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Gong M, Bai N, Su J, Wang Y, Wei Y, Zhang Q. Transcriptome analysis of Gossypium reveals the molecular mechanisms of Ca 2+ signaling pathway on arsenic tolerance induced by arbuscular mycorrhizal fungi. Front Microbiol 2024; 15:1362296. [PMID: 38591035 PMCID: PMC11000422 DOI: 10.3389/fmicb.2024.1362296] [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: 01/24/2024] [Accepted: 03/05/2024] [Indexed: 04/10/2024] Open
Abstract
Introduction Arbuscular mycorrhizal fungi (AMF) have been demonstrated their ability to enhance the arsenic (As) tolerance of host plants, and making the utilization of mycorrhizal plants a promising and practical approach for remediating As-contaminated soils. However, comprehensive transcriptome analysis to reveal the molecular mechanism of As tolerance in the symbiotic process between AMF and host plants is still limited. Methods In this study, transcriptomic analysis of Gossypium seedlings was conducted with four treatments: non-inoculated Gossypium under non-As stress (CK0), non-inoculated Gossypium under As stress (CK100), F. mosseae-inoculated Gossypium under non-As stress (FM0), and F. mosseae-inoculated Gossypium under As stress (FM100). Results Our results showed that inoculation with F. mosseae led to a reduction in net fluxes of Ca2+, while increasing Ca2+ contents in the roots and leaves of Gossypium under the same As level in soil. Notably, 199 and 3129 differentially expressed genes (DEGs) were specially regulated by F. mosseae inoculation under As stress and non-As stress, respectively. Through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation and enrichment analyses, we found that under As stress, F. mosseae inoculation up-regulated a significant number of genes related to the Ca2+ signaling pathway genes, involved in cellular process, membrane part, and signal transduction. This suggests a potential role in mitigating As tolerance in Gossypium seedlings. Furthermore, our analysis identified specific DEGs in transcription factor families, including ERF, MYB, NAC, and WRKY, that were upregulated by F. mosseae inoculation. Conversely, MYB and HB-other were down-regulated. The ERF and MYB families exhibited the highest number of up- and down-regulated DEGs, respectively, which were speculated to play an important role in alleviating the As toxicity of Gossypium. Discussion Our findings provided valuable insights into the molecular theoretical basis of the Ca2+ signaling pathway in improving As tolerance of mycorrhizal plants in the future.
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Affiliation(s)
- Minggui Gong
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, China
| | - Na Bai
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, China
| | - Jiajie Su
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, China
| | - Yuan Wang
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, China
| | - Yanan Wei
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, China
| | - Qiaoming Zhang
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, China
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Zhang Q, Gong M, Xu S, Wei Y, Yuan J, Chang Q. Rhizophagus intraradices improves arsenic tolerance in Sophora viciifolia Hance. ANN MICROBIOL 2022. [DOI: 10.1186/s13213-022-01668-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Purpose
Arbuscular mycorrhizal fungi (AMF) are capable of protecting host plants against heavy metal toxicity, whereas rare knowledge has been acquired on the underlying effects of AMF on woody leguminous species under arsenic (As) stress. This study was aimed that whether AMF inoculation improves the As tolerance in Sophora viciifolia (a king of leguminous shrub).
Methods
S. viciifolia seedlings were inoculated with AMF Rhizophagus intraradices, and then the seedlings were grown at three levels (0, 50, and 100 mg As kg−1 soil) of As-polluted soil by performing the potted experiments. The plant growth, photosynthetic parameter, oxidative damage, antioxidant enzyme activities and gene expression of phytochelatin synthase in R. intraradices- and non-inoculated S. davidii seedlings under the different levels of As stress were analyzed.
Result
Compared with non-inoculated S. viciifolia at the identical As level, R. intraradices-inoculated S. viciifolia were higher in the shoot and root dry weight, plant height, root length, photosynthetic rate, stomatal conductance, transpiration rate, maximal photochemical efficiency of PSII photochemistry, actual quantum yield, and photochemical quenching values, while the intercellular CO2 concentration and non-photochemical quenching values were lower. As-induced oxidative stress generating malondialdehyde, hydrogen peroxide and superoxide in the S. viciifolia leaves and roots reduced significantly by R. intraradices inoculation, whereas the activities of antioxidative enzymes (e.g., superoxide dismutase, peroxidase, and catalase) in S. viciifolia leaves and roots were increased by R. intraradices inoculation. Notably, R. intraradices inoculation up-regulated the gene expression of S. viciifolia phytochelatins in the leaves and roots.
Conclusion
These results demonstrated that R. intraradices inoculation enhanced the As tolerance in S. viciifolia seedlings by improving the plant growth, gas exchange, chlorophyll fluorescence, reactive oxygen species, antioxidant enzymes and gene expression of S. viciifolia phytochelatins. The present study verified a multifarious positive role of AMF for woody leguminous species under As stress.
