes, which is a signature of balancing selection. Haploblocks are usually shorter than 1000 nucleotides, and collectively cover about 10% of the S. commune genome. LD tends to be substantially higher for pairs of nonsynonymous variants encoding amino acids that interact within the protein. There is a substantial correlation between LDs at the same pairs of nonsynonymous mutations in the USA and the Russian populations. These patterns indicate that selection in S. commune involves positive epistasis due to compensatory interactions between nonsynonymous alleles. When less polymorphic species are studied, analogous patterns can be detected only through interspecific comparisons. Changes to DNA known as mutations may alter how the proteins and other components of a cell work, and thus play an important role in allowing living things to evolve new traits and abilities over many generations. Whether a mutation is beneficial or harmful may differ depending on the genetic background of the individual – that is, depending on other mutations present in other positions within the same gene – due to a phenomenon called epistasis. Epistasis is known to affect how various species accumulate differences in their DNA compared to each other over time. For example, a mutation that is rare in humans and known to cause disease may be widespread in other primates because its negative effect is canceled out by another mutation that is standard for these species but absent in humans. However, it remains unclear whether epistasis plays a significant part in shaping genetic differences between individuals of the same species. A type of fungus known as Schizophyllum commune lives on rotting wood and is found across the world. It is one of the most genetically diverse species currently known, so there is a higher chance of pairs of compensatory mutations occurring and persisting for a long time in S. commune than in most other species, providing a unique opportunity to study epistasis. Here, Stolyarova et al. studied two distinct populations of S. commune, one from the USA and one from Russia. The team found that – unlike in humans, flies and other less genetically diverse species – epistasis maintains combinations of mutations in S. commune that individually would be harmful to the fungus but together compensate for each other. For example, pairs of mutations affecting specific molecules known as amino acids – the building blocks of proteins – that physically interact with each other tended to be found together in the same individuals. One potential downside of having pairs of compensatory mutations in the genome is that when the organism reproduces, the process of making sex cells may split up these pairs so that harmful mutations are inherited without their partner mutations. Thus, epistasis may have helped shape the way S. commune and other genetically diverse species have evolved.
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Affiliation(s)
| | - Tatiana V Neretina
- Biological Faculty, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Elena A Zvyagina
- Biological Faculty, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Anna V Fedotova
- Skolkovo Institute of Science and Technology, Moscow, Russian Federation
| | - Alexey Kondrashov
- Department of Ecology and Evolutionary Biology, University of Michigan-Ann Arbor, Ann Arbor, United States
| | - Georgii A Bazykin
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Moscow, Russian Federation
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11
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van den Brandhof JG, Wösten HAB. Risk assessment of fungal materials. Fungal Biol Biotechnol 2022; 9:3. [PMID: 35209958 PMCID: PMC8876125 DOI: 10.1186/s40694-022-00134-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 02/18/2022] [Indexed: 12/12/2022] Open
Abstract
Sustainable fungal materials have a high potential to replace non-sustainable materials such as those used for packaging or as an alternative for leather and textile. The properties of fungal materials depend on the type of fungus and substrate, the growth conditions and post-treatment of the material. So far, fungal materials are mainly made with species from the phylum Basidiomycota, selected for the mechanical and physical properties they provide. However, for mycelium materials to be implemented in society on a large scale, selection of fungal species should also be based on a risk assessment of the potential to be pathogenic, form mycotoxins, attract insects, or become an invasive species. Moreover, production processes should be standardized to ensure reproducibility and safety of the product.
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Affiliation(s)
- Jeroen G van den Brandhof
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Han A B Wösten
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
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12
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van Brenk B, Wösten HAB. A screening method for decoloration of xenobiotic dyes by fungi. J Microbiol Methods 2021; 188:106301. [PMID: 34389364 DOI: 10.1016/j.mimet.2021.106301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/08/2021] [Accepted: 08/08/2021] [Indexed: 10/20/2022]
Abstract
Wood degrading fungi are often screened for their ability to degrade xenobiotics such as dyes. Dye decoloration by these fungi on solid media could until now only be assessed qualitatively. We here describe a fast quantitative method to screen for dye decoloration on such media. Decoloration of crystal violet (CV), malachite green (MG), orange G (OG), rose bengal (RB) and remazol brilliant blue R (RBBR) by 124 isolates of the basidiomycete Schizophyllum commune was quantified with a flatbed scanner and the CIE-L*a*b* model. Colour and intensity changes were calculated with the Euclidean distance formula. More than 10 strains showed high MG decoloration. Isolates 136, 140 and 213 showed superior CV decoloration, while OG was most effectively decolorized by isolates 183, 216 and 227. Six strains showed high RB decoloration with isolate 216 being superior. The latter strain was also highly active on RBBR together with isolates 177 and 227. Together, dye decoloration was highly variable between the 124 isolates but strain 216 showed high activity on 3 out of 5 dyes. The fast screening method described in this paper enables identification of strains effectively decolorizing dyes.
