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Lee SJ, Risse E, Mateus ID, Sanders IR. Evolution of unexpected diversity in a putative mating type locus and its correlation with genome variability reveals likely asexuality in the model mycorrhizal fungus Rhizophagus irregularis. BMC Genomics 2024; 25:888. [PMID: 39304834 DOI: 10.1186/s12864-024-10770-9] [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: 08/18/2023] [Accepted: 09/04/2024] [Indexed: 09/22/2024] Open
Abstract
BACKGROUND Arbuscular mycorrhizal fungi (AMF) form mutualistic partnerships with approximately 80% of plant species. AMF, and their diversity, play a fundamental role in plant growth, driving plant diversity, and global carbon cycles. Knowing whether AMF are sexual or asexual has fundamental consequences for how they can be used in agricultural applications. Evidence for and against sexuality in the model AMF, Rhizophagus irregularis, has been proposed. The discovery of a putative mating-type locus (MAT locus) in R. irregularis, and the previously suggested recombination among nuclei of a dikaryon R. irregularis isolate, potentially suggested sexuality. Unless undergoing frequent sexual reproduction, evolution of MAT-locus diversity is expected to be very low. Additionally, in sexual species, MAT-locus evolution is decoupled from the evolution of arbitrary genome-wide loci. RESULTS We studied MAT-locus diversity of R. irregularis. This was then compared to diversification in a phosphate transporter gene (PTG), that is not involved in sex, and to genome-wide divergence, defined by 47,378 single nucleotide polymorphisms. Strikingly, we found unexpectedly high MAT-locus diversity indicating that either it is not involved in sex, or that AMF are highly active in sex. However, a strongly congruent evolutionary history of the MAT-locus, PTG and genome-wide arbitrary loci allows us to reject both the hypothesis that the MAT-locus is involved in mating and that the R. irregularis lineage is sexual. CONCLUSION Our finding shapes the approach to developing more effective AMF strains and is highly informative as it suggests that introduced strains applied in agriculture will not exchange DNA with native populations.
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Affiliation(s)
- Soon-Jae Lee
- Department of Ecology and Evolution, University of Lausanne, Lausanne, 1015, Switzerland
| | - Eric Risse
- Department of Ecology and Evolution, University of Lausanne, Lausanne, 1015, Switzerland
| | - Ivan D Mateus
- Department of Ecology and Evolution, University of Lausanne, Lausanne, 1015, Switzerland
| | - Ian R Sanders
- Department of Ecology and Evolution, University of Lausanne, Lausanne, 1015, Switzerland.
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Manyara D, Sánchez-García M, Montoliu-Nerin M, Rosling A. Detection of rare variants among nuclei populating the arbuscular mycorrhizal fungal model species Rhizophagus irregularis DAOM197198. G3 (BETHESDA, MD.) 2024; 14:jkae074. [PMID: 38656424 DOI: 10.1093/g3journal/jkae074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 03/27/2024] [Indexed: 04/26/2024]
Abstract
Identifying genuine polymorphic variants is a significant challenge in sequence data analysis, although detecting low-frequency variants in sequence data is essential for estimating demographic parameters and investigating genetic processes, such as selection, within populations. Arbuscular mycorrhizal (AM) fungi are multinucleate organisms, in which individual nuclei collectively operate as a population, and the extent of genetic variation across nuclei has long been an area of scientific interest. In this study, we investigated the patterns of polymorphism discovery and the alternate allele frequency distribution by comparing polymorphism discovery in 2 distinct genomic sequence datasets of the AM fungus model species, Rhizophagus irregularis strain DAOM197198. The 2 datasets used in this study are publicly available and were generated either from pooled spores and hyphae or amplified single nuclei from a single spore. We also estimated the intraorganismal variation within the DAOM197198 strain. Our results showed that the 2 datasets exhibited different frequency patterns for discovered variants. The whole-organism dataset showed a distribution spanning low-, intermediate-, and high-frequency variants, whereas the single-nucleus dataset predominantly featured low-frequency variants with smaller proportions in intermediate and high frequencies. Furthermore, single nucleotide polymorphism density estimates within both the whole organism and individual nuclei confirmed the low intraorganismal variation of the DAOM197198 strain and that most variants are rare. Our study highlights the methodological challenges associated with detecting low-frequency variants in AM fungal whole-genome sequence data and demonstrates that alternate alleles can be reliably identified in single nuclei of AM fungi.
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Affiliation(s)
- David Manyara
- Department of Ecology and Genetics, Uppsala University, Uppsala 752 36, Sweden
| | - Marisol Sánchez-García
- Department of Ecology and Genetics, Uppsala University, Uppsala 752 36, Sweden
- Uppsala Biocentre, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala 750 07, Sweden
| | - Merce Montoliu-Nerin
- Department of Ecology and Genetics, Uppsala University, Uppsala 752 36, Sweden
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Madrid 28223, Spain
| | - Anna Rosling
- Department of Ecology and Genetics, Uppsala University, Uppsala 752 36, Sweden
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3
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Petijová L, Henzelyová J, Kuncová J, Matoušková M, Čellárová E. In silico prediction of polyketide biosynthetic gene clusters in the genomes of Hypericum-borne endophytic fungi. BMC Genomics 2024; 25:555. [PMID: 38831295 PMCID: PMC11149221 DOI: 10.1186/s12864-024-10475-z] [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: 06/20/2023] [Accepted: 05/29/2024] [Indexed: 06/05/2024] Open
Abstract
BACKGROUND The search for new bioactive natural compounds with anticancer activity is still of great importance. Even though their potential for diagnostics and treatment of cancer has already been proved, the availability is still limited. Hypericin, a naphthodianthrone isolated essentially from plant source Hypericum perforatum L. along with other related anthraquinones and bisanthraquinones belongs to this group of compounds. Although it has been proven that hypericin is synthesized by the polyketide pathway in plants, none of the candidate genes coding for key enzymes has been experimentally validated yet. Despite the rare occurrence of anthraquinones in plants, their presence in microorganisms, including endophytic fungi, is quite common. Unlike plants, several biosynthetic genes grouped into clusters (BGCs) in fungal endophytes have already been characterized. RESULTS The aim of this work was to predict, identify and characterize the anthraquinone BGCs in de novo assembled and functionally annotated genomes of selected endophytic fungal isolates (Fusarium oxysporum, Plectosphaerella cucumerina, Scedosporium apiospermum, Diaporthe eres, Canariomyces subthermophilus) obtained from different tissues of Hypericum spp. The number of predicted type I polyketide synthase (PKS) BGCs in the studied genomes varied. The non-reducing type I PKS lacking thioesterase domain and adjacent discrete gene encoding protein with product release function were identified only in the genomes of C. subthermophilus and D. eres. A candidate bisanthraquinone BGC was predicted in C. subthermophilus genome and comprised genes coding the enzymes that catalyze formation of the basic anthraquinone skeleton (PKS, metallo-beta-lactamase, decarboxylase, anthrone oxygenase), putative dimerization enzyme (cytochrome P450 monooxygenase), other tailoring enzymes (oxidoreductase, dehydrogenase/reductase), and non-catalytic proteins (fungal transcription factor, transporter protein). CONCLUSIONS The results provide an insight into genetic background of anthraquinone biosynthesis in Hypericum-borne endophytes. The predicted bisanthraquinone gene cluster represents a basis for functional validation of the candidate biosynthetic genes in a simple eukaryotic system as a prospective biotechnological alternative for production of hypericin and related bioactive anthraquinones.
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Affiliation(s)
- Linda Petijová
- Department of Genetics, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Mánesova 23, Košice, 04154, Slovakia.
| | - Jana Henzelyová
- Department of Genetics, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Mánesova 23, Košice, 04154, Slovakia
| | - Júlia Kuncová
- Department of Genetics, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Mánesova 23, Košice, 04154, Slovakia
| | - Martina Matoušková
- Department of Genetics, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Mánesova 23, Košice, 04154, Slovakia
| | - Eva Čellárová
- Department of Genetics, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Mánesova 23, Košice, 04154, Slovakia
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4
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van Creij J, Auxier B, An J, Wijfjes RY, Bergin C, Rosling A, Bisseling T, Pan Z, Limpens E. Stochastic nuclear organization and host-dependent allele contribution in Rhizophagus irregularis. BMC Genomics 2023; 24:53. [PMID: 36709253 PMCID: PMC9883914 DOI: 10.1186/s12864-023-09126-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 01/10/2023] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Arbuscular mycorrhizal (AM) fungi are arguably the most important symbionts of plants, offering a range of benefits to their hosts. However, the provisioning of these benefits does not appear to be uniform among AM fungal individuals, with genetic variation between fungal symbionts having a substantial impact on plant performance. Interestingly, genetic variation has also been reported within fungal individuals, which contain millions of haploid nuclei sharing a common cytoplasm. In the model AM fungus, Rhizophagus irregularis, several isolates have been reported to be dikaryotes, containing two genetically distinct types of nuclei recognized based on their mating-type (MAT) locus identity. However, their extremely coenocytic nature and lack of a known single nucleus stage has raised questions on the origin, distribution and dynamics of this genetic variation. RESULTS Here we performed DNA and RNA sequencing at the mycelial individual, single spore and single nucleus levels to gain insight into the dynamic genetic make-up of the dikaryote-like R. irregularis C3 isolate and the effect of different host plants on its genetic variation. Our analyses reveal that parallel spore and root culture batches can have widely variable ratios of two main genotypes in C3. Additionally, numerous polymorphisms were found with frequencies that deviated significantly from the general genotype ratio, indicating a diverse population of slightly different nucleotypes. Changing host plants did not show consistent host effects on nucleotype ratio's after multiple rounds of subculturing. Instead, we found a major effect of host plant-identity on allele-specific expression in C3. CONCLUSION Our analyses indicate a highly dynamic/variable genetic organization in different isolates of R. irregularis. Seemingly random fluctuations in nucleotype ratio's upon spore formation, recombination events, high variability of non-tandemly repeated rDNA sequences and host-dependent allele expression all add levels of variation that may contribute to the evolutionary success of these widespread symbionts.