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Dauphin B, de Freitas Pereira M, Kohler A, Grigoriev IV, Barry K, Na H, Amirebrahimi M, Lipzen A, Martin F, Peter M, Croll D. Cryptic genetic structure and copy-number variation in the ubiquitous forest symbiotic fungus Cenococcum geophilum. Environ Microbiol 2021; 23:6536-6556. [PMID: 34472169 PMCID: PMC9293092 DOI: 10.1111/1462-2920.15752] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/27/2021] [Accepted: 08/30/2021] [Indexed: 01/22/2023]
Abstract
Ectomycorrhizal (ECM) fungi associated with plants constitute one of the most successful symbiotic interactions in forest ecosystems. ECM support trophic exchanges with host plants and are important factors for the survival and stress resilience of trees. However, ECM clades often harbour morpho-species and cryptic lineages, with weak morphological differentiation. How this relates to intraspecific genome variability and ecological functioning is poorly known. Here, we analysed 16 European isolates of the ascomycete Cenococcum geophilum, an extremely ubiquitous forest symbiotic fungus with no known sexual or asexual spore-forming structures but with a massively enlarged genome. We carried out whole-genome sequencing to identify single-nucleotide polymorphisms. We found no geographic structure at the European scale but divergent lineages within sampling sites. Evidence for recombination was restricted to specific cryptic lineages. Lineage differentiation was supported by extensive copy-number variation. Finally, we confirmed heterothallism with a single MAT1 idiomorph per genome. Synteny analyses of the MAT1 locus revealed substantial rearrangements and a pseudogene of the opposite MAT1 idiomorph. Our study provides the first evidence for substantial genome-wide structural variation, lineage-specific recombination and low continent-wide genetic differentiation in C. geophilum. Our study provides a foundation for targeted analyses of intra-specific functional variation in this major symbiosis.
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Affiliation(s)
| | - Maíra de Freitas Pereira
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland.,INRAE, UMR 1136 INRAE-University of Lorraine, Interactions Arbres/Microorganismes, Laboratory of Excellence ARBRE, INRAE-Grand Est, Champenoux, France
| | - Annegret Kohler
- INRAE, UMR 1136 INRAE-University of Lorraine, Interactions Arbres/Microorganismes, Laboratory of Excellence ARBRE, INRAE-Grand Est, Champenoux, France
| | - Igor V Grigoriev
- Department of Plant and Microbial Biology, University of California, Berkeley, USA.,U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, USA
| | - Kerrie Barry
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, USA
| | - Hyunsoo Na
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, USA
| | - Mojgan Amirebrahimi
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, USA
| | - Anna Lipzen
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, USA
| | - Francis Martin
- INRAE, UMR 1136 INRAE-University of Lorraine, Interactions Arbres/Microorganismes, Laboratory of Excellence ARBRE, INRAE-Grand Est, Champenoux, France
| | - Martina Peter
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
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Morin E, Miyauchi S, San Clemente H, Chen ECH, Pelin A, de la Providencia I, Ndikumana S, Beaudet D, Hainaut M, Drula E, Kuo A, Tang N, Roy S, Viala J, Henrissat B, Grigoriev IV, Corradi N, Roux C, Martin FM. Comparative genomics of Rhizophagus irregularis, R. cerebriforme, R. diaphanus and Gigaspora rosea highlights specific genetic features in Glomeromycotina. THE NEW PHYTOLOGIST 2019; 222:1584-1598. [PMID: 30636349 DOI: 10.1111/nph.15687] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 12/28/2018] [Indexed: 05/21/2023]
Abstract
Glomeromycotina is a lineage of early diverging fungi that establish arbuscular mycorrhizal (AM) symbiosis with land plants. Despite their major ecological role, the genetic basis of their obligate mutualism remains largely unknown, hindering our understanding of their evolution and biology. We compared the genomes of Glomerales (Rhizophagus irregularis, Rhizophagus diaphanus, Rhizophagus cerebriforme) and Diversisporales (Gigaspora rosea) species, together with those of saprotrophic Mucoromycota, to identify gene families and processes associated with these lineages and to understand the molecular underpinning of their symbiotic lifestyle. Genomic features in Glomeromycotina appear to be very similar with a very high content in transposons and protein-coding genes, extensive duplications of protein kinase genes, and loss of genes coding for lignocellulose degradation, thiamin biosynthesis and cytosolic fatty acid synthase. Most symbiosis-related genes in R. irregularis and G. rosea are specific to Glomeromycotina. We also confirmed that the present species have a homokaryotic genome organisation. The high interspecific diversity of Glomeromycotina gene repertoires, affecting all known protein domains, as well as symbiosis-related orphan genes, may explain the known adaptation of Glomeromycotina to a wide range of environmental settings. Our findings contribute to an increasingly detailed portrait of genomic features defining the biology of AM fungi.