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Affiliation(s)
- Brigit van Brenk
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, the Netherlands
| | - Han A B Wösten
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, the Netherlands.
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13
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Pereira D, Oggenfuss U, McDonald BA, Croll D. Population genomics of transposable element activation in the highly repressive genome of an agricultural pathogen. Microb Genom 2021; 7:000540. [PMID: 34424154 PMCID: PMC8549362 DOI: 10.1099/mgen.0.000540] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 02/03/2021] [Indexed: 12/13/2022] Open
Abstract
The activity of transposable elements (TEs) can be an important driver of genetic diversity with TE-mediated mutations having a wide range of fitness consequences. To avoid deleterious effects of TE activity, some fungi have evolved highly sophisticated genomic defences to reduce TE proliferation across the genome. Repeat-induced point mutation (RIP) is a fungal-specific TE defence mechanism efficiently targeting duplicated sequences. The rapid accumulation of RIPs is expected to deactivate TEs over the course of a few generations. The evolutionary dynamics of TEs at the population level in a species with highly repressive genome defences is poorly understood. Here, we analyse 366 whole-genome sequences of Parastagonospora nodorum, a fungal pathogen of wheat with efficient RIP. A global population genomics analysis revealed high levels of genetic diversity and signs of frequent sexual recombination. Contrary to expectations for a species with RIP, we identified recent TE activity in multiple populations. The TE composition and copy numbers showed little divergence among global populations regardless of the demographic history. Miniature inverted-repeat transposable elements (MITEs) and terminal repeat retrotransposons in miniature (TRIMs) were largely underlying recent intra-species TE expansions. We inferred RIP footprints in individual TE families and found that recently active, high-copy TEs have possibly evaded genomic defences. We find no evidence that recent positive selection acted on TE-mediated mutations rather that purifying selection maintained new TE insertions at low insertion frequencies in populations. Our findings highlight the complex evolutionary equilibria established by the joint action of TE activity, selection and genomic repression.
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Affiliation(s)
- Danilo Pereira
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
- Present address: Max Planck Institute for Evolutionary Biology, August-Thienemann-Straße 2, D-24306 Plön, Germany
| | - Ursula Oggenfuss
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Bruce A. McDonald
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
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14
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Alm Rosenblad M, Abramova A, Lind U, Ólason P, Giacomello S, Nystedt B, Blomberg A. Genomic Characterization of the Barnacle Balanus improvisus Reveals Extreme Nucleotide Diversity in Coding Regions. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2021; 23:402-416. [PMID: 33931810 PMCID: PMC8270832 DOI: 10.1007/s10126-021-10033-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 04/05/2021] [Indexed: 05/11/2023]
Abstract
Barnacles are key marine crustaceans in several habitats, and they constitute a common practical problem by causing biofouling on man-made marine constructions and ships. Despite causing considerable ecological and economic impacts, there is a surprising void of basic genomic knowledge, and a barnacle reference genome is lacking. We here set out to characterize the genome of the bay barnacle Balanus improvisus (= Amphibalanus improvisus) based on short-read whole-genome sequencing and experimental genome size estimation. We show both experimentally (DNA staining and flow cytometry) and computationally (k-mer analysis) that B. improvisus has a haploid genome size of ~ 740 Mbp. A pilot genome assembly rendered a total assembly size of ~ 600 Mbp and was highly fragmented with an N50 of only 2.2 kbp. Further assembly-based and assembly-free analyses revealed that the very limited assembly contiguity is due to the B. improvisus genome having an extremely high nucleotide diversity (π) in coding regions (average π ≈ 5% and average π in fourfold degenerate sites ≈ 20%), and an overall high repeat content (at least 40%). We also report on high variation in the α-octopamine receptor OctA (average π = 3.6%), which might increase the risk that barnacle populations evolve resistance toward antifouling agents. The genomic features described here can help in planning for a future high-quality reference genome, which is urgently needed to properly explore and understand proteins of interest in barnacle biology and marine biotechnology and for developing better antifouling strategies.