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Affiliation(s)
- Jelle van Creij
- grid.4818.50000 0001 0791 5666Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, Wageningen, The Netherlands
| | - Ben Auxier
- grid.4818.50000 0001 0791 5666Laboratory of Genetics, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, Wageningen, The Netherlands
| | - Jianyong An
- grid.4818.50000 0001 0791 5666Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, Wageningen, The Netherlands ,grid.411626.60000 0004 1798 6793Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, 102206 China
| | - Raúl Y. Wijfjes
- grid.4818.50000 0001 0791 5666Laboratory of Bioinformatics, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, Wageningen, The Netherlands ,grid.5252.00000 0004 1936 973XCurrent affiliation: Faculty of Biology, Ludwig Maximilian University of Munich, Munich, Germany
| | - Claudia Bergin
- grid.8993.b0000 0004 1936 9457Department of Cell and Molecular Biology, Uppsala University, and Microbial Single Cell Genomics Facility, Science for Life Laboratory, Uppsala, Sweden
| | - Anna Rosling
- grid.8993.b0000 0004 1936 9457Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-75236 Uppsala, Sweden
| | - Ton Bisseling
- grid.4818.50000 0001 0791 5666Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, Wageningen, The Netherlands ,grid.411626.60000 0004 1798 6793Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, 102206 China
| | - Zhiyong Pan
- grid.35155.370000 0004 1790 4137Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region, Ministry of Agriculture), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Erik Limpens
- grid.4818.50000 0001 0791 5666Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, Wageningen, The Netherlands
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Zhou J, Kuyper TW, Feng G. A trade-off between space exploration and mobilization of organic phosphorus through associated microbiomes enables niche differentiation of arbuscular mycorrhizal fungi on the same root. SCIENCE CHINA. LIFE SCIENCES 2023:10.1007/s11427-022-2261-1. [PMID: 36811801 DOI: 10.1007/s11427-022-2261-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 12/19/2022] [Indexed: 02/24/2023]
Abstract
Ecology seeks to explain species coexistence, but experimental tests of mechanisms for coexistence are difficult to conduct. We synthesized an arbuscular mycorrhizal (AM) fungal community with three fungal species that differed in their capacity of foraging for orthophosphate (P) due to differences in soil exploration. We tested whether AM fungal species-specific hyphosphere bacterial assemblages recruited by hyphal exudates enabled differentiation among the fungi in the capacity of mobilizing soil organic P (Po). We found that the less efficient space explorer, Gigaspora margarita, obtained less 13C from the plant, whereas it had higher efficiencies in Po mobilization and alkaline phosphatase (AlPase) production per unit C than the two efficient space explorers, Rhizophagusintraradices and Funneliformis mosseae. Each AM fungus was associated with a distinct alp gene harboring bacterial assemblage, and the alp gene abundance and Po preference of the microbiome associated with the less efficient space explorer were higher than those of the two other species. We conclude that the traits of AM fungal associated bacterial consortia cause niche differentiation. The trade-off between foraging ability and the ability to recruit effective Po mobilizing microbiomes is a mechanism that allows co-existence of AM fungal species in a single plant root and surrounding soil habitat.
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Affiliation(s)
- Jiachao Zhou
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Thomas W Kuyper
- Soil Biology Group, Wageningen University & Research, Wageningen, 6700 AA, The Netherlands
| | - Gu Feng
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China.
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6
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McGale E, Sanders IR. Integrating plant and fungal quantitative genetics to improve the ecological and agricultural applications of mycorrhizal symbioses. Curr Opin Microbiol 2022; 70:102205. [PMID: 36201974 DOI: 10.1016/j.mib.2022.102205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 08/12/2022] [Accepted: 08/18/2022] [Indexed: 01/25/2023]
Abstract
Finding and targeting genes that quantitatively contribute to agricultural and ecological processes progresses food production and conservation efforts. Typically, quantitative genetic approaches link variants in a single organism's genome with a trait of interest. Recently, genome-to-genome mapping has found genome variants interacting between species to produce the result of a multiorganism (including multikingdom) interaction. These were plant and bacterial pathogen genome interactions; plant-fungal coquantitative genetics have not yet been applied. Plant-mycorrhizae symbioses exist across most biomes, for a majority of land plants, including crop plants, and manipulate many traits from single organisms to ecosystems for which knowing the genetic basis would be useful. The availability of Rhizophagus irregularis mycorrhizal isolates, with genomic information, makes dual-genome methods with beneficial mutualists accessible and imminent.
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Affiliation(s)
- Erica McGale
- Department of Ecology and Evolution, Biophore Building, University of Lausanne, 1015 Lausanne, Switzerland
| | - Ian R Sanders
- Department of Ecology and Evolution, Biophore Building, University of Lausanne, 1015 Lausanne, Switzerland.
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7
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Lofgren LA, Ross BS, Cramer RA, Stajich JE. The pan-genome of Aspergillus fumigatus provides a high-resolution view of its population structure revealing high levels of lineage-specific diversity driven by recombination. PLoS Biol 2022; 20:e3001890. [PMID: 36395320 PMCID: PMC9714929 DOI: 10.1371/journal.pbio.3001890] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 12/01/2022] [Accepted: 10/26/2022] [Indexed: 11/18/2022] Open
Abstract
Aspergillus fumigatus is a deadly agent of human fungal disease where virulence heterogeneity is thought to be at least partially structured by genetic variation between strains. While population genomic analyses based on reference genome alignments offer valuable insights into how gene variants are distributed across populations, these approaches fail to capture intraspecific variation in genes absent from the reference genome. Pan-genomic analyses based on de novo assemblies offer a promising alternative to reference-based genomics with the potential to address the full genetic repertoire of a species. Here, we evaluate 260 genome sequences of A. fumigatus including 62 newly sequenced strains, using a combination of population genomics, phylogenomics, and pan-genomics. Our results offer a high-resolution assessment of population structure and recombination frequency, phylogenetically structured gene presence-absence variation, evidence for metabolic specificity, and the distribution of putative antifungal resistance genes. Although A. fumigatus disperses primarily via asexual conidia, we identified extraordinarily high levels of recombination with the lowest linkage disequilibrium decay value reported for any fungal species to date. We provide evidence for 3 primary populations of A. fumigatus, with recombination occurring only rarely between populations and often within them. These 3 populations are structured by both gene variation and distinct patterns of gene presence-absence with unique suites of accessory genes present exclusively in each clade. Accessory genes displayed functional enrichment for nitrogen and carbohydrate metabolism suggesting that populations may be stratified by environmental niche specialization. Similarly, the distribution of antifungal resistance genes and resistance alleles were often structured by phylogeny. Altogether, the pan-genome of A. fumigatus represents one of the largest fungal pan-genomes reported to date including many genes unrepresented in the Af293 reference genome. These results highlight the inadequacy of relying on a single-reference genome-based approach for evaluating intraspecific variation and the power of combined genomic approaches to elucidate population structure, genetic diversity, and putative ecological drivers of clinically relevant fungi.
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Affiliation(s)
- Lotus A. Lofgren
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, California, United States of America
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Brandon S. Ross
- Dartmouth Geisel School of Medicine in the Department of Microbiology and Immunology, Dartmouth, Hanover, New Hampshire, United States of America
| | - Robert A. Cramer
- Dartmouth Geisel School of Medicine in the Department of Microbiology and Immunology, Dartmouth, Hanover, New Hampshire, United States of America
| | - Jason E. Stajich
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, California, United States of America
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8
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Mateus ID, Auxier B, Ndiaye MMS, Cruz J, Lee SJ, Sanders IR. Reciprocal recombination genomic signatures in the symbiotic arbuscular mycorrhizal fungi Rhizophagus irregularis. PLoS One 2022; 17:e0270481. [PMID: 35776745 PMCID: PMC9249182 DOI: 10.1371/journal.pone.0270481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 06/12/2022] [Indexed: 11/24/2022] Open
Abstract
Arbuscular mycorrhizal fungi (AMF) are part of the most widespread fungal-plant symbiosis. They colonize at least 80% of plant species, promote plant growth and plant diversity. These fungi are multinucleated and contain either one or two haploid nuclear genotypes (monokaryon and dikaryon) identified by the alleles at a putative mating-type locus. This taxon has been considered as an ancient asexual scandal because of the lack of observable sexual structures. Despite identification of a putative mating-type locus and functional activation of genes related to mating when two isolates co-exist, it remains unknown if the AMF life cycle involves a sexual or parasexual stage. We used publicly available genome sequences to test if Rhizophagus irregularis dikaryon genomes display signatures of sexual reproduction in the form of reciprocal recombination patterns, or if they display exclusively signatures of parasexual reproduction involving gene conversion. We used short-read and long-read sequence data to identify nucleus-specific alleles within dikaryons and then compared them to orthologous gene sequences from related monokaryon isolates displaying the same putative MAT-types as the dikaryon. We observed that the two nucleus-specific alleles of the dikaryon A5 are more related to the homolog sequences of monokaryon isolates displaying the same putative MAT-type than between each other. We also observed that these nucleus-specific alleles displayed reciprocal recombination signatures. These results confirm that dikaryon and monokaryon isolates displaying the same putative MAT-type are related in their life-cycle. These results suggest that a genetic exchange mechanism, involving reciprocal recombination in dikaryon genomes, allows AMF to generate genetic diversity.
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Affiliation(s)
- Ivan D. Mateus
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- * E-mail:
| | - Ben Auxier
- Laboratory of Genetics, Wageningen University, Wageningen, The Netherlands
| | - Mam M. S. Ndiaye
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Joaquim Cruz
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Soon-Jae Lee
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Ian R. Sanders
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
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Lakovic M, Rillig MC. A Nuclei-Based Conceptual Model of (Eco)evolutionary Dynamics in Fungal Heterokaryons. Front Microbiol 2022; 13:914040. [PMID: 35711750 PMCID: PMC9194903 DOI: 10.3389/fmicb.2022.914040] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/10/2022] [Indexed: 11/21/2022] Open
Abstract
Filamentous fungi are characterised by specific features, such as multinuclearity, coexistence of genetically different nuclei and nuclear movement across the mycelial network. These attributes make them an interesting, yet rather underappreciated, system for studying (eco)evolutionary dynamics. This is especially noticeable among theoretical studies, where rather few consider nuclei and their role in (eco)evolutionary dynamics. To encourage such theoretical approaches, we here provide an overview of existing research on nuclear genotype heterogeneity (NGH) and its sources, such as mutations and vegetative non-self-fusion. We then discuss the resulting intra-mycelial nuclear dynamics and the potential consequences for fitness and adaptation. Finally, we formulate a nuclei-based conceptual framework, which considers three levels of selection: a single nucleus, a subpopulation of nuclei and the mycelium. We compare this framework to other concepts, for example those that consider only the mycelium as the level of selection, and outline the benefits of our approach for studying (eco)evolutionary dynamics. Our concept should serve as a baseline for modelling approaches, such as individual-based simulations, which will contribute greatly to our understanding of multilevel selection and (eco)evolutionary dynamics in filamentous fungi.