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Affiliation(s)
- Emmanuelle Morin
- Institut National de la Recherche Agronomique, Université de Lorraine, Unité Mixte de Recherche Interactions Arbres/Microorganismes, Centre INRA-Grand Est-Nancy, 54280, Champenoux, France
| | - Shingo Miyauchi
- Institut National de la Recherche Agronomique, Université de Lorraine, Unité Mixte de Recherche Interactions Arbres/Microorganismes, Centre INRA-Grand Est-Nancy, 54280, Champenoux, France
| | - Hélène San Clemente
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, UPS, CNRS, 24 Chemin de Borde Rouge-Auzeville, 31320, Castanet-Tolosan, France
| | - Eric C H Chen
- Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Adrian Pelin
- Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | | | - Steve Ndikumana
- Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Denis Beaudet
- Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Mathieu Hainaut
- CNRS, UMR 7257, Aix-Marseille Université, 13007, Marseille, France
| | - Elodie Drula
- CNRS, UMR 7257, Aix-Marseille Université, 13007, Marseille, France
| | - Alan Kuo
- US Department of Energy Joint Genome Institute (JGI), Walnut Creek, CA, 94598, USA
| | - Nianwu Tang
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, UPS, CNRS, 24 Chemin de Borde Rouge-Auzeville, 31320, Castanet-Tolosan, France
| | - Sébastien Roy
- Agronutrition- rue Pierre et Marie Curie, Immeuble BIOSTEP, 31670, Labège, France
| | - Julie Viala
- Agronutrition- rue Pierre et Marie Curie, Immeuble BIOSTEP, 31670, Labège, France
| | - Bernard Henrissat
- CNRS, UMR 7257, Aix-Marseille Université, 13007, Marseille, France
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, 13007, Marseille, France
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute (JGI), Walnut Creek, CA, 94598, USA
| | - Nicolas Corradi
- Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Christophe Roux
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, UPS, CNRS, 24 Chemin de Borde Rouge-Auzeville, 31320, Castanet-Tolosan, France
| | - Francis M Martin
- Institut National de la Recherche Agronomique, Université de Lorraine, Unité Mixte de Recherche Interactions Arbres/Microorganismes, Centre INRA-Grand Est-Nancy, 54280, Champenoux, France
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forest University, 100080, Beijing, China
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Chen ECH, Mathieu S, Hoffrichter A, Sedzielewska-Toro K, Peart M, Pelin A, Ndikumana S, Ropars J, Dreissig S, Fuchs J, Brachmann A, Corradi N. Single nucleus sequencing reveals evidence of inter-nucleus recombination in arbuscular mycorrhizal fungi. eLife 2018; 7:e39813. [PMID: 30516133 PMCID: PMC6281316 DOI: 10.7554/elife.39813] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 11/16/2018] [Indexed: 12/18/2022] Open
Abstract
Eukaryotes thought to have evolved clonally for millions of years are referred to as ancient asexuals. The oldest group among these are the arbuscular mycorrhizal fungi (AMF), which are plant symbionts harboring hundreds of nuclei within one continuous cytoplasm. Some AMF strains (dikaryons) harbor two co-existing nucleotypes but there is no direct evidence that such nuclei recombine in this life-stage, as is expected for sexual fungi. Here, we show that AMF nuclei with distinct genotypes can undergo recombination. Inter-nuclear genetic exchange varies in frequency among strains, and despite recombination all nuclear genomes have an average similarity of at least 99.8%. The present study demonstrates that AMF can generate genetic diversity via meiotic-like processes in the absence of observable mating. The AMF dikaryotic life-stage is a primary source of nuclear variability in these organisms, highlighting its potential for strain enhancement of these symbionts.
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Affiliation(s)
- Eric CH Chen
- Department of BiologyUniversity of OttawaOttawaCanada
| | | | - Anne Hoffrichter
- Institute of Genetics, Faculty of BiologyLudwig Maximilian University of MunichMunichGermany
| | - Kinga Sedzielewska-Toro
- Institute of Genetics, Faculty of BiologyLudwig Maximilian University of MunichMunichGermany
| | - Max Peart
- Department of BiologyUniversity of OttawaOttawaCanada
| | - Adrian Pelin
- Department of BiologyUniversity of OttawaOttawaCanada
| | | | - Jeanne Ropars
- Department of BiologyUniversity of OttawaOttawaCanada
| | - Steven Dreissig
- Leibniz Institute of Plant Genetics and Crop Plant ResearchGaterslebenGermany
| | - Jorg Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant ResearchGaterslebenGermany
| | - Andreas Brachmann
- Institute of Genetics, Faculty of BiologyLudwig Maximilian University of MunichMunichGermany
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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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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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Sbrana C, Strani P, Pepe A, de Novais CB, Giovannetti M. Divergence of Funneliformis mosseae populations over 20 years of laboratory cultivation, as revealed by vegetative incompatibility and molecular analysis. MYCORRHIZA 2018; 28:329-341. [PMID: 29574495 DOI: 10.1007/s00572-018-0830-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 03/13/2018] [Indexed: 06/08/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) are widespread, important plant symbionts. They absorb and translocate mineral nutrients from the soil to host plants through an extensive extraradical mycelium, consisting of indefinitely large networks of nonseptate, multinucleated hyphae which may be interconnected by hyphal fusions (anastomoses). This work investigated whether different lineages of the same isolate may lose the ability to establish successful anastomoses, becoming vegetatively incompatible, when grown separately. The occurrence of hyphal incompatibility among five lineages of Funneliformis mosseae, originated from the same ancestor isolate and grown in vivo for more than 20 years in different European locations, was assessed by systematic detection of anastomosis frequency and cytological studies. Anastomosis frequencies ranged from 60 to 80% within the same lineage and from 17 to 44% among different lineages. The consistent detection of protoplasm continuity and nuclei in perfect fusions showed active protoplasm flow both within and between lineages. In pairings between different lineages, post-fusion incompatible reactions occurred in 6-48% of hyphal contacts and pre-fusion incompatibility in 2-17%. Molecular fingerprinting profiles showed genetic divergence among lineages, with overall Jaccard similarity indices ranging from 0.85 to 0.95. Here, phenotypic divergence among the five F. mosseae lineages was demonstrated by the reduction of their ability to form anastomosis and the detection of high levels of vegetative incompatibility. Our data suggest that potential genetic divergence may occur in AMF over only 20 years and represent the basis for detailed studies on the relationship between genes regulating anastomosis formation and hyphal compatibility in AMF.