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Affiliation(s)
- Magnus Alm Rosenblad
- Deparment of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg , Sweden
| | - Anna Abramova
- Deparment of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg , Sweden
| | - Ulrika Lind
- Deparment of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg , Sweden
| | - Páll Ólason
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Husargatan 3, 752 37, Uppsala, Sweden
| | - Stefania Giacomello
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Box 1031, 17121, Solna, Sweden
| | - Björn Nystedt
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Husargatan 3, 752 37, Uppsala, Sweden
| | - Anders Blomberg
- Deparment of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg , Sweden.
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15
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Stability across the Whole Nuclear Genome in the Presence and Absence of DNA Mismatch Repair. Cells 2021; 10:cells10051224. [PMID: 34067668 PMCID: PMC8156620 DOI: 10.3390/cells10051224] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/13/2021] [Accepted: 05/14/2021] [Indexed: 01/06/2023] Open
Abstract
We describe the contribution of DNA mismatch repair (MMR) to the stability of the eukaryotic nuclear genome as determined by whole-genome sequencing. To date, wild-type nuclear genome mutation rates are known for over 40 eukaryotic species, while measurements in mismatch repair-defective organisms are fewer in number and are concentrated on Saccharomyces cerevisiae and human tumors. Well-studied organisms include Drosophila melanogaster and Mus musculus, while less genetically tractable species include great apes and long-lived trees. A variety of techniques have been developed to gather mutation rates, either per generation or per cell division. Generational rates are described through whole-organism mutation accumulation experiments and through offspring–parent sequencing, or they have been identified by descent. Rates per somatic cell division have been estimated from cell line mutation accumulation experiments, from systemic variant allele frequencies, and from widely spaced samples with known cell divisions per unit of tissue growth. The latter methods are also used to estimate generational mutation rates for large organisms that lack dedicated germlines, such as trees and hyphal fungi. Mechanistic studies involving genetic manipulation of MMR genes prior to mutation rate determination are thus far confined to yeast, Arabidopsis thaliana, Caenorhabditis elegans, and one chicken cell line. A great deal of work in wild-type organisms has begun to establish a sound baseline, but far more work is needed to uncover the variety of MMR across eukaryotes. Nonetheless, the few MMR studies reported to date indicate that MMR contributes 100-fold or more to genome stability, and they have uncovered insights that would have been impossible to obtain using reporter gene assays.
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16
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Bezmenova AV, Zvyagina EA, Fedotova AV, Kasianov AS, Neretina TV, Penin AA, Bazykin GA, Kondrashov AS. Rapid Accumulation of Mutations in Growing Mycelia of a Hypervariable Fungus Schizophyllum commune. Mol Biol Evol 2021; 37:2279-2286. [PMID: 32243532 PMCID: PMC7403608 DOI: 10.1093/molbev/msaa083] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The basidiomycete Schizophyllum commune has the highest level of genetic polymorphism known among living organisms. In a previous study, it was also found to have a moderately high per-generation mutation rate of 2×10−8, likely contributing to its high polymorphism. However, this rate has been measured only in an experiment on Petri dishes, and it is unclear how it translates to natural populations. Here, we used an experimental design that measures the rate of accumulation of de novo mutations in a linearly growing mycelium. We show that S. commune accumulates mutations at a rate of 1.24×10−7 substitutions per nucleotide per meter of growth, or ∼2.04×10−11 per nucleotide per cell division. In contrast to what has been observed in a number of species with extensive vegetative growth, this rate does not decline in the course of propagation of a mycelium. As a result, even a moderate per-cell-division mutation rate in S. commune can translate into a very high per-generation mutation rate when the number of cell divisions between consecutive meiosis is large.