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Affiliation(s)
- Milica Lakovic
- Institut für Biologie, Freie Universität Berlin, Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research, Berlin, Germany
| | - Matthias C Rillig
- Institut für Biologie, Freie Universität Berlin, Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research, Berlin, Germany
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10
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Stengel A, Stanke KM, Quattrone AC, Herr JR. Improving Taxonomic Delimitation of Fungal Species in the Age of Genomics and Phenomics. Front Microbiol 2022; 13:847067. [PMID: 35250961 PMCID: PMC8892103 DOI: 10.3389/fmicb.2022.847067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Accepted: 01/28/2022] [Indexed: 01/04/2023] Open
Abstract
Species concepts have long provided a source of debate among biologists. These lively debates have been important for reaching consensus on how to communicate across scientific disciplines and for advancing innovative strategies to study evolution, population biology, ecology, natural history, and disease epidemiology. Species concepts are also important for evaluating variability and diversity among communities, understanding biogeographical distributions, and identifying causal agents of disease across animal and plant hosts. While there have been many attempts to address the concept of species in the fungi, there are several concepts that have made taxonomic delimitation especially challenging. In this review we discuss these major challenges and describe methodological approaches that show promise for resolving ambiguity in fungal taxonomy by improving discrimination of genetic and functional traits. We highlight the relevance of eco-evolutionary theory used in conjunction with integrative taxonomy approaches to improve the understanding of interactions between environment, ecology, and evolution that give rise to distinct species boundaries. Beyond recent advances in genomic and phenomic methods, bioinformatics tools and modeling approaches enable researchers to test hypothesis and expand our knowledge of fungal biodiversity. Looking to the future, the pairing of integrative taxonomy approaches with multi-locus genomic sequencing and phenomic techniques, such as transcriptomics and proteomics, holds great potential to resolve many unknowns in fungal taxonomic classification.
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Affiliation(s)
- Ashley Stengel
- Complex Biosystems Interdisciplinary Life Sciences, University of Nebraska-Lincoln, Lincoln, NE, United States
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Kimberly M. Stanke
- Complex Biosystems Interdisciplinary Life Sciences, University of Nebraska-Lincoln, Lincoln, NE, United States
- Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Amanda C. Quattrone
- Complex Biosystems Interdisciplinary Life Sciences, University of Nebraska-Lincoln, Lincoln, NE, United States
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, United States
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Joshua R. Herr
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, United States
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, United States
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, United States
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11
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Sbrana C, Agnolucci M, Avio L, Giovannini L, Palla M, Turrini A, Giovannetti M. Mycorrhizal Symbionts and Associated Bacteria: Potent Allies to Improve Plant Phosphorus Availability and Food Security. Front Microbiol 2022; 12:797381. [PMID: 35082769 PMCID: PMC8784594 DOI: 10.3389/fmicb.2021.797381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 12/16/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Cristiana Sbrana
- National Research Council (CNR), Institute of Agricultural Biology and Biotechnology, Pisa, Italy
| | - Monica Agnolucci
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Luciano Avio
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Luca Giovannini
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Michela Palla
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Alessandra Turrini
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Manuela Giovannetti
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
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12
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Robbins C, Cruz Corella J, Aletti C, Seiler R, Mateus ID, Lee S, Masclaux FG, Sanders IR. Generation of unequal nuclear genotype proportions in Rhizophagus irregularis progeny causes allelic imbalance in gene transcription. THE NEW PHYTOLOGIST 2021; 231:1984-2001. [PMID: 34085297 PMCID: PMC8457141 DOI: 10.1111/nph.17530] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 05/25/2021] [Indexed: 05/05/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) form mutualisms with most plant species. The model AMF Rhizophagus irregularis is common in many ecosystems and naturally forms homokaryons and dikaryons. Quantitative variation in allele frequencies in clonally dikaryon offspring suggests they disproportionately inherit two distinct nuclear genotypes from their parent. This is interesting, because such progeny strongly and differentially affect plant growth. Neither the frequency and magnitude of this occurrence nor its effect on gene transcription are known. Using reduced representation genome sequencing, transcriptomics, and quantitative analysis tools, we show that progeny of homokaryons and dikaryons are qualitatively genetically identical to the parent. However, dikaryon progeny differ quantitatively due to unequal inheritance of nuclear genotypes. Allele frequencies of actively transcribed biallelic genes resembled the frequencies of the two nuclear genotypes. More biallelic genes showed transcription of both alleles than monoallelic transcription, but biallelic transcription was less likely with greater allelic divergence. Monoallelic transcription levels of biallelic genes were reduced compared with biallelic gene transcription, a finding consistent with genomic conflict. Given that genetic variation in R. irregularis is associated with plant growth, our results establish quantitative genetic variation as a future consideration when selecting AMF lines to improve plant production.
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Affiliation(s)
- Chanz Robbins
- Department of Ecology and EvolutionUniversity of LausanneBiophore BuildingLausanne1015Switzerland
| | - Joaquim Cruz Corella
- Department of Ecology and EvolutionUniversity of LausanneBiophore BuildingLausanne1015Switzerland
| | - Consolée Aletti
- Department of Ecology and EvolutionUniversity of LausanneBiophore BuildingLausanne1015Switzerland
| | - Réjane Seiler
- Department of Ecology and EvolutionUniversity of LausanneBiophore BuildingLausanne1015Switzerland
| | - Ivan D. Mateus
- Department of Ecology and EvolutionUniversity of LausanneBiophore BuildingLausanne1015Switzerland
| | - Soon‐Jae Lee
- Department of Ecology and EvolutionUniversity of LausanneBiophore BuildingLausanne1015Switzerland
| | - Frédéric G. Masclaux
- Group of Genetic MedicineGeneva University HospitalBuilding DGeneva1205Switzerland
| | - Ian R. Sanders
- Department of Ecology and EvolutionUniversity of LausanneBiophore BuildingLausanne1015Switzerland
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13
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Chaturvedi A, Cruz Corella J, Robbins C, Loha A, Menin L, Gasilova N, Masclaux FG, Lee SJ, Sanders IR. The methylome of the model arbuscular mycorrhizal fungus, Rhizophagus irregularis, shares characteristics with early diverging fungi and Dikarya. Commun Biol 2021; 4:901. [PMID: 34294866 PMCID: PMC8298701 DOI: 10.1038/s42003-021-02414-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 07/01/2021] [Indexed: 12/16/2022] Open
Abstract
Early-diverging fungi (EDF) are distinct from Dikarya and other eukaryotes, exhibiting high N6-methyldeoxyadenine (6mA) contents, rather than 5-methylcytosine (5mC). As plants transitioned to land the EDF sub-phylum, arbuscular mycorrhizal fungi (AMF; Glomeromycotina) evolved a symbiotic lifestyle with 80% of plant species worldwide. Here we show that these fungi exhibit 5mC and 6mA methylation characteristics that jointly set them apart from other fungi. The model AMF, R. irregularis, evolved very high levels of 5mC and greatly reduced levels of 6mA. However, unlike the Dikarya, 6mA in AMF occurs at symmetrical ApT motifs in genes and is associated with their transcription. 6mA is heterogeneously distributed among nuclei in these coenocytic fungi suggesting functional differences among nuclei. While far fewer genes are regulated by 6mA in the AMF genome than in EDF, most strikingly, 6mA methylation has been specifically retained in genes implicated in components of phosphate regulation; the quintessential hallmark defining this globally important symbiosis. Anurag Chaturvedi et al. use long-read PacBio sequencing and LC-MS to profile 5mC and 6mA DNA methylation in the model arbuscular mycorrhizal fungus, Rhizophagus irregularis. Their results suggest that R. irregularis shows methylation profiles distinct from other early-diverging fungi, and Dikarya and provide further insight into how these fungi may have adapted to form symbiotic relationships with important plant species.
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Affiliation(s)
- Anurag Chaturvedi
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Environmental Genomics Group, School of Biosciences, The University of Birmingham, Birmingham, UK
| | - Joaquim Cruz Corella
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Chanz Robbins
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Anita Loha
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | - Laure Menin
- Institute of Chemical Sciences and Engineering, Swiss Federal Institute of Technology Lausanne (EPFL), SSMI, Batochime, Lausanne, Switzerland
| | - Natalia Gasilova
- Institute of Chemical Sciences and Engineering, Swiss Federal Institute of Technology Lausanne (EPFL), SSMI, Batochime, Lausanne, Switzerland
| | - Frédéric G Masclaux
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Soon-Jae Lee
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Ian R Sanders
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.
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14
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Mironenko NV, Orina AS, Kovalenko NM. Nuclear Genetic Polymorphism in Pyrenophora tritici-repentis Strains for ToxA and ToxB Effector Genes. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421040098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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15
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Kokkoris V, Chagnon PL, Yildirir G, Clarke K, Goh D, MacLean AM, Dettman J, Stefani F, Corradi N. Host identity influences nuclear dynamics in arbuscular mycorrhizal fungi. Curr Biol 2021; 31:1531-1538.e6. [PMID: 33545043 DOI: 10.1016/j.cub.2021.01.035] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 11/19/2020] [Accepted: 01/12/2021] [Indexed: 02/07/2023]
Abstract
The arbuscular mycorrhizal fungi (AMF) are involved in one of the most ecologically important symbioses on the planet, occurring within the roots of most land plants.1 Knowledge of even basic elements of AM fungal biology is still poor, with the discovery that AMF may in fact have a sexual life cycle being only very recently reported.2-5 AMF produce asexual spores that contain up to several thousand individual haploid nuclei6 of either largely uniform genotypes (AMF homokaryons) or nuclei originating from two parental genotypes2-5 (AMF dikaryons or heterokaryons). In contrast to the sexual dikaryons in the phyla Ascomycota and Basidiomycota,7,8 in which pairs of nuclei coexist in single hyphal compartments, AMF dikaryons carry several thousand nuclei in a coenocytic mycelium. Here, we set out to better understand the dynamics of this unique multinucleate condition by combining molecular analyses with advanced microscopy and modeling. Herein, we report that select AMF dikaryotic strains carry the distinct nucleotypes in equal proportions to one another, whereas others show an unequal distribution of parental nucleotypes. In both cases, the relative proportions within a given strain are inherently stable. Simulation models suggest that AMF dikaryons may be maintained through nuclear cooperation dynamics. Remarkably, we report that these nuclear ratios shift dramatically in response to plant host identity, revealing a previously unknown layer of genetic complexity and dynamism within the intimate interactions that occur between the partners of a prominent terrestrial symbiosis.