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Affiliation(s)
- Cristiana Sbrana
- CNR-Institute of Agricultural Biology and Biotechnology, UOS Pisa, Pisa, Italy.
| | - Patrizia Strani
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Alessandra Pepe
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Candido Barreto de Novais
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
- Forestry Institute, Federal Rural University of Rio de Janeiro, Seropédica, Brazil
| | - Manuela Giovannetti
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
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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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Kamel L, Keller-Pearson M, Roux C, Ané JM. Biology and evolution of arbuscular mycorrhizal symbiosis in the light of genomics. THE NEW PHYTOLOGIST 2017; 213:531-536. [PMID: 27780291 DOI: 10.1111/nph.14263] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 07/27/2016] [Indexed: 06/06/2023]
Abstract
531 I. 531 II. 532 III. 532 IV. 534 V. 534 535 References 535 SUMMARY: Arbuscular mycorrhizal (AM) fungi associate with the vast majority of land plants, providing mutual nutritional benefits and protecting hosts against biotic and abiotic stresses. Significant progress was made recently in our understanding of the genomic organization, the obligate requirements, and the sexual nature of these fungi through the release and subsequent mining of genome sequences. Genomic and genetic approaches also improved our understanding of the signal repertoire used by AM fungi and their plant hosts to recognize each other for the initiation and maintenance of this association. Evolutionary and bioinformatic analyses of host and nonhost plant genomes represent novel ways with which to decipher host mechanisms controlling these associations and shed light on the stepwise acquisition of this genetic toolkit during plant evolution. Mining fungal and plant genomes along with evolutionary and genetic approaches will improve understanding of these symbiotic associations and, in the long term, their usefulness in agricultural settings.
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Affiliation(s)
- Laurent Kamel
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, UPS, CNRS 24 Chemin de Borde Rouge-Auzeville, BP 42617, 31326, Castanet-Tolosan, France
- Agronutrition SA, rue Pierre et Marie Curie Immeuble Biostep, 31670, Labège, France
| | - Michelle Keller-Pearson
- Department of Bacteriology, University of Wisconsin - Madison, Madison, WI, 53706, USA
- Department of Plant Pathology, University of Wisconsin - Madison, Madison, WI, 53706, USA
| | - Christophe Roux
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, UPS, CNRS 24 Chemin de Borde Rouge-Auzeville, BP 42617, 31326, Castanet-Tolosan, France
| | - Jean-Michel Ané
- Department of Bacteriology, University of Wisconsin - Madison, Madison, WI, 53706, USA
- Department of Agronomy, University of Wisconsin - Madison, Madison, WI, 53706, USA
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Ropars J, Toro KS, Noel J, Pelin A, Charron P, Farinelli L, Marton T, Krüger M, Fuchs J, Brachmann A, Corradi N. Evidence for the sexual origin of heterokaryosis in arbuscular mycorrhizal fungi. Nat Microbiol 2016; 1:16033. [PMID: 27572831 DOI: 10.1038/nmicrobiol.2016.33] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 02/23/2016] [Indexed: 12/30/2022]
Abstract
Sexual reproduction is ubiquitous among eukaryotes, and fully asexual lineages are extremely rare. Prominent among ancient asexual lineages are the arbuscular mycorrhizal fungi (AMF), a group of plant symbionts with a multinucleate cytoplasm. Genomic divergence among co-existing nuclei was proposed to drive the evolutionary success of AMF in the absence of sex(1), but this hypothesis has been contradicted by recent genome analyses that failed to find significant genetic diversity within an AMF isolate(2,3). Here, we set out to resolve issues surrounding the genome organization and sexual potential of AMF by exploring the genomes of five isolates of Rhizophagus irregularis, a model AMF. We find that genetic diversity in this species varies among isolates and is structured in a homo-dikaryon-like manner usually linked with the existence of a sexual life cycle. We also identify a putative AMF mating-type locus, containing two genes with structural and evolutionary similarities with the mating-type locus of some Dikarya. Our analyses suggest that this locus may be multi-allelic and that AMF could be heterothallic and bipolar. These findings reconcile opposing views on the genome organization of these ubiquitous plant symbionts and open avenues for strain improvement and environmental application of these organisms.