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Affiliation(s)
| | | | - Anna V Fedotova
- Center of Life Sciences, Skoltech, Moscow, Russia.,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Artem S Kasianov
- Kharkevich Institute for Information Transmission Problems, Moscow, Russia.,Vavilov Institute of General Genetics, Moscow, Russia
| | - Tatiana V Neretina
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.,Kharkevich Institute for Information Transmission Problems, Moscow, Russia.,N. A. Pertsov White Sea Biological Station, Lomonosov Moscow State University, Primorskiy, Russia
| | - Aleksey A Penin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.,Kharkevich Institute for Information Transmission Problems, Moscow, Russia
| | - Georgii A Bazykin
- Center of Life Sciences, Skoltech, Moscow, Russia.,Kharkevich Institute for Information Transmission Problems, Moscow, Russia
| | - Alexey S Kondrashov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.,Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI
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17
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Choi Y, Nguyen HTK, Lee TS, Kim JK, Choi J. Genetic Diversity and Dye-Decolorizing Spectrum of Schizophyllum commune Population. J Microbiol Biotechnol 2020; 30:1525-1535. [PMID: 32807761 PMCID: PMC9728380 DOI: 10.4014/jmb.2006.06049] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/10/2020] [Accepted: 08/11/2020] [Indexed: 12/15/2022]
Abstract
Synthetic dyes are widely used in various industries and their wastage causes severe environmental problems while being hazardous to human health, leading to the need for eco-friendly degradation techniques. The split-gill fungus Schizophyllum commune, which is found worldwide, has the potential to degrade all components of the lignocellulosic biomass and is a candidate for the treatment of synthetic dyes. A systematic molecular analysis of 75 Korean and 6 foreign S. commune strains has revealed the high genetic diversity of this population and its important contribution to the total diversity of S. commune. We examined the dye decolorization ability of this population and revealed 5 excellent strains that strongly decolorized 3 dyes: Crystal Violet, Congo Red and Methylene Blue. Finally, comparison of dye decolorization ability and the phylogenetic identification of these strains generalized their genetic and physiological diversity. This study provides an initial resource for physiological and genetic research projects as well as the bioremediation of textile dyes.
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Affiliation(s)
- Yongjun Choi
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 22012, Republic of Korea
| | - Ha Thi Kim Nguyen
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 22012, Republic of Korea
| | - Tae Soo Lee
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 22012, Republic of Korea
| | - Jae Kwang Kim
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 22012, Republic of Korea,Corresponding authors J.K.Kim Phone: +82-32-835-8241 Fax: +82-32-835-0763 E-mail:
| | - Jaehyuk Choi
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 22012, Republic of Korea,J.Choi Phone: +82-32-835-8242 Fax: +82-32-835-0763 E-mail:
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18
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Towards Genomic Criteria for Delineating Fungal Species. J Fungi (Basel) 2020; 6:jof6040246. [PMID: 33114441 PMCID: PMC7711752 DOI: 10.3390/jof6040246] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 10/15/2020] [Accepted: 10/23/2020] [Indexed: 02/06/2023] Open
Abstract
The discussion of fungal species delineation has yet to reach a consensus, despite the advancements in technology, which helped modernise traditional approaches. In particular, the phylogenetic species concept was one of the tools that has been used with considerable success across the fungal kingdom. The fast rise of fungal genomics provides an unprecedented opportunity to expand measuring the relatedness of fungal strains to the level of whole genomes. However, the use of genomic information in taxonomy has only just begun, and few methodological guidelines have been suggested so far. Here, a simple approach of computationally measuring genomic distances and their use as a standard for species delineation is investigated. A fixed threshold genomic distance calculated by the quick and easy-to-use tools Mash and Dashing proved to be an unexpectedly widely applicable and robust criterion for determining whether two genomes belong to the same or to different species. The accuracy of species delineation in an uncurated dataset of GenBank fungal genomes was close to 90%—and exceeded 90% with minimal curation. As expected, the discriminative power of this approach was lower at higher taxonomic ranks, but still significantly larger than zero. Simple instructions for calculation of a genomic distance between two genomes and species similarity thresholds at different k-mer sizes are suggested. The calculation of genomic distance is identified as a powerful approach for delineating fungal species and is proposed—not as the only criterion—but as an additional tool in the versatile toolbox of fungal taxonomy.
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19
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Wisselink M, Aanen DK, van ’t Padje A. The Longevity of Colonies of Fungus-Growing Termites and the Stability of the Symbiosis. INSECTS 2020; 11:E527. [PMID: 32823564 PMCID: PMC7469218 DOI: 10.3390/insects11080527] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/08/2020] [Accepted: 08/10/2020] [Indexed: 01/10/2023]
Abstract
The agricultural mutualistic symbiosis between macrotermitine termites and Termitomyces fungi is obligate for both partners. The termites provide a protective growth environment for the fungus by cultivating it inside their colony and providing it with foraged plant material. The termites use the fungus for plant substrate degradation, and the production of asexual fruiting bodies for nourishment and re-inoculation of the fungus garden. The termite colony can reach an age of up to several decades, during which time it is believed that a single fungal monoculture is asexually propagated by the offspring of a single founding royal pair. The termite-fungus mutualism has a long evolutionary history dating back more than 30 million years. Both on the time-scale of a termite colony lifespan and that of the mutualistic symbiosis, questions arise about stability. We address the physical stability of the mound, the termite colony and the monoculture fungal garden during a colony's lifetime. On the long-term evolutionary scale, we address the stability of the symbiosis, where horizontal transmission of the symbiotic fungus raises the question of how the mutualistic interaction between host and symbiont persists over generations.