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Affiliation(s)
- Vasilis Kokkoris
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada; Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON K1A 0C6, Canada.
| | - Pierre-Luc Chagnon
- Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Sherbrooke Est, Montreal, QC H1X 2B2, Canada
| | - Gökalp Yildirir
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Kelsey Clarke
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada; Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON K1A 0C6, Canada
| | - Dane Goh
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Allyson M MacLean
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Jeremy Dettman
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON K1A 0C6, Canada
| | - Franck Stefani
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON K1A 0C6, Canada
| | - Nicolas Corradi
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada.
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Peña R, Robbins C, Corella JC, Thuita M, Masso C, Vanlauwe B, Signarbieux C, Rodriguez A, Sanders IR. Genetically Different Isolates of the Arbuscular Mycorrhizal Fungus Rhizophagus irregularis Induce Differential Responses to Stress in Cassava. FRONTIERS IN PLANT SCIENCE 2020; 11:596929. [PMID: 33424891 PMCID: PMC7793890 DOI: 10.3389/fpls.2020.596929] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 11/10/2020] [Indexed: 05/12/2023]
Abstract
Water scarcity negatively impacts global crop yields and climate change is expected to greatly increase the severity of future droughts. The use of arbuscular mycorrhizal fungi (AMF) can potentially mitigate the effects of water stress in plants. Cassava is a crop that feeds approximately 800 million people daily. Genetically different isolates of the AMF R. irregularis as well as their clonal progeny have both been shown to greatly alter cassava growth in field conditions. Given that cassava experiences seasonal drought in many of the regions in which it is cultivated, we evaluated whether intraspecific variation in R. irregularis differentially alters physiological responses of cassava to water stress. In a first experiment, conducted in field conditions in Western Kenya, cassava was inoculated with two genetically different R. irregularis isolates and their clonal progeny. All cassava plants exhibited physiological signs of stress during the dry period, but the largest differences occurred among plants inoculated with clonal progeny of each of the two parental fungal isolates. Because drought had not been experimentally manipulated in the field, we conducted a second experiment in the greenhouse where cassava was inoculated with two genetically different R. irregularis isolates and subjected to drought, followed by re-watering, to allow recovery. Physiological stress responses of cassava to drought differed significantly between plants inoculated with the two different fungi. However, plants that experienced higher drought stress also recovered at a faster rate following re-watering. We conclude that intraspecific genetic variability in AMF significantly influences cassava physiological responses during water stress. This highlights the potential of using naturally existing variation in AMF to improve cassava tolerance undergoing water stress. However, the fact that clonal progeny of an AMF isolate can differentially affect how cassava copes with natural drought stress in field conditions, highlights the necessity to understand additional factors, beyond genetic variation, which can account for such large differences in cassava responses to drought.
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Affiliation(s)
- Ricardo Peña
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Chanz Robbins
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Joaquim Cruz Corella
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Moses Thuita
- International Institute for Tropical Agriculture (IITA) Kenya, Nairobi, Kenya
| | - Cargele Masso
- International Institute for Tropical Agriculture (IITA) Cameroon, Yaoundé, Cameroon
| | - Bernard Vanlauwe
- International Institute for Tropical Agriculture (IITA) Kenya, Nairobi, Kenya
| | - Constant Signarbieux
- Laboratory of Ecological Systems (ECOS), Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Alia Rodriguez
- Department of Biology, National University of Colombia, Bogotá, Colombia
| | - Ian R. Sanders
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
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17
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Liu J, Liu X, Zhang Q, Li S, Sun Y, Lu W, Ma C. Response of alfalfa growth to arbuscular mycorrhizal fungi and phosphate-solubilizing bacteria under different phosphorus application levels. AMB Express 2020; 10:200. [PMID: 33141419 PMCID: PMC7609620 DOI: 10.1186/s13568-020-01137-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 10/21/2020] [Indexed: 12/26/2022] Open
Abstract
Alfalfa (Medicago sativa L.) is an important forage legume in farming and animal husbandry systems. This study assessed the effects of arbuscular mycorrhizal fungi (AMF) and phosphate-solubilizing bacteria (PSB) on alfalfa growth under different phosphorus application levels. In this experiment, a complete randomized block design was used. The following four bacterial applications were used: inoculation of Funneliformis mosseae (Fm), inoculation of Bacillus megaterium (Bm), inoculation of mixed species (Fm × Bm) and noninoculation treatment (CK). Phosphorus (P) treatment was applied at the following four levels: 0 mg kg−1 (P0), 50 mg kg−1 (P1), 100 mg kg−1 (P2) and 150 mg P kg−1 (P3). The results showed that with the increase in phosphorus application, each index increased first and then decreased. The J2 treatment was significantly greater than the J0 treatment (P < 0.05) under the same bacterial treatment. In each cropping period the difference in each index to alfalfa was extremely significant under J, P treatment and J × P interactive treatment (P < 0.01). The indexes were compared by membership function. The priority order was as follows: J3P2 > J1P2 > J3P1 treatment. Therefore, when phosphorus was applied at 100 mg kg−1, the mixed inoculation of Fm × Bm was optimal, benefitting mycorrhiza growth and the production performance of alfalfa.
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18
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Mosaic fungal individuals have the potential to evolve within a single generation. Sci Rep 2020; 10:17625. [PMID: 33077756 PMCID: PMC7572425 DOI: 10.1038/s41598-020-74679-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 10/06/2020] [Indexed: 01/25/2023] Open
Abstract
Although cells of mushroom-producing fungi typically contain paired haploid nuclei (n + n), most Armillaria gallica vegetative cells are uninucleate. As vegetative nuclei are produced by fusions of paired haploid nuclei, they are thought to be diploid (2n). Here we report finding haploid vegetative nuclei in A. gallica at multiple sites in southeastern Massachusetts, USA. Sequencing multiple clones of a single-copy gene isolated from single hyphal filaments revealed nuclear heterogeneity both among and within hyphae. Cytoplasmic bridges connected hyphae in field-collected and cultured samples, and we propose nuclear migration through bridges maintains this nuclear heterogeneity. Growth studies demonstrate among- and within-hypha phenotypic variation for growth in response to gallic acid, a plant-produced antifungal compound. The existence of both genetic and phenotypic variation within vegetative hyphae suggests that fungal individuals have the potential to evolve within a single generation in response to environmental variation over time and space.
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19
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Quintero-Corrales C, Ángeles-Argáiz R, Jaramillo-Correa JP, Piñero D, Garibay-Orijel R, Mastretta-Yanes A. Allopatric instead of parapatric divergence in an ectomycorrhizal fungus (Laccaria trichodermophora) in tropical sky-islands. FUNGAL ECOL 2020. [DOI: 10.1016/j.funeco.2020.100966] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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20
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Naranjo‐Ortiz MA, Gabaldón T. Fungal evolution: cellular, genomic and metabolic complexity. Biol Rev Camb Philos Soc 2020; 95:1198-1232. [PMID: 32301582 PMCID: PMC7539958 DOI: 10.1111/brv.12605] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 03/31/2020] [Accepted: 04/02/2020] [Indexed: 12/13/2022]
Abstract
The question of how phenotypic and genomic complexity are inter-related and how they are shaped through evolution is a central question in biology that historically has been approached from the perspective of animals and plants. In recent years, however, fungi have emerged as a promising alternative system to address such questions. Key to their ecological success, fungi present a broad and diverse range of phenotypic traits. Fungal cells can adopt many different shapes, often within a single species, providing them with great adaptive potential. Fungal cellular organizations span from unicellular forms to complex, macroscopic multicellularity, with multiple transitions to higher or lower levels of cellular complexity occurring throughout the evolutionary history of fungi. Similarly, fungal genomes are very diverse in their architecture. Deep changes in genome organization can occur very quickly, and these phenomena are known to mediate rapid adaptations to environmental changes. Finally, the biochemical complexity of fungi is huge, particularly with regard to their secondary metabolites, chemical products that mediate many aspects of fungal biology, including ecological interactions. Herein, we explore how the interplay of these cellular, genomic and metabolic traits mediates the emergence of complex phenotypes, and how this complexity is shaped throughout the evolutionary history of Fungi.
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Affiliation(s)
- Miguel A. Naranjo‐Ortiz
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyDr. Aiguader 88, Barcelona08003Spain
| | - Toni Gabaldón
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyDr. Aiguader 88, Barcelona08003Spain
- Department of Experimental Sciences, Universitat Pompeu Fabra (UPF)Dr. Aiguader 88, 08003BarcelonaSpain
- ICREAPg. Lluís Companys 23, 08010BarcelonaSpain
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21
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Kokkoris V, Stefani F, Dalpé Y, Dettman J, Corradi N. Nuclear Dynamics in the Arbuscular Mycorrhizal Fungi. TRENDS IN PLANT SCIENCE 2020; 25:765-778. [PMID: 32534868 DOI: 10.1016/j.tplants.2020.05.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 04/30/2020] [Accepted: 05/20/2020] [Indexed: 05/09/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) are plant root symbionts that continuously carry thousands of nuclei in their spores and hyphae. This unique cellular biology raises fundamental questions regarding their nuclear dynamics. This review aims to address these by synthesizing current knowledge of nuclear content and behavior in these ubiquitous soil fungi. Overall, we find that that nuclear counts, as well as the nuclei shape and organization, vary drastically both within and among species in this group. By comparing these features with those of other fungi, we highlight unique aspects of the AMF nuclear biology that require further attention. The potential implications of the observed nuclear variability for the biology and evolution of these widespread plant symbionts are discussed.
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Affiliation(s)
- Vasilis Kokkoris
- Department of Biology, University of Ottawa, ON, Ottawa, K1N 6N5, Canada; Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, ON, Ottawa, K1A 0C5, Canada.
| | - Franck Stefani
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, ON, Ottawa, K1A 0C5, Canada
| | - Yolande Dalpé
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, ON, Ottawa, K1A 0C5, Canada
| | - Jeremy Dettman
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, ON, Ottawa, K1A 0C5, Canada
| | - Nicolas Corradi
- Department of Biology, University of Ottawa, ON, Ottawa, K1N 6N5, Canada.