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Affiliation(s)
- Jeanne Ropars
- Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | | | - Jessica Noel
- Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Adrian Pelin
- Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Philippe Charron
- Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Laurent Farinelli
- FASTERIS S.A., Ch. du Pont-du-Centenaire 109, PO Box 28, CH-1228 Plan-les-Ouates, Switzerland
| | - Timea Marton
- Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Manuela Krüger
- Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ottawa, Ontario, Canada.,Institute of Botany, Academy of Sciences of the Czech Republic, Zámek 1, Průhonice, CZ-25243, Czech Republic
| | - Jörg Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany
| | - Andreas Brachmann
- LMU Munich, Faculty of Biology, Genetics, D-82152 Planegg-Martinsried, Germany
| | - Nicolas Corradi
- Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
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12
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Tang N, San Clemente H, Roy S, Bécard G, Zhao B, Roux C. A Survey of the Gene Repertoire of Gigaspora rosea Unravels Conserved Features among Glomeromycota for Obligate Biotrophy. Front Microbiol 2016; 7:233. [PMID: 26973612 PMCID: PMC4771724 DOI: 10.3389/fmicb.2016.00233] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 02/15/2016] [Indexed: 01/22/2023] Open
Abstract
Arbuscular mycorrhizal (AM) fungi are a diverse group of soil fungi (Glomeromycota) that form the most ancient mutualistic association termed AM symbiosis with a majority of land plants, improving their nutrition uptake and resistance to stresses. In contrast to their great ecological implications, the knowledge of the molecular biological mechanisms involved is still scant, partly due to the limited genomic resources available. Here, we describe the gene repertoire of a new AM fungus Gigaspora rosea (Diversisporales). Among the 86332 non-redundant virtual transcripts assembled, 15346 presented similarities with proteins in the Refseq database and 10175 were assigned with GO terms. KOG and Interpro domain annotations clearly showed an enrichment of genes involved in signal transduction in G. rosea. KEGG pathway analysis indicates that most primary metabolic processes are active in G. rosea. However, as for Rhizophagus irregularis, several metabolic genes were not found, including the fatty acid synthase (FAS) gene. This finding supports the hypothesis that AM fungi depend on the lipids produced by their hosts. Furthermore, the presence of a large number of transporters and 100s of secreted proteins, together with the reduced number of plant cell wall degrading enzymes could be interpreted as an evolutionary adaptation to its mutualistic obligate biotrophy. The detection of meiosis-related genes suggests that G. rosea might use a cryptic sexual process. Lastly, a phylogeny of basal fungi clearly shows Glomeromycota as a sister clade to Mucoromycotina, not only to the Mucorales or Mortierellales. The characterization of the gene repertoire from an AM fungal species belonging to the order of Diversisporales and its comparison with the gene sets of R. irregularis (Glomerales) and Gigaspora margarita (Diversisporales), reveal that AM fungi share several features linked to mutualistic obligate biotrophy. This work contributes to lay the foundation for forthcoming studies into the genomics of Diversisporales, and also illuminates the utility of comparing gene repertoires of species from Diversisporales and other clades of Glomeromycota to gain more insights into the genetics and evolution of this fungal group.
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Affiliation(s)
- Nianwu Tang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural UniversityWuhan, China
- CNRS, Laboratoire de Recherche en Sciences Végétales, UMR, Université Paul Sabatier – Université de ToulouseCastanet Tolosan, France
| | - Hélène San Clemente
- CNRS, Laboratoire de Recherche en Sciences Végétales, UMR, Université Paul Sabatier – Université de ToulouseCastanet Tolosan, France
| | - Sébastien Roy
- AGRONUTRITION Laboratoire de BiotechnologiesToulouse, France
| | - Guillaume Bécard
- CNRS, Laboratoire de Recherche en Sciences Végétales, UMR, Université Paul Sabatier – Université de ToulouseCastanet Tolosan, France
| | - Bin Zhao
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Christophe Roux
- CNRS, Laboratoire de Recherche en Sciences Végétales, UMR, Université Paul Sabatier – Université de ToulouseCastanet Tolosan, France
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13
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Ropars J, Corradi N. Homokaryotic vs heterokaryotic mycelium in arbuscular mycorrhizal fungi: different techniques, different results? THE NEW PHYTOLOGIST 2015; 208:638-641. [PMID: 25952991 DOI: 10.1111/nph.13448] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Affiliation(s)
- Jeanne Ropars
- Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Nicolas Corradi
- Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
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14
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Abstract
Research over the past two decades shows that both recombination and clonality are likely to contribute to the reproduction of all fungi. This view of fungi is different from the historical and still commonly held view that a large fraction of fungi are exclusively clonal and that some fungi have been exclusively clonal for hundreds of millions of years. Here, we first will consider how these two historical views have changed. Then we will examine the impact on fungal research of the concept of restrained recombination [Tibayrenc M, Ayala FJ (2012) Proc Natl Acad Sci USA 109 (48):E3305-E3313]. Using animal and human pathogenic fungi, we examine extrinsic restraints on recombination associated with bottlenecks in genetic variation caused by geographic dispersal and extrinsic restraints caused by shifts in reproductive mode associated with either disease transmission or hybridization. Using species of the model yeast Saccharomyces and the model filamentous fungus Neurospora, we examine intrinsic restraints on recombination associated with mating systems that range from strictly clonal at one extreme to fully outbreeding at the other and those that lie between, including selfing and inbreeding. We also consider the effect of nomenclature on perception of reproductive mode and a means of comparing the relative impact of clonality and recombination on fungal populations. Last, we consider a recent hypothesis suggesting that fungi thought to have the most severe intrinsic constraints on recombination actually may have the fewest.