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Affiliation(s)
| | - Duur K. Aanen
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands; (M.W.); (A.v.P.)
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20
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Czuppon P, Constable GWA. Invasion and Extinction Dynamics of Mating Types Under Facultative Sexual Reproduction. Genetics 2019; 213:567-580. [PMID: 31391266 PMCID: PMC6781889 DOI: 10.1534/genetics.119.302306] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 08/04/2019] [Indexed: 01/08/2023] Open
Abstract
In sexually reproducing isogamous species, syngamy between gametes is generally not indiscriminate, but rather restricted to occurring between complementary self-incompatible mating types. A longstanding question regards the evolutionary pressures that control the number of mating types observed in natural populations, which ranges from two to many thousands. Here, we describe a population genetic null model of this reproductive system, and derive expressions for the stationary probability distribution of the number of mating types, the establishment probability of a newly arising mating type, and the mean time to extinction of a resident type. Our results yield that the average rate of sexual reproduction in a population correlates positively with the expected number of mating types observed. We further show that the low number of mating types predicted in the rare-sex regime is primarily driven by low invasion probabilities of new mating type alleles, with established resident alleles being very stable over long evolutionary periods. Moreover, our model naturally exhibits varying selection strength dependent on the number of resident mating types. This results in higher extinction and lower invasion rates for an increasing number of residents.
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Affiliation(s)
- Peter Czuppon
- Center for Interdisciplinary Research in Biology, CNRS, Collège de France, PSL Research University, 75231 Paris, France
- Institute of Ecology and Environmental Sciences of Paris, Sorbonne Université, UPEC, CNRS, IRD, INRA, 75252 Paris, France
| | - George W A Constable
- Department of Mathematical Sciences, The University of Bath, BA2 7AY, United Kingdom
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21
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Maintenance of High Genome Integrity over Vegetative Growth in the Fairy-Ring Mushroom Marasmius oreades. Curr Biol 2019; 29:2758-2765.e6. [PMID: 31402298 DOI: 10.1016/j.cub.2019.07.025] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/25/2019] [Accepted: 07/09/2019] [Indexed: 01/06/2023]
Abstract
Most mutations in coding regions of the genome are deleterious, causing selection to favor mechanisms that minimize the mutational load over time [1-5]. DNA replication during cell division is a major source of new mutations. It is therefore important to limit the number of cell divisions between generations, particularly for large and long-lived organisms [6-9]. The germline cells of animals and the slowly dividing cells in plant meristems are adaptations to control the number of mutations that accumulate over generations [9-11]. Fungi lack a separated germline while harboring species with very large and long-lived individuals that appear to maintain highly stable genomes within their mycelia [8, 12, 13]. Here, we studied genomic mutation accumulation in the fairy-ring mushroom Marasmius oreades. We generated a chromosome-level genome assembly using a combination of cutting-edge DNA sequencing technologies and re-sequenced 40 samples originating from six individuals of this fungus. The low number of mutations recovered in the sequencing data suggests the presence of an unknown mechanism that works to maintain extraordinary genome integrity over vegetative growth in M. oreades. The highly structured growth pattern of M. oreades allowed us to estimate the number of cell divisions leading up to each sample [14, 15], and from this data, we infer an incredibly low per mitosis mutation rate (3.8 × 10-12 mutations per site and cell division) as one of several possible explanations for the low number of identified mutations.
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22
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Fungal species boundaries in the genomics era. Fungal Genet Biol 2019; 131:103249. [PMID: 31279976 DOI: 10.1016/j.fgb.2019.103249] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 05/21/2019] [Accepted: 06/28/2019] [Indexed: 12/30/2022]
Abstract
Genomic data has opened new possibilities to understand how organisms change over time, and could enable the discovery of previously undescribed species. Although taxonomy used to be based on phenotypes, molecular data has frequently revealed that morphological traits are insufficient to describe biodiversity. Genomics holds the promise of revealing even more genetic discontinuities, but the parameters on how to describe species from genomic data remain unclear. Fungi have been a successful case in which the use of molecular markers has uncovered the existence of genetic boundaries where no crosses are possible. In this minireview, we highlight recent advances, propose a set of standards to use genomic sequences to uncover species boundaries, point out potential pitfalls, and present possible future research directions.