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22
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Savary R, Dupuis C, Masclaux FG, Mateus ID, Rojas EC, Sanders IR. Genetic variation and evolutionary history of a mycorrhizal fungus regulate the currency of exchange in symbiosis with the food security crop cassava. THE ISME JOURNAL 2020; 14:1333-1344. [PMID: 32066875 PMCID: PMC7242447 DOI: 10.1038/s41396-020-0606-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 01/16/2020] [Accepted: 01/30/2020] [Indexed: 12/19/2022]
Abstract
Most land plants form symbioses with arbuscular mycorrhizal fungi (AMF). Diversity of AMF increases plant community productivity and plant diversity. For decades, it was known that plants trade carbohydrates for phosphate with their fungal symbionts. However, recent studies show that plant-derived lipids probably represent the most essential currency of exchange. Understanding the regulation of plant genes involved in the currency of exchange is crucial to understanding stability of this mutualism. Plants encounter many different AMF genotypes that vary greatly in the benefit they confer to plants. Yet the role that fungal genetic variation plays in the regulation of this currency has not received much attention. We used a high-resolution phylogeny of one AMF species (Rhizophagus irregularis) to show that fungal genetic variation drives the regulation of the plant fatty acid pathway in cassava (Manihot esculenta); a pathway regulating one of the essential currencies of trade in the symbiosis. The regulation of this pathway was explained by clearly defined patterns of fungal genome-wide variation representing the precise fungal evolutionary history. This represents the first demonstrated link between the genetics of AMF and reprogramming of an essential plant pathway regulating the currency of exchange in the symbiosis. The transcription factor RAM1 was also revealed as the dominant gene in the fatty acid plant gene co-expression network. Our study highlights the crucial role of variation in fungal genomes in the trade of resources in this important symbiosis and also opens the door to discovering characteristics of AMF genomes responsible for interactions between AMF and cassava that will lead to optimal cassava growth.
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Affiliation(s)
- Romain Savary
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Cindy Dupuis
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland
| | - Frédéric G Masclaux
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland
- Vital-IT Group, Swiss Institute of Bioinformatics, University of Lausanne, 1015, Lausanne, Switzerland
| | - Ivan D Mateus
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland
| | - Edward C Rojas
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871, Copenhagen, Denmark
| | - Ian R Sanders
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland.
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23
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Masclaux FG, Wyss T, Pagni M, Rosikiewicz P, Sanders IR. Investigating unexplained genetic variation and its expression in the arbuscular mycorrhizal fungus Rhizophagus irregularis: A comparison of whole genome and RAD sequencing data. PLoS One 2019; 14:e0226497. [PMID: 31881076 PMCID: PMC6934306 DOI: 10.1371/journal.pone.0226497] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 11/27/2019] [Indexed: 12/19/2022] Open
Abstract
Arbuscular mycorrhizal fungi (AMF) are important symbionts of plants. Recently, studies of the AMF Rhizophagus irregularis recorded within-isolate genetic variation that does not completely match the proposed homokaryon or heterokaryon state (where heterokaryons comprise a population of two distinct nucleus genotypes). We re-analysed published data showing that bi-allelic sites (and their frequencies), detected in proposed homo- and heterokaryote R. irregularis isolates, were similar across independent studies using different techniques. This indicated that observed within-fungus genetic variation was not an artefact of sequencing and that such within- fungus genetic variation possibly exists. We then looked to see if bi-allelic transcripts from three R. irregularis isolates matched those observed in the genome as this would give a strong indication of whether bi-allelic sites recorded in the genome were reliable variants. In putative homokaryon isolates, very few bi-allelic transcripts matched those in the genome. In a putative heterokaryon, a large number of bi-allelic transcripts matched those in the genome. Bi-allelic transcripts also occurred in the same frequency in the putative heterokaryon as predicted from allele frequency in the genome. Our results indicate that while within-fungus genome variation in putative homokaryon and heterokaryon AMF was highly similar in 2 independent studies, there was little support that this variation is transcribed in homokaryons. In contrast, within-fungus variation thought to be segregated among two nucleus genotypes in a heterokaryon isolate was indeed transcribed in a way that is proportional to that seen in the genome.
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Affiliation(s)
- Frédéric G. Masclaux
- Department of Ecology and Evolution, University of Lausanne, Switzerland
- Vital-IT Group, Swiss Institute of Bioinformatics, Switzerland
| | - Tania Wyss
- Department of Ecology and Evolution, University of Lausanne, Switzerland
| | - Marco Pagni
- Vital-IT Group, Swiss Institute of Bioinformatics, Switzerland
| | - Pawel Rosikiewicz
- Department of Ecology and Evolution, University of Lausanne, Switzerland
| | - Ian R. Sanders
- Department of Ecology and Evolution, University of Lausanne, Switzerland
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24
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The role of in vitro cultivation on symbiotic trait and function variation in a single species of arbuscular mycorrhizal fungus. Fungal Biol 2019; 123:732-744. [DOI: 10.1016/j.funbio.2019.06.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 06/11/2019] [Accepted: 06/18/2019] [Indexed: 11/23/2022]
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25
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Mateus ID, Masclaux FG, Aletti C, Rojas EC, Savary R, Dupuis C, Sanders IR. Dual RNA-seq reveals large-scale non-conserved genotype × genotype-specific genetic reprograming and molecular crosstalk in the mycorrhizal symbiosis. THE ISME JOURNAL 2019; 13:1226-1238. [PMID: 30647457 PMCID: PMC6474227 DOI: 10.1038/s41396-018-0342-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 11/05/2018] [Accepted: 12/11/2018] [Indexed: 01/19/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) impact plant growth and are a major driver of plant diversity and productivity. We quantified the contribution of intra-specific genetic variability in cassava (Manihot esculenta) and Rhizophagus irregularis to gene reprogramming in symbioses using dual RNA-sequencing. A large number of cassava genes exhibited altered transcriptional responses to the fungus but transcription of most of these plant genes (72%) responded in a different direction or magnitude depending on the plant genotype. Two AMF isolates displayed large differences in their transcription, but the direction and magnitude of the transcriptional responses for a large number of these genes was also strongly influenced by the genotype of the plant host. This indicates that unlike the highly conserved plant genes necessary for the symbiosis establishment, most of the plant and fungal gene transcriptional responses are not conserved and are greatly influenced by plant and fungal genetic differences, even at the within-species level. The transcriptional variability detected allowed us to identify an extensive gene network showing the interplay in plant-fungal reprogramming in the symbiosis. Key genes illustrated that the two organisms jointly program their cytoskeleton organization during growth of the fungus inside roots. Our study reveals that plant and fungal genetic variation has a strong role in shaping the genetic reprograming in response to symbiosis, indicating considerable genotype × genotype interactions in the mycorrhizal symbiosis. Such variation needs to be considered in order to understand the molecular mechanisms between AMF and their plant hosts in natural communities.
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Affiliation(s)
- Ivan D Mateus
- Department of Ecology and Evolution, University of Lausanne, Biophore Building, 1015, Lausanne, Switzerland
| | - Frédéric G Masclaux
- Department of Ecology and Evolution, University of Lausanne, Biophore Building, 1015, Lausanne, Switzerland
- Vital-IT, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Consolée Aletti
- Department of Ecology and Evolution, University of Lausanne, Biophore Building, 1015, Lausanne, Switzerland
| | - Edward C Rojas
- Department of Ecology and Evolution, University of Lausanne, Biophore Building, 1015, Lausanne, Switzerland
| | - Romain Savary
- Department of Ecology and Evolution, University of Lausanne, Biophore Building, 1015, Lausanne, Switzerland
| | - Cindy Dupuis
- Department of Ecology and Evolution, University of Lausanne, Biophore Building, 1015, Lausanne, Switzerland
| | - Ian R Sanders
- Department of Ecology and Evolution, University of Lausanne, Biophore Building, 1015, Lausanne, Switzerland.
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26
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Kokkoris V, Miles T, Hart MM. The role of in vitro cultivation on asymbiotic trait variation in a single species of arbuscular mycorrhizal fungus. Fungal Biol 2019; 123:307-317. [PMID: 30928039 DOI: 10.1016/j.funbio.2019.01.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 12/29/2018] [Accepted: 01/17/2019] [Indexed: 01/13/2023]
Abstract
Cultivating arbuscular mycorrhizal (AM) fungi in vitro is an efficient way to produce material for industry and research. However, such artificial growing conditions may impose selective pressure on fungi grown in vitro over many generations. We hypothesized that isolates subjected to long term propagation in vitro may develop increasingly ruderal traits. We proposed a predictive framework for the effect of in vitro cultivation on asymbiotic AM fungal traits. Using photomicrography and image processing, we analyzed morphology and growth traits for 14 isolates representing an in vitro cultivation gradient from 0 to >80 generations in vitro. We investigated the range of trait variation among asymbiotic growth of arbuscular mycorrhizal (AM) fungus isolates (Rhizoglomus irregulare). Spore dormancy was strongly associated with in vitro cultivation. We observed extremely high levels of inter-isolate variation for most fungal traits, but this was not related to time in vitro. Our results indicate that intra-specific diversity may have a strong ecological role in AM fungal communities.
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Affiliation(s)
- Vasilis Kokkoris
- Department of Biology, University of British Columbia, Okanagan Campus, 3333 University Way, Kelowna, BC V1V 1V7, Canada.
| | - Thea Miles
- Department of Biology, University of British Columbia, Okanagan Campus, 3333 University Way, Kelowna, BC V1V 1V7, Canada
| | - Miranda M Hart
- Department of Biology, University of British Columbia, Okanagan Campus, 3333 University Way, Kelowna, BC V1V 1V7, Canada
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27
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Scott TW, Kiers ET, Cooper GA, dos Santos M, West SA. Evolutionary maintenance of genomic diversity within arbuscular mycorrhizal fungi. Ecol Evol 2019; 9:2425-2435. [PMID: 30891190 PMCID: PMC6405528 DOI: 10.1002/ece3.4834] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 11/23/2018] [Accepted: 11/26/2018] [Indexed: 01/12/2023] Open
Abstract
Most organisms are built from a single genome. In striking contrast, arbuscular mycorrhizal fungi appear to maintain genomic variation within an individual fungal network. Arbuscular mycorrhizal fungi dwell in the soil, form mutualistic networks with plants, and bear multiple, potentially genetically diverse nuclei within a network. We explore, from a theoretical perspective, why such genetic diversity might be maintained within individuals. We consider selection acting within and between individual fungal networks. We show that genetic diversity could provide a benefit at the level of the individual, by improving growth in variable environments, and that this can stabilize genetic diversity even in the presence of nuclear conflict. Arbuscular mycorrhizal fungi complicate our understanding of organismality, but our findings offer a way of understanding such biological anomalies.