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Zou YN, Huang YM, Wu QS, He XH. Mycorrhiza-induced lower oxidative burst is related with higher antioxidant enzyme activities, net H2O2 effluxes, and Ca2+ influxes in trifoliate orange roots under drought stress. MYCORRHIZA 2015; 25:143-52. [PMID: 25085218 DOI: 10.1007/s00572-014-0598-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 07/24/2014] [Indexed: 05/06/2023]
Abstract
Mechanisms of arbuscular mycorrhiza (AM)-induced lower oxidative burst of host plants under drought stress (DS) are not elucidated. A noninvasive microtest technology (NMT) was used to investigate the effects of Funneliformis mosseae on net fluxes of root hydrogen peroxide (H2O2) and calcium ions (Ca2+) in 5-month-old Poncirus trifoliata, in combination with catalase (CAT) and superoxide dismutase (SOD) activities as well as tissue superoxide radical (O2•-) and H2O2 concentrations under DS and well-watered (WW) conditions. A 2-month DS (55% maximum water holding capacity of growth substrates) significantly inhibited AM fungal root colonization, while AM symbiosis significantly increased plant biomass production, irrespective of water status. F. mosseae inoculation generally increased SOD and CAT activity but decreased O2•- and H2O2 concentrations in leaves and roots under WW and DS. Compared with non-AM seedlings, roots of AM seedlings had significantly higher net H2O2 effluxes and net Ca2+ influxes, especially in the meristem zone, but lower net H2O2 efflux in the elongation zone. Net Ca2+ influxes into roots were significantly positively correlated with root net H2O2 effluxes but negatively with root H2O2 concentrations. Results from this study suggest that AM-induced lower oxidative burst is related with higher antioxidant enzyme activities, root net H2O2 effluxes, and Ca2+ influxes under WW and DS.
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Affiliation(s)
- Ying-Ning Zou
- College of Horticulture and Gardening/Institute of Root Biology, Yangtze University, 88 Jingmi Road, Jingzhou, Hubei, 434025, People's Republic of China
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16
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Milgroom MG, Jiménez-Gasco MDM, Olivares García C, Drott MT, Jiménez-Díaz RM. Recombination between clonal lineages of the asexual fungus Verticillium dahliae detected by genotyping by sequencing. PLoS One 2014; 9:e106740. [PMID: 25181515 PMCID: PMC4152335 DOI: 10.1371/journal.pone.0106740] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2014] [Accepted: 08/09/2014] [Indexed: 11/18/2022] Open
Abstract
Most asexual species of fungi have either lost sexuality recently, or they experience recombination by cryptic sexual reproduction. Verticillium dahliae is a plant-pathogenic, ascomycete fungus with no known sexual stage, even though related genera have well-described sexual reproduction. V. dahliae reproduces mitotically and its population structure is highly clonal. However, previously described discrepancies in phylogenetic relationships among clonal lineages may be explained more parsimoniously by recombination than mutation; therefore, we looked for evidence of recombination within and between clonal lineages. Genotyping by sequencing was performed on 141 V. dahliae isolates from diverse geographic and host origins, resulting in 26,748 single-nucleotide polymorphisms (SNPs). We found a strongly clonal population structure with the same lineages as described previously by vegetative compatibility groups (VCGs) and molecular markers. We detected 443 recombination events, evenly distributed throughout the genome. Most recombination events detected were between clonal lineages, with relatively few recombinant haplotypes detected within lineages. The only three isolates with mating type MAT1-1 had recombinant SNP haplotypes; all other isolates had mating type MAT1-2. We found homologs of eight meiosis-specific genes in the V. dahliae genome, all with conserved or partially conserved protein domains. The extent of recombination and molecular signs of sex in (mating-type and meiosis-specific genes) suggest that V. dahliae clonal lineages arose by recombination, even though the current population structure is markedly clonal. Moreover, the detection of new lineages may be evidence that sexual reproduction has occurred recently and may potentially occur under some circumstances. We speculate that the current clonal population structure, despite the sexual origin of lineages, has arisen, in part, as a consequence of agriculture and selection for adaptation to agricultural cropping systems.