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23
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The rate of facultative sex governs the number of expected mating types in isogamous species. Nat Ecol Evol 2018; 2:1168-1175. [DOI: 10.1038/s41559-018-0580-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 05/16/2018] [Indexed: 01/30/2023]
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24
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Abstract
The first eukaryotic genome to be sequenced was fungal, and there continue to be more sequenced genomes in the kingdom Fungi than in any other eukaryotic kingdom. Comparison of these genomes reveals many sources of genetic variation, from single nucleotide polymorphisms to horizontal gene transfer and on to changes in the arrangement and number of chromosomes, not to mention endofungal bacteria and viruses. Population genomics shows that all sources generate variation all the time and implicate natural selection as the force maintaining genome stability. Variation in wild populations is a rich resource for associating genetic variation with phenotypic variation, whether through quantitative trait locus mapping, genome-wide association studies, or reverse ecology. Subjects of studies associating genetic and phenotypic variation include model fungi, e.g., Saccharomyces and Neurospora, but pioneering studies have also been made with fungi pathogenic to plants, e.g., Pyricularia (= Magnaporthe), Zymoseptoria, and Fusarium, and to humans, e.g., Coccidioides, Cryptococcus, and Candida.
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25
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Nieuwenhuis BPS, James TY. The frequency of sex in fungi. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2015.0540. [PMID: 27619703 DOI: 10.1098/rstb.2015.0540] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/15/2016] [Indexed: 12/16/2022] Open
Abstract
Fungi are a diverse group of organisms with a huge variation in reproductive strategy. While almost all species can reproduce sexually, many reproduce asexually most of the time. When sexual reproduction does occur, large variation exists in the amount of in- and out-breeding. While budding yeast is expected to outcross only once every 10 000 generations, other fungi are obligate outcrossers with well-mixed panmictic populations. In this review, we give an overview of the costs and benefits of sexual and asexual reproduction in fungi, and the mechanisms that evolved in fungi to reduce the costs of either mode. The proximate molecular mechanisms potentiating outcrossing and meiosis appear to be present in nearly all fungi, making them of little use for predicting outcrossing rates, but also suggesting the absence of true ancient asexual lineages. We review how population genetic methods can be used to estimate the frequency of sex in fungi and provide empirical data that support a mixed mode of reproduction in many species with rare to frequent sex in between rounds of mitotic reproduction. Finally, we highlight how these estimates might be affected by the fungus-specific mechanisms that evolved to reduce the costs of sexual and asexual reproduction.This article is part of the themed issue 'Weird sex: the underappreciated diversity of sexual reproduction'.
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Affiliation(s)
- Bart P S Nieuwenhuis
- Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden
| | - Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, 830 North University, Ann Arbor, MI 48109-1048, USA
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26
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Chung CL, Lee TJ, Akiba M, Lee HH, Kuo TH, Liu D, Ke HM, Yokoi T, Roa MB, Lu MYJ, Chang YY, Ann PJ, Tsai JN, Chen CY, Tzean SS, Ota Y, Hattori T, Sahashi N, Liou RF, Kikuchi T, Tsai IJ. Comparative and population genomic landscape of Phellinus noxius
: A hypervariable fungus causing root rot in trees. Mol Ecol 2017; 26:6301-6316. [DOI: 10.1111/mec.14359] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 09/08/2017] [Accepted: 09/11/2017] [Indexed: 01/21/2023]
Affiliation(s)
- Chia-Lin Chung
- Department of Plant Pathology and Microbiology; National Taiwan University; Taipei City Taiwan
- Master Program for Plant Medicine; National Taiwan University; Taipei City Taiwan
| | - Tracy J. Lee
- Biodiversity Research Center; Academia Sinica; Taipei City Taiwan
- Biodiversity Program; Taiwan International Graduate Program; Academia Sinica and National Taiwan Normal University; Taipei City Taiwan
- Department of Life Science; National Taiwan Normal University; Taipei City Taiwan
| | - Mitsuteru Akiba
- Department of Forest Microbiology; Forestry and Forest Products Research Institute; Tsukuba Japan
| | - Hsin-Han Lee
- Department of Plant Pathology and Microbiology; National Taiwan University; Taipei City Taiwan
| | - Tzu-Hao Kuo
- Biodiversity Research Center; Academia Sinica; Taipei City Taiwan
| | - Dang Liu
- Biodiversity Research Center; Academia Sinica; Taipei City Taiwan