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Affiliation(s)
| | - E. Toby Kiers
- Institute of Ecological Sciences, Faculty of Earth and Life SciencesVrije UniversiteitAmsterdamThe Netherlands
| | | | - Miguel dos Santos
- Department of ZoologyUniversity of OxfordOxfordUK
- Department of Social Psychology and Social Neuroscience, Institute of PsychologyUniversity of BernBernSwitzerland
| | - Stuart A. West
- Department of ZoologyUniversity of OxfordOxfordUK
- Magdalen CollegeOxfordUK
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28
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Chen ECH, Morin E, Beaudet D, Noel J, Yildirir G, Ndikumana S, Charron P, St-Onge C, Giorgi J, Krüger M, Marton T, Ropars J, Grigoriev IV, Hainaut M, Henrissat B, Roux C, Martin F, Corradi N. High intraspecific genome diversity in the model arbuscular mycorrhizal symbiont Rhizophagus irregularis. THE NEW PHYTOLOGIST 2018; 220:1161-1171. [PMID: 29355972 DOI: 10.1111/nph.14989] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 12/03/2017] [Indexed: 05/20/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) are known to improve plant fitness through the establishment of mycorrhizal symbioses. Genetic and phenotypic variations among closely related AMF isolates can significantly affect plant growth, but the genomic changes underlying this variability are unclear. To address this issue, we improved the genome assembly and gene annotation of the model strain Rhizophagus irregularis DAOM197198, and compared its gene content with five isolates of R. irregularis sampled in the same field. All isolates harbor striking genome variations, with large numbers of isolate-specific genes, gene family expansions, and evidence of interisolate genetic exchange. The observed variability affects all gene ontology terms and PFAM protein domains, as well as putative mycorrhiza-induced small secreted effector-like proteins and other symbiosis differentially expressed genes. High variability is also found in active transposable elements. Overall, these findings indicate a substantial divergence in the functioning capacity of isolates harvested from the same field, and thus their genetic potential for adaptation to biotic and abiotic changes. Our data also provide a first glimpse into the genome diversity that resides within natural populations of these symbionts, and open avenues for future analyses of plant-AMF interactions that link AMF genome variation with plant phenotype and fitness.
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Affiliation(s)
- Eric C H Chen
- Department of Biology, University of Ottawa, Ottawa, ON, K1N9A7, Canada
| | - Emmanuelle Morin
- Institut National de la Recherche Agronomique (INRA), Unité Mixte de Recherche 1136 Interactions Arbres/Microorganismes, Laboratoire D'excellence Recherches Avancées sur la Biologie de l'Arbre et les Ecosystèmes Forestiers (ARBRE), Centre INRA-Grand Est-Nancy, Champenoux, 54280, France
| | - Denis Beaudet
- Department of Biology, University of Ottawa, Ottawa, ON, K1N9A7, Canada
| | - Jessica Noel
- Department of Biology, University of Ottawa, Ottawa, ON, K1N9A7, Canada
| | - Gokalp Yildirir
- Department of Biology, University of Ottawa, Ottawa, ON, K1N9A7, Canada
| | - Steve Ndikumana
- Department of Biology, University of Ottawa, Ottawa, ON, K1N9A7, Canada
| | - Philippe Charron
- Department of Biology, University of Ottawa, Ottawa, ON, K1N9A7, Canada
| | - Camille St-Onge
- Department of Biology, University of Ottawa, Ottawa, ON, K1N9A7, Canada
| | - John Giorgi
- Department of Biology, University of Ottawa, Ottawa, ON, K1N9A7, Canada
| | - Manuela Krüger
- Department of Biology, University of Ottawa, Ottawa, ON, K1N9A7, Canada
| | - Timea Marton
- Department of Biology, University of Ottawa, Ottawa, ON, K1N9A7, Canada
| | - Jeanne Ropars
- Department of Biology, University of Ottawa, Ottawa, ON, K1N9A7, Canada
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute (JGI), Walnut Creek, CA, 94598, USA
| | - Matthieu Hainaut
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, 13288, France
- INRA, USC 1408 AFMB, Marseille, F-13288, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, 13288, France
- INRA, USC 1408 AFMB, Marseille, F-13288, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Christophe Roux
- Laboratoire de Recherche en Sciences Végétales, UPS, CNRS 24 Chemin de Borde Rouge-Auzeville, Université de Toulouse, Castanet-Tolosan, 31326, France
| | - Francis Martin
- Institut National de la Recherche Agronomique (INRA), Unité Mixte de Recherche 1136 Interactions Arbres/Microorganismes, Laboratoire D'excellence Recherches Avancées sur la Biologie de l'Arbre et les Ecosystèmes Forestiers (ARBRE), Centre INRA-Grand Est-Nancy, Champenoux, 54280, France
| | - Nicolas Corradi
- Department of Biology, University of Ottawa, Ottawa, ON, K1N9A7, Canada
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Sanders IR. Sex, plasticity, and biologically significant variation in one Glomeromycotina species. THE NEW PHYTOLOGIST 2018; 220:968-970. [PMID: 29480929 DOI: 10.1111/nph.15049] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Affiliation(s)
- Ian R Sanders
- Department of Ecology & Evolution, University of Lausanne, Biophore Building, 1015, Lausanne, Switzerland
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30
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Mathieu S, Cusant L, Roux C, Corradi N. Arbuscular mycorrhizal fungi: intraspecific diversity and pangenomes. THE NEW PHYTOLOGIST 2018; 220:1129-1134. [PMID: 29949657 DOI: 10.1111/nph.15275] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 05/21/2018] [Indexed: 06/08/2023]
Abstract
Contents Summary 1129 I. Introduction 1129 II. Intraspecific phenotypic variation and the plant host 1130 III. High inter-isolate genetic diversity in model AMF 1130 IV. Genome diversity within the model AM fungus Rhizophagus irregularis 1131 V. Pangenomes and the future of AMF ecological genomics 1131 Acknowledgements 1133 References 1133 SUMMARY: Arbuscular mycorrhizal fungi (AMF) are ubiquitous plant symbionts with an intriguing population biology. Conspecific AMF strains can vary substantially at the genetic and phenotypic levels, leading to direct and quantifiable variation in plant growth. Recent studies have shown that high intraspecific diversity is very common in AMF, and not only found in model species. Studies have also revealed how the phenotype of conspecific isolates varies depending on the plant host, highlighting the functional relevance of intraspecific phenotypic plasticity for the AMF ecology and mycorrhizal symbiosis. Recent work has also demonstrated that conspecific isolates of the model AMF Rhizophagus irregularis harbor large and highly variable pangenomes, highlighting the potential role of intraspecific genome diversity for the ecological adaptation of these symbionts.
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Affiliation(s)
- Stephanie Mathieu
- Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Loïc Cusant
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, UPS, CNRS 24 Chemin de Borde Rouge-Auzeville, Castanet-Tolosan, France
| | - Christophe Roux
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, UPS, CNRS 24 Chemin de Borde Rouge-Auzeville, Castanet-Tolosan, France
| | - Nicolas Corradi
- Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
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31
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Bruns TD, Corradi N, Redecker D, Taylor JW, Öpik M. Glomeromycotina: what is a species and why should we care? THE NEW PHYTOLOGIST 2018; 220:963-967. [PMID: 29165821 DOI: 10.1111/nph.14913] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A workshop at the recent International Conference on Mycorrhiza was focused on species recognition in Glomeromycotina and parts of their basic biology that define species. The workshop was motivated by the paradigm-shifting evidence derived from genomic data for sex and for the lack of heterokaryosis, and by published exchanges in Science that were based on different species concepts and have led to differing views of dispersal and endemism in these fungi. Although a lively discussion ensued, there was general agreement that species recognition in the group is in need of more attention, and that many basic assumptions about the biology of these important fungi including sexual or clonal reproduction, similarity or dissimilarity of nuclei within an individual, and species boundaries need to be re-examined and scrutinized with current techniques.
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Affiliation(s)
- Thomas D Bruns
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720-3102, USA
| | - Nicolas Corradi
- Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Dirk Redecker
- Agroécologie, Université de Bourgogne Franche-Comté, INRA, CNRS, AgroSup Dijon, F-21000, Dijon, France
| | - John W Taylor
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720-3102, USA
| | - Maarja Öpik
- University of Tartu, 40 Lai Street, 51005, Tartu, Estonia
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32
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Savary R, Villard L, Sanders IR. Within-species phylogenetic relatedness of a common mycorrhizal fungus affects evenness in plant communities through effects on dominant species. PLoS One 2018; 13:e0198537. [PMID: 30462644 PMCID: PMC6248901 DOI: 10.1371/journal.pone.0198537] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 10/16/2018] [Indexed: 12/17/2022] Open
Abstract
Arbuscular mycorrhizal fungi (AMF) have been shown to influence plant community structure and diversity. Studies based on single plant-single AMF isolate experiments show that within AMF species variation leads to large differential growth responses of different plant species. Because of these differential effects, genetic differences among isolates of an AMF species could potentially have strong effects on the structure of plant communities. We tested the hypothesis that within species variation in the AMF Rhizophagus irregularis significantly affects plant community structure and plant co-existence. We took advantage of a recent genetic characterization of several isolates using double-digest restriction-site associated DNA sequencing (ddRADseq). This allowed us to test not only for the impact of within AMF species variation on plant community structure but also for the role of the R. irregularis phylogeny on plant community metrics. Nine isolates of R. irregularis, belonging to three different genetic groups (Gp1, Gp3 and Gp4), were used as either single inoculum or as mixed diversity inoculum. Plants in a mesocosm representing common species that naturally co-exist in European grasslands were inoculated with the different AMF treatments. We found that within-species differences in R. irregularis did not strongly influence the performance of individual plants or the structure of the overall plant community. However, the evenness of the plant community was affected by the phylogeny of the fungal isolates, where more closely-related AMF isolates were more likely to affect plant community evenness in a similar way compared to more genetically distant isolates. This study underlines the effect of within AMF species variability on plant community structure. While differential effects of the AMF isolates were not strong, a single AMF species had enough functional variability to change the equilibrium of a plant community in a way that is associated with the evolutionary history of the fungus.