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Affiliation(s)
- Michael G. Milgroom
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America
| | - María del Mar Jiménez-Gasco
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Concepción Olivares García
- College of Agriculture and Forestry, University of Córdoba, and Institute for Sustainable Agriculture, CSIC, Campus de Excelencia Internacional Agroalimentario, ceiA3, Córdoba, Spain
| | - Milton T. Drott
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America
| | - Rafael M. Jiménez-Díaz
- College of Agriculture and Forestry, University of Córdoba, and Institute for Sustainable Agriculture, CSIC, Campus de Excelencia Internacional Agroalimentario, ceiA3, Córdoba, Spain
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17
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Chi J, Parrow MW, Dunthorn M. Cryptic Sex in Symbiodinium
(Alveolata, Dinoflagellata) is Supported by an Inventory of Meiotic Genes. J Eukaryot Microbiol 2014; 61:322-7. [DOI: 10.1111/jeu.12110] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Jingyun Chi
- Department of Ecology; University of Kaiserslautern; Erwin Schrödinger Strasse 14 D-67663 Kaiserslautern Germany
| | - Matthew W. Parrow
- Department of Biology; University of North Carolina at Charlotte; 9201 University City Boulevard Charlotte North Carolina 28223 USA
| | - Micah Dunthorn
- Department of Ecology; University of Kaiserslautern; Erwin Schrödinger Strasse 14 D-67663 Kaiserslautern Germany
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18
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Lin K, Limpens E, Zhang Z, Ivanov S, Saunders DGO, Mu D, Pang E, Cao H, Cha H, Lin T, Zhou Q, Shang Y, Li Y, Sharma T, van Velzen R, de Ruijter N, Aanen DK, Win J, Kamoun S, Bisseling T, Geurts R, Huang S. Single nucleus genome sequencing reveals high similarity among nuclei of an endomycorrhizal fungus. PLoS Genet 2014; 10:e1004078. [PMID: 24415955 PMCID: PMC3886924 DOI: 10.1371/journal.pgen.1004078] [Citation(s) in RCA: 172] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Accepted: 11/18/2013] [Indexed: 12/03/2022] Open
Abstract
Nuclei of arbuscular endomycorrhizal fungi have been described as highly diverse due to their asexual nature and absence of a single cell stage with only one nucleus. This has raised fundamental questions concerning speciation, selection and transmission of the genetic make-up to next generations. Although this concept has become textbook knowledge, it is only based on studying a few loci, including 45S rDNA. To provide a more comprehensive insight into the genetic makeup of arbuscular endomycorrhizal fungi, we applied de novo genome sequencing of individual nuclei of Rhizophagus irregularis. This revealed a surprisingly low level of polymorphism between nuclei. In contrast, within a nucleus, the 45S rDNA repeat unit turned out to be highly diverged. This finding demystifies a long-lasting hypothesis on the complex genetic makeup of arbuscular endomycorrhizal fungi. Subsequent genome assembly resulted in the first draft reference genome sequence of an arbuscular endomycorrhizal fungus. Its length is 141 Mbps, representing over 27,000 protein-coding gene models. We used the genomic sequence to reinvestigate the phylogenetic relationships of Rhizophagus irregularis with other fungal phyla. This unambiguously demonstrated that Glomeromycota are more closely related to Mucoromycotina than to its postulated sister Dikarya.
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Affiliation(s)
- Kui Lin
- Laboratory of Computational Molecular Biology, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Erik Limpens
- Laboratory of Molecular Biology, Department of Plant Science, Wageningen University, Wageningen, The Netherlands
| | - Zhonghua Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Sino-Dutch Joint Lab of Horticultural Genomics, Beijing, China
| | - Sergey Ivanov
- Laboratory of Molecular Biology, Department of Plant Science, Wageningen University, Wageningen, The Netherlands
| | | | - Desheng Mu
- Novome Biotech Inc., Zhongguancun Life Science Park, Beijing, China
| | - Erli Pang
- Laboratory of Computational Molecular Biology, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Huifen Cao
- Laboratory of Computational Molecular Biology, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Hwangho Cha
- Laboratory of Computational Molecular Biology, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Tao Lin
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Sino-Dutch Joint Lab of Horticultural Genomics, Beijing, China
| | - Qian Zhou
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Sino-Dutch Joint Lab of Horticultural Genomics, Beijing, China
| | - Yi Shang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Sino-Dutch Joint Lab of Horticultural Genomics, Beijing, China
| | - Ying Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Sino-Dutch Joint Lab of Horticultural Genomics, Beijing, China
| | - Trupti Sharma
- Laboratory of Molecular Biology, Department of Plant Science, Wageningen University, Wageningen, The Netherlands
| | - Robin van Velzen
- Laboratory of Molecular Biology, Department of Plant Science, Wageningen University, Wageningen, The Netherlands
| | - Norbert de Ruijter
- Laboratory of Cell Biology, Department of Plant Science, Wageningen University, Wageningen, The Netherlands
| | - Duur K. Aanen
- Laboratory of Genetics, Department of Plant Science, Wageningen University, Wageningen, The Netherlands
| | - Joe Win
- The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Sophien Kamoun
- The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Ton Bisseling
- Laboratory of Molecular Biology, Department of Plant Science, Wageningen University, Wageningen, The Netherlands
- College of Science, King Saud University, Riyadh, Saudi Arabia
| | - René Geurts
- Laboratory of Molecular Biology, Department of Plant Science, Wageningen University, Wageningen, The Netherlands
| | - Sanwen Huang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Sino-Dutch Joint Lab of Horticultural Genomics, Beijing, China
- Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
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19
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Riley R, Charron P, Idnurm A, Farinelli L, Dalpé Y, Martin F, Corradi N. Extreme diversification of the mating type-high-mobility group (MATA-HMG) gene family in a plant-associated arbuscular mycorrhizal fungus. THE NEW PHYTOLOGIST 2014; 201:254-268. [PMID: 24033097 DOI: 10.1111/nph.12462] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 07/22/2013] [Indexed: 06/02/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) are important plant symbionts that have long been considered evolutionary anomalies because of their apparent long-term lack of sexuality, but recent explorations of available DNA sequence have challenged this notion by revealing the presence of homologues of fungal mating type-high-mobility group (MATA-HMG) and core meiotic genes in these organisms. To obtain more insights into the sexual potential of AMF, homologues of MATA-HMGs were sought in the transcriptome of three AMF isolates, and their functional and evolutionary trajectories were studied in genetically divergent strains of Rhizophagus irregularis using conventional and quantitative PCR procedures. Our analyses revealed the presence of at least 76 homologues of MATA-HMGs in R. irregularis isolates. None of these was found to be surrounded by genes generally found near other known fungal mating type loci, but here we report the presence of a 9-kb-long region in the AMF R. irregularis harbouring a total of four tandem-repeated MATA-HMGs; a feature that highlights a potentially elevated intragenomic diversity in this AMF species. The present study provides intriguing insights into the genome evolution of R. irregularis, and represents a stepping stone for understanding the potential of these fungi to undergo cryptic sex.