- Genome and Systems Biology Degree Program; National Taiwan University and Academia Sinica; Taipei City Taiwan
| | - Huei-Mien Ke
- Biodiversity Research Center; Academia Sinica; Taipei City Taiwan
| | - Toshiro Yokoi
- Department of Forest Microbiology; Forestry and Forest Products Research Institute; Tsukuba Japan
| | - Marylette B. Roa
- Biodiversity Research Center; Academia Sinica; Taipei City Taiwan
- Philippine Genome Center; University of the Philippines Diliman; Quezon City Philippines
| | - Mei-Yeh J. Lu
- Biodiversity Research Center; Academia Sinica; Taipei City Taiwan
| | - Ya-Yun Chang
- Department of Plant Pathology and Microbiology; National Taiwan University; Taipei City Taiwan
| | - Pao-Jen Ann
- Plant Pathology Division; Taiwan Agricultural Research Institute; Taichung City Taiwan
| | - Jyh-Nong Tsai
- Plant Pathology Division; Taiwan Agricultural Research Institute; Taichung City Taiwan
| | - Chien-Yu Chen
- Department of Bio-industrial Mechatronics Engineering; National Taiwan University; Taipei City Taiwan
| | - Shean-Shong Tzean
- Department of Plant Pathology and Microbiology; National Taiwan University; Taipei City Taiwan
| | - Yuko Ota
- Department of Forest Microbiology; Forestry and Forest Products Research Institute; Tsukuba Japan
- College of Bioresource Sciences; Nihon University; Fujisawa Japan
| | - Tsutomu Hattori
- Department of Forest Microbiology; Forestry and Forest Products Research Institute; Tsukuba Japan
| | - Norio Sahashi
- Department of Forest Microbiology; Forestry and Forest Products Research Institute; Tsukuba Japan
| | - Ruey-Fen Liou
- Department of Plant Pathology and Microbiology; National Taiwan University; Taipei City Taiwan
- Master Program for Plant Medicine; National Taiwan University; Taipei City Taiwan
| | - Taisei Kikuchi
- Division of Parasitology; Faculty of Medicine; University of Miyazaki; Miyazaki Japan
| | - Isheng J. Tsai
- Biodiversity Research Center; Academia Sinica; Taipei City Taiwan
- Biodiversity Program; Taiwan International Graduate Program; Academia Sinica and National Taiwan Normal University; Taipei City Taiwan
- Department of Life Science; National Taiwan Normal University; Taipei City Taiwan
- Genome and Systems Biology Degree Program; National Taiwan University and Academia Sinica; Taipei City Taiwan
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Cariou M, Duret L, Charlat S. How and how much does RAD-seq bias genetic diversity estimates? BMC Evol Biol 2016; 16:240. [PMID: 27825303 PMCID: PMC5100275 DOI: 10.1186/s12862-016-0791-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 10/06/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND RAD-seq is a powerful tool, increasingly used in population genomics. However, earlier studies have raised red flags regarding possible biases associated with this technique. In particular, polymorphism on restriction sites results in preferential sampling of closely related haplotypes, so that RAD data tends to underestimate genetic diversity. RESULTS Here we (1) clarify the theoretical basis of this bias, highlighting the potential confounding effects of population structure and selection, (2) confront predictions to real data from in silico digestion of full genomes and (3) provide a proof of concept toward an ABC-based correction of the RAD-seq bias. Under a neutral and panmictic model, we confirm the previously established relationship between the true polymorphism and its RAD-based estimation, showing a more pronounced bias when polymorphism is high. Using more elaborate models, we show that selection, resulting in heterogeneous levels of polymorphism along the genome, exacerbates the bias and leads to a more pronounced underestimation. On the contrary, spatial genetic structure tends to reduce the bias. We confront the neutral and panmictic model to "ideal" empirical data (in silico RAD-sequencing) using full genomes from natural populations of the fruit fly Drosophila melanogaster and the fungus Shizophyllum commune, harbouring respectively moderate and high genetic diversity. In D. melanogaster, predictions fit the model, but the small difference between the true and RAD polymorphism makes this comparison insensitive to deviations from the model. In the highly polymorphic fungus, the model captures a large part of the bias but makes inaccurate predictions. Accordingly, ABC corrections based on this model improve the estimations, albeit with some imprecisions. CONCLUSION The RAD-seq underestimation of genetic diversity associated with polymorphism in restriction sites becomes more pronounced when polymorphism is high. In practice, this means that in many systems where polymorphism does not exceed 2 %, the bias is of minor importance in the face of other sources of uncertainty, such as heterogeneous bases composition or technical artefacts. The neutral panmictic model provides a practical mean to correct the bias through ABC, albeit with some imprecisions. More elaborate ABC methods might integrate additional parameters, such as population structure and selection, but their opposite effects could hinder accurate corrections.