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Affiliation(s)
- Romain Savary
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Lucas Villard
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Ian R. Sanders
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
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33
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Allen JL, McKenzie SK, Sleith RS, Alter SE. First genome-wide analysis of the endangered, endemic lichen Cetradonia linearis reveals isolation by distance and strong population structure. AMERICAN JOURNAL OF BOTANY 2018; 105:1556-1567. [PMID: 30157288 DOI: 10.1002/ajb2.1150] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 06/14/2018] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY Lichenized fungi are evolutionarily diverse and ecologically important, but little is known about the processes that drive their diversification and genetic differentiation. Distributions are often assumed to be wholly shaped by ecological requirements rather than dispersal limitations. Furthermore, although asexual and sexual reproductive structures are observable, the lack of information about recombination rates makes inferences about reproductive strategies difficult. We investigated the population genomics of Cetradonia linearis, a federally endangered lichen in the southern Appalachians of eastern North America, to test the relative contributions of environmental and geographic distance in shaping genetic structure, and to characterize the mating system and genome-wide recombination. METHODS Whole-genome shotgun sequencing was conducted to generate data for 32 individuals of C. linearis. A reference genome was assembled, and reads from all samples were aligned to generate a set of single-nucleotide polymorphisms for further analyses. KEY RESULTS We found evidence for low rates of recombination and for isolation by distance, but not for isolation by environment. The species is putatively unisexual, given that only one mating-type locus was found. Hindcast species distribution models and the distribution of genetic diversity support C. linearis having a larger range during the Last Glacial Maximum in the southern portion of its current extent. CONCLUSIONS Our findings contribute to the understanding of factors that shape genetic diversity in C. linearis and in fungi more broadly. Because all populations are highly genetically differentiated, the extirpation of any population would mean the loss of unique genetic diversity; therefore, our results support the continued conservation of this species.
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Affiliation(s)
- Jessica L Allen
- The New York Botanical Garden, 2900 Southern Blvd., Bronx, New York, 10458, USA
- The Graduate Center, City University of New York, 365 5th Avenue, New York, New York, 10016, USA
| | - Sean K McKenzie
- Rockefeller University, 1230 York Avenue, New York, New York, 10065, USA
| | - Robin S Sleith
- The New York Botanical Garden, 2900 Southern Blvd., Bronx, New York, 10458, USA
- The Graduate Center, City University of New York, 365 5th Avenue, New York, New York, 10016, USA
| | - S Elizabeth Alter
- The Graduate Center, City University of New York, 365 5th Avenue, New York, New York, 10016, USA
- Biology Department, York College, 94-20 Guy R Brewer Blvd., Jamaica, New York, 11451, USA
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34
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Noë R, Kiers ET. Mycorrhizal Markets, Firms, and Co-ops. Trends Ecol Evol 2018; 33:777-789. [PMID: 30177306 DOI: 10.1016/j.tree.2018.07.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Revised: 07/26/2018] [Accepted: 07/31/2018] [Indexed: 12/22/2022]
Abstract
The nutrient exchange mutualism between arbuscular mycorrhizal fungi (AMFs) and their host plants qualifies as a biological market, but several complications have hindered its appropriate use. First, fungal 'trading agents' are hard to identify because AMFs are potentially heterokaryotic, that is, they may contain large numbers of polymorphic nuclei. This means it is difficult to define and study a fungal 'individual' acting as an independent agent with a specific trading strategy. Second, because nutrient exchanges occur via communal structures (arbuscules), this temporarily reduces outbidding competition and transaction costs and hence resembles exchanges among divisions of firms, rather than traditional trade on markets. We discuss how fungal nuclei may coordinate their trading strategies, but nevertheless retain some independence, similar to human co-operatives (co-ops).
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Affiliation(s)
- Ronald Noë
- Department of Psychology, Université de Strasbourg, Strasbourg, France.
| | - E Toby Kiers
- Department of Ecological Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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35
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Korinsak S, Tangphatsornruang S, Pootakham W, Wanchana S, Plabpla A, Jantasuriyarat C, Patarapuwadol S, Vanavichit A, Toojinda T. Genome-wide association mapping of virulence gene in rice blast fungus Magnaporthe oryzae using a genotyping by sequencing approach. Genomics 2018; 111:661-668. [PMID: 29775784 DOI: 10.1016/j.ygeno.2018.05.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 05/04/2018] [Accepted: 05/11/2018] [Indexed: 01/22/2023]
Abstract
Magnaporthe oryzae is a fungal pathogen causing blast disease in many plant species. In this study, seventy three isolates of M. oryzae collected from rice (Oryza sativa) in 1996-2014 were genotyped using a genotyping-by-sequencing approach to detect genetic variation. An association study was performed to identify single nucleotide polymorphisms (SNPs) associated with virulence genes using 831 selected SNP and infection phenotypes on local and improved rice varieties. Population structure analysis revealed eight subpopulations. The division into eight groups was not related to the degree of virulence. Association mapping showed five SNPs associated with fungal virulence on chromosome 1, 2, 3, 4 and 7. The SNP on chromosome 1 was associated with virulence against RD6-Pi7 and IRBL7-M which might be linked to the previously reported AvrPi7.
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Affiliation(s)
- Siripar Korinsak
- Plant Breeding Program, Faculty of Agriculture at Kamphaeng Saen, Kesetsart University, Nakhon Pathom 73140, Thailand
| | - Sithichoke Tangphatsornruang
- National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Pahonyothin Road, Khlong Nueng, Khlong Luang, PathumThani 12120, Thailand
| | - Wirulda Pootakham
- National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Pahonyothin Road, Khlong Nueng, Khlong Luang, PathumThani 12120, Thailand
| | - Samart Wanchana
- National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Pahonyothin Road, Khlong Nueng, Khlong Luang, PathumThani 12120, Thailand
| | - Anucha Plabpla
- Interdisciplinary Graduate Program in Genetic Engineering, Kasetsart University, Bangkok 10900, Thailand
| | | | - Sujin Patarapuwadol
- Department of Plant Pathology, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand
| | - Apichart Vanavichit
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand; Rice Science Center, Kasetsart University, Kamphaeng Saen, Nakhon Pathom 73140, Thailand
| | - Theerayut Toojinda
- National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Pahonyothin Road, Khlong Nueng, Khlong Luang, PathumThani 12120, Thailand.
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36
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Masclaux FG, Wyss T, Mateus-Gonzalez ID, Aletti C, Sanders IR. Variation in allele frequencies at the bg112 locus reveals unequal inheritance of nuclei in a dikaryotic isolate of the fungus Rhizophagus irregularis. MYCORRHIZA 2018; 28:369-377. [PMID: 29675619 DOI: 10.1007/s00572-018-0834-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 04/05/2018] [Indexed: 05/26/2023]
Abstract
The genetic state of the arbuscular mycorrhizal fungus species Rhizophagus irregularis differs among isolates, including both homokaryotic and dikaryotic isolates. Via the production of multi-nucleate axexual spores, siblings of dikaryotic isolates may inherit unequal frequencies of nucleotypes. Using bg112, a microsatellite marker, previous studies revealed that lines deriving from single spores of the dikaryotic R. irregularis isolate C3 differed in their proportions of different alleles. A genomic study of single nuclei of R. irregularis, however, suggested that this marker was a multi-copy locus and that therefore it was inappropriate to study the inheritance of nuclei in dikaryotic isolates. In this study, we first analysed whole genome data of several R. irregularis isolates and demonstrated that bg112 is indeed a single copy locus in these genomes. Thus, the bg112 locus is a suitable marker to study the relative frequency of nucleotypes in R. irregularis. Second, by using amplicon sequencing, we confirmed the existence of one allele of bg112 in two homokaryotic isolates (DAOM197198 and C2) and two alleles in the dikaryotic isolate (C3). Finally, we found that the relative proportions of two bg112 alleles differed significantly among dikaryotic single-spore lines derived from isolate C3, indicating that genetically different nucleotypes are inherited unequally in this dikaryotic R. irregularis isolate.
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Affiliation(s)
- Frédéric G Masclaux
- Department of Ecology and Evolution, Biophore Building, University of Lausanne, 1015, Lausanne, Switzerland
- Vital-IT Group, Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Tania Wyss
- Department of Ecology and Evolution, Biophore Building, University of Lausanne, 1015, Lausanne, Switzerland
| | - Ivan D Mateus-Gonzalez
- Department of Ecology and Evolution, Biophore Building, University of Lausanne, 1015, Lausanne, Switzerland
| | - Consolée Aletti
- Department of Ecology and Evolution, Biophore Building, University of Lausanne, 1015, Lausanne, Switzerland
| | - Ian R Sanders
- Department of Ecology and Evolution, Biophore Building, University of Lausanne, 1015, Lausanne, Switzerland.
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37
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Savary R, Masclaux FG, Wyss T, Droh G, Cruz Corella J, Machado AP, Morton JB, Sanders IR. A population genomics approach shows widespread geographical distribution of cryptic genomic forms of the symbiotic fungus Rhizophagus irregularis. THE ISME JOURNAL 2018; 12:17-30. [PMID: 29027999 PMCID: PMC5739010 DOI: 10.1038/ismej.2017.153] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 07/20/2017] [Accepted: 08/21/2017] [Indexed: 11/26/2022]
Abstract
Arbuscular mycorrhizal fungi (AMF; phylum Gomeromycota) associate with plants forming one of the most successful microbe-plant associations. The fungi promote plant diversity and have a potentially important role in global agriculture. Plant growth depends on both inter- and intra-specific variation in AMF. It was recently reported that an unusually large number of AMF taxa have an intercontinental distribution, suggesting long-distance gene flow for many AMF species, facilitated by either long-distance natural dispersal mechanisms or human-assisted dispersal. However, the intercontinental distribution of AMF species has been questioned because the use of very low-resolution markers may be unsuitable to detect genetic differences among geographically separated AMF, as seen with some other fungi. This has been untestable because of the lack of population genomic data, with high resolution, for any AMF taxa. Here we use phylogenetics and population genomics to test for intra-specific variation in Rhizophagus irregularis, an AMF species for which genome sequence information already exists. We used ddRAD sequencing to obtain thousands of markers distributed across the genomes of 81 R. irregularis isolates and related species. Based on 6 888 variable positions, we observed significant genetic divergence into four main genetic groups within R. irregularis, highlighting that previous studies have not captured underlying genetic variation. Despite considerable genetic divergence, surprisingly, the variation could not be explained by geographical origin, thus also supporting the hypothesis for at least one AMF species of widely dispersed AMF genotypes at an intercontinental scale. Such information is crucial for understanding AMF ecology, and how these fungi can be used in an environmentally safe way in distant locations.