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Affiliation(s)
- Rohan Riley
- Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Philippe Charron
- Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Alexander Idnurm
- Division of Cell Biology and Biophysics, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, MO, USA
| | - Laurent Farinelli
- FASTERIS S.A., Ch. du Pont-du-Centenaire 109, PO Box 28, CH-1228, Plan-les-Ouates, Switzerland
| | - Yolande Dalpé
- Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, ON, K1A 0C6, Canada
| | - Francis Martin
- UMR INRA-UHP 'Interaction Arbres/Micro-Organismes', Centre INRA de Nancy, Champenoux, France
| | - Nicolas Corradi
- Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
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20
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Chi J, Mahé F, Loidl J, Logsdon J, Dunthorn M. Meiosis gene inventory of four ciliates reveals the prevalence of a synaptonemal complex-independent crossover pathway. Mol Biol Evol 2013; 31:660-72. [PMID: 24336924 DOI: 10.1093/molbev/mst258] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
To establish which meiosis genes are present in ciliates, and to look for clues as to which recombination pathways may be treaded by them, four genomes were inventoried for 11 meiosis-specific and 40 meiosis-related genes. We found that the set of meiosis genes shared by Tetrahymena thermophila, Paramecium tetraurelia, Ichthyophthirius multifiliis, and Oxytricha trifallax is consistent with the prevalence of a Mus81-dependent class II crossover pathway that is considered secondary in most model eukaryotes. There is little evidence for a canonical class I crossover pathway that requires the formation of a synaptonemal complex (SC). This gene inventory suggests that meiotic processes in ciliates largely depend on mitotic repair proteins for executing meiotic recombination. We propose that class I crossovers and SCs were reduced sometime during the evolution of ciliates. Consistent with this reduction, we provide microscopic evidence for the presence only of degenerate SCs in Stylonychia mytilus. In addition, lower nonsynonymous to synonymous mutation rates of some of the meiosis genes suggest that, in contrast to most other nuclear genes analyzed so far, meiosis genes in ciliates are largely evolving at a slower rate than those genes in fungi and animals.
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Affiliation(s)
- Jingyun Chi
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, Germany
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21
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Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis. Proc Natl Acad Sci U S A 2013; 110:20117-22. [PMID: 24277808 DOI: 10.1073/pnas.1313452110] [Citation(s) in RCA: 444] [Impact Index Per Article: 40.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The mutualistic symbiosis involving Glomeromycota, a distinctive phylum of early diverging Fungi, is widely hypothesized to have promoted the evolution of land plants during the middle Paleozoic. These arbuscular mycorrhizal fungi (AMF) perform vital functions in the phosphorus cycle that are fundamental to sustainable crop plant productivity. The unusual biological features of AMF have long fascinated evolutionary biologists. The coenocytic hyphae host a community of hundreds of nuclei and reproduce clonally through large multinucleated spores. It has been suggested that the AMF maintain a stable assemblage of several different genomes during the life cycle, but this genomic organization has been questioned. Here we introduce the 153-Mb haploid genome of Rhizophagus irregularis and its repertoire of 28,232 genes. The observed low level of genome polymorphism (0.43 SNP per kb) is not consistent with the occurrence of multiple, highly diverged genomes. The expansion of mating-related genes suggests the existence of cryptic sex-related processes. A comparison of gene categories confirms that R. irregularis is close to the Mucoromycotina. The AMF obligate biotrophy is not explained by genome erosion or any related loss of metabolic complexity in central metabolism, but is marked by a lack of genes encoding plant cell wall-degrading enzymes and of genes involved in toxin and thiamine synthesis. A battery of mycorrhiza-induced secreted proteins is expressed in symbiotic tissues. The present comprehensive repertoire of R. irregularis genes provides a basis for future research on symbiosis-related mechanisms in Glomeromycota.
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