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Affiliation(s)
- Marie Cariou
- Université de Lyon, Université Lyon 1, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, 43 boulevard du 11 novembre 1918, Villeurbanne, F-69622 France
- Current address: Laboratory of Evolutionary Genetics and Ecology, URBE, University of Namur, Rue de Bruxelles 61, 5000 Namur, Belgium
| | - Laurent Duret
- Université de Lyon, Université Lyon 1, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, 43 boulevard du 11 novembre 1918, Villeurbanne, F-69622 France
| | - Sylvain Charlat
- Université de Lyon, Université Lyon 1, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, 43 boulevard du 11 novembre 1918, Villeurbanne, F-69622 France
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Freihorst D, Brunsch M, Wirth S, Krause K, Kniemeyer O, Linde J, Kunert M, Boland W, Kothe E. Smelling the difference: Transcriptome, proteome and volatilome changes after mating. Fungal Genet Biol 2016; 112:2-11. [PMID: 27593501 DOI: 10.1016/j.fgb.2016.08.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 08/24/2016] [Accepted: 08/30/2016] [Indexed: 10/21/2022]
Abstract
Mushrooms, such as Schizophyllum commune, have a specific odor. Whether this is linked to mating, prerequisite for mushroom formation, or also found in monokaryotic, unmated strains, was investigated with a comprehensive study on the transcriptome and proteome of this model organism. Mating interactions were investigated using a complete, cytosolic proteome map for unmated, monokaryotic, as well as for mated, dikaryotic mycelia. The regulations of the proteome were compared to transcriptional changes upon mating and to changes in smell by volatilome studies. We could show a good overlap between proteome and transcriptome data, but extensive posttranslational regulation was identified for more than 80% of transcripts. This suggests down-stream regulation upon interaction of mating partners and formation of the dikaryon that is competent to form fruiting bodies. The volatilome was shown to respond to mating by a broader spectrum of volatiles and increased emission of the mushroom smell molecules 3-octanone and 1-octen-3-ol, as well as ethanol and β-bisabolol in the dikaryon. Putatively involved biosynthetic proteins like alcohol dehydrogenases, Ppo-like oxygenases, or sesquiterpene synthases showed correlating transcriptional regulation depending on either mono- or dikaryotic stages.
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Affiliation(s)
- Daniela Freihorst
- Friedrich Schiller University, Institute of Microbiology, Microbial Communication, Neugasse 25, 07743 Jena, Germany
| | - Melanie Brunsch
- Friedrich Schiller University, Institute of Microbiology, Microbial Communication, Neugasse 25, 07743 Jena, Germany
| | - Sophia Wirth
- Friedrich Schiller University, Institute of Microbiology, Microbial Communication, Neugasse 25, 07743 Jena, Germany
| | - Katrin Krause
- Friedrich Schiller University, Institute of Microbiology, Microbial Communication, Neugasse 25, 07743 Jena, Germany
| | - Olaf Kniemeyer
- Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Adolf-Reichwein-Straße 23, 07745 Jena, Germany
| | - Jörg Linde
- Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Adolf-Reichwein-Straße 23, 07745 Jena, Germany
| | - Maritta Kunert
- Max Planck Institute for Chemical Ecology, Department of Bioorganic Chemistry, Hans-Knöll-Straße 8, 07745 Jena, Germany
| | - Wilhelm Boland
- Max Planck Institute for Chemical Ecology, Department of Bioorganic Chemistry, Hans-Knöll-Straße 8, 07745 Jena, Germany
| | - Erika Kothe
- Friedrich Schiller University, Institute of Microbiology, Microbial Communication, Neugasse 25, 07743 Jena, Germany.
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James TY. Why mushrooms have evolved to be so promiscuous: Insights from evolutionary and ecological patterns. FUNGAL BIOL REV 2015. [DOI: 10.1016/j.fbr.2015.10.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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