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Affiliation(s)
- Romain Savary
- Department of Ecology and Evolution, Biophore Building, University of Lausanne, Lausanne, Switzerland
| | - Frédéric G Masclaux
- Department of Ecology and Evolution, Biophore Building, University of Lausanne, Lausanne, Switzerland
- Vital-IT Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Tania Wyss
- Department of Ecology and Evolution, Biophore Building, University of Lausanne, Lausanne, Switzerland
| | - Germain Droh
- Department of Ecology and Evolution, Biophore Building, University of Lausanne, Lausanne, Switzerland
- Laboratoire de Génétique, Unité de Formation et de Recherche en Biosciences, Université Félix Houphouet Boigny, Abidjan, Ivory Coast
| | - Joaquim Cruz Corella
- Department of Ecology and Evolution, Biophore Building, University of Lausanne, Lausanne, Switzerland
| | - Ana Paula Machado
- Department of Ecology and Evolution, Biophore Building, University of Lausanne, Lausanne, Switzerland
| | - Joseph B Morton
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, USA
| | - Ian R Sanders
- Department of Ecology and Evolution, Biophore Building, University of Lausanne, Lausanne, Switzerland
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38
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Grewe F, Huang JP, Leavitt SD, Lumbsch HT. Reference-based RADseq resolves robust relationships among closely related species of lichen-forming fungi using metagenomic DNA. Sci Rep 2017; 7:9884. [PMID: 28852019 PMCID: PMC5575168 DOI: 10.1038/s41598-017-09906-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 07/31/2017] [Indexed: 01/13/2023] Open
Abstract
Despite increasing availability of phylogenomic datasets, strategies to generate genome-scale data from organisms involved in symbiotic relationships remains challenging. Restriction site-associated DNA sequencing (RADseq) can effectively generated reduced representation genomic loci. However, when using metagenomic DNA from inseparable symbiotic organisms, RADseq loci may belong to any number of the organisms involved in these intimate associations. In this study, we explored the potential for a reference-based RADseq approach to generate data for lichen-forming fungi from metagenomic DNA extracted from intact lichens. We simulated RAD data from draft genomes of closely related lichenized fungi to test if RADseq can reconstruct robust evolutionary relationships. Subsequently, we generated empirical RADseq data from metagenomic lichen DNA, with RADseq loci mapped back to a reference genome to exclude loci from other lichen symbionts that are represented in metagenomic libraries. In all cases, phylogenetic reconstructions using RADseq loci recovered diversification histories consistent with a previous study based on more comprehensive genome sampling. Furthermore, RADseq loci were found to resolve relationships among closely related species, which were otherwise indistinguishable using a phylogenetic species recognition criterion. Our studies revealed that a modified, reference-based RADseq approach can successfully be implemented to generate symbiont-specific phylogenomic data from metagenomic reads.
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Affiliation(s)
- Felix Grewe
- Integrative Research Center, Science and Education, Field Museum of Natural History, 1400S Lake Shore Drive, Chicago, IL, 60605, USA.
| | - Jen-Pen Huang
- Integrative Research Center, Science and Education, Field Museum of Natural History, 1400S Lake Shore Drive, Chicago, IL, 60605, USA
| | - Steven D Leavitt
- Integrative Research Center, Science and Education, Field Museum of Natural History, 1400S Lake Shore Drive, Chicago, IL, 60605, USA.,Department of Biology & M. L. Bean Life Science Museum, Brigham Young University, Provo, UT, 84602, USA
| | - H Thorsten Lumbsch
- Integrative Research Center, Science and Education, Field Museum of Natural History, 1400S Lake Shore Drive, Chicago, IL, 60605, USA
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39
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Glynou K, Ali T, Kia SH, Thines M, Maciá-Vicente JG. Genotypic diversity in root-endophytic fungi reflects efficient dispersal and environmental adaptation. Mol Ecol 2017; 26:4618-4630. [PMID: 28667772 DOI: 10.1111/mec.14231] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 04/09/2017] [Accepted: 06/08/2017] [Indexed: 12/25/2022]
Abstract
Studying community structure and dynamics of plant-associated fungi is the basis for unravelling their interactions with hosts and ecosystem functions. A recent sampling revealed that only a few fungal groups, as defined by internal transcribed spacer region (ITS) sequence similarity, dominate culturable root endophytic communities of nonmycorrhizal Microthlaspi spp. plants across Europe. Strains of these fungi display a broad phenotypic and functional diversity, which suggests a genetic variability masked by ITS clustering into operational taxonomic units (OTUs). The aims of this study were to identify how genetic similarity patterns of these fungi change across environments and to evaluate their ability to disperse and adapt to ecological conditions. A first ITS-based haplotype analysis of ten widespread OTUs mostly showed a low to moderate genotypic differentiation, with the exception of a group identified as Cadophora sp. that was highly diverse. A multilocus phylogeny based on additional genetic loci (partial translation elongation factor 1α, beta-tubulin and actin) and amplified fragment length polymorphism profiling of 185 strains representative of the five dominant OTUs revealed a weak association of genetic differences with geography and environmental conditions, including bioclimatic and soil factors. Our findings suggest that dominant culturable root endophytic fungi have efficient dispersal capabilities, and that their distribution is little affected by environmental filtering. Other processes, such as inter- and intraspecific biotic interactions, may be more important for the local assembly of their communities.
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Affiliation(s)
- Kyriaki Glynou
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany.,Integrative Fungal Research Cluster (IPF), Frankfurt am Main, Germany
| | - Tahir Ali
- Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
| | - Sevda Haghi Kia
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany.,Integrative Fungal Research Cluster (IPF), Frankfurt am Main, Germany
| | - Marco Thines
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany.,Integrative Fungal Research Cluster (IPF), Frankfurt am Main, Germany.,Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
| | - Jose G Maciá-Vicente
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany.,Integrative Fungal Research Cluster (IPF), Frankfurt am Main, Germany
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40
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Rosikiewicz P, Bonvin J, Sanders IR. Cost-efficient production of in vitro Rhizophagus irregularis. MYCORRHIZA 2017; 27:477-486. [PMID: 28210812 PMCID: PMC5486606 DOI: 10.1007/s00572-017-0763-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 01/27/2017] [Indexed: 05/09/2023]
Abstract
One of the bottlenecks in mycorrhiza research is that arbuscular mycorrhizal fungi (AMF) have to be cultivated with host plant roots. Some AMF species, such as Rhizophagus irregularis, can be grown in vitro on dual-compartment plates, where fungal material can be harvested from a fungus-only compartment. Plant roots often grow into this fungus compartment, and regular root trimming is required if the fungal material needs to be free of traces of plant material. Trimming also increases unwanted contamination by other microorganisms. We compared 22 different culture types and conditions to a widely used dual-compartment culture system that we refer to as the "standard system." We found two modified culture systems that allowed high spore production and low rates of contamination. We then compared the two modified culture systems with the standard system in more detail. In the two modified culture systems versus the standard system, a comparable number of spores were produced per plate, the necessity for root trimming was reduced, and there was significantly diminished contamination in the fungal compartment. A cost analysis showed that both modified culture systems were more economic than the standard culture system for the production of the same number of non-contaminated spores. The two modified culture systems provide an economic alternative for the production of contaminant-free fungal material which is ideal for studies requiring AMF DNA or RNA for genetics, genomics, and transcriptomic studies or for studies requiring relatively large amounts of fungal material for greenhouse experiments.
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Affiliation(s)
- Pawel Rosikiewicz
- Department of Ecology and Evolution, University of Lausanne, Biophore Building, 1015, Lausanne, Switzerland
| | - Jérémy Bonvin
- Department of Ecology and Evolution, University of Lausanne, Biophore Building, 1015, Lausanne, Switzerland
| | - Ian R Sanders
- Department of Ecology and Evolution, University of Lausanne, Biophore Building, 1015, Lausanne, Switzerland.
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41
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Corradi N, Brachmann A. Fungal Mating in the Most Widespread Plant Symbionts? TRENDS IN PLANT SCIENCE 2017; 22:175-183. [PMID: 27876487 DOI: 10.1016/j.tplants.2016.10.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 10/26/2016] [Accepted: 10/28/2016] [Indexed: 06/06/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) are relevant plant symbionts whose hyphae and spores carry hundreds of coexisting nuclei with supposedly divergent genomes but no sign of sexual reproduction. This unusual biology suggested that conventional fungal mating is not amendable to optimize strains for plant growth, but recent evidence of sexual-related nuclear inheritance in these organisms is now challenging this widespread notion. Here, we outline our knowledge of AMF genetics within a historical context, and discuss how past and new information in this area changed our understanding of AMF biology. We also highlight the mating-related processes in AMF, and propose new research avenues and approaches that could lead to a better application of these organisms for agricultural and environmental practices.
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Affiliation(s)
- Nicolas Corradi
- Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ottawa, ON, Canada.
| | - Andreas Brachmann
- LMU Munich, Faculty of Biology, Genetics, D-82152 Planegg-Martinsried, Germany
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42
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Nadimi M, Stefani FOP, Hijri M. The large (134.9 kb) mitochondrial genome of the glomeromycete Funneliformis mosseae. MYCORRHIZA 2016; 26:747-755. [PMID: 27246226 DOI: 10.1007/s00572-016-0710-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 05/23/2016] [Indexed: 06/05/2023]
Abstract
Funneliformis mosseae is among the most ecologically and economically important glomeromycete species and occurs both in natural and disturbed areas in a wide range of habitats and climates. In this study, we report the sequencing of the complete mitochondrial (mt) genome of F. mosseae isolate FL299 using 454 pyrosequencing and Illumina HiSeq technologies. This mt genome is a full-length circular chromosome of 134,925 bp, placing it among the largest mitochondrial DNAs (mtDNAs) in the fungal kingdom. A comparative analysis with publically available arbuscular mycorrhizal fungal mtDNAs revealed that the mtDNA of F. mosseae FL299 contained a very large number of insertions contributing to its expansion. The gene synteny was completely reshuffled compared to previously published glomeromycotan mtDNAs and several genes were oriented in an anti-sense direction. Furthermore, the presence of different types of introns and insertions in rnl (14 introns) made this gene very distinctive in Glomeromycota. The presence of alternative genetic codes in both initiation (GUG) and termination (UGA) codons was another new feature in this mtDNA compared to previously published glomeromycotan mt genomes. The phylogenetic analysis inferred from the analysis of 14 protein mt genes confirmed the position of the Glomeromycota clade as a sister group of Mortierellomycotina. This mt genome is the largest observed so far in Glomeromycota and the first mt genome within the Funneliformis clade, providing new opportunities to better understand their evolution and to develop molecular markers.
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Affiliation(s)
- Maryam Nadimi
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, QC, H1X 2B2, Canada
| | - Franck O P Stefani
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, QC, H1X 2B2, Canada
| | - Mohamed Hijri
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, QC, H1X 2B2, Canada.
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