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Ament-Velásquez SL, Vogan AA, Wallerman O, Hartmann FE, Gautier V, Silar P, Giraud T, Johannesson H. High-Quality Genome Assemblies of 4 Members of the Podospora anserina Species Complex. Genome Biol Evol 2024; 16:evae034. [PMID: 38386982 PMCID: PMC10936905 DOI: 10.1093/gbe/evae034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/29/2023] [Accepted: 02/17/2024] [Indexed: 02/24/2024] Open
Abstract
The filamentous fungus Podospora anserina is a model organism used extensively in the study of molecular biology, senescence, prion biology, meiotic drive, mating-type chromosome evolution, and plant biomass degradation. It has recently been established that P. anserina is a member of a complex of 7 closely related species. In addition to P. anserina, high-quality genomic resources are available for 2 of these taxa. Here, we provide chromosome-level annotated assemblies of the 4 remaining species of the complex, as well as a comprehensive data set of annotated assemblies from a total of 28 Podospora genomes. We find that all 7 species have genomes of around 35 Mb arranged in 7 chromosomes that are mostly collinear and less than 2% divergent from each other at genic regions. We further attempt to resolve their phylogenetic relationships, finding significant levels of phylogenetic conflict as expected from a rapid and recent diversification.
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Affiliation(s)
- S Lorena Ament-Velásquez
- Division of Population Genetics, Department of Zoology, Stockholm University, 106 91 Stockholm, Sweden
| | - Aaron A Vogan
- Systematic Biology, Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden
| | - Ola Wallerman
- Department of Medical Biochemistry and Microbiology, Comparative Genetics and Functional Genomics, Uppsala University, 752 37 Uppsala, Sweden
| | - Fanny E Hartmann
- Ecologie Systematique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, 91198 Gif-sur-Yvette, France
| | - Valérie Gautier
- Laboratoire Interdisciplinaire des Energies de Demain (LIED), Université de Paris Cité, F-75013 Paris, France
| | - Philippe Silar
- Laboratoire Interdisciplinaire des Energies de Demain (LIED), Université de Paris Cité, F-75013 Paris, France
| | - Tatiana Giraud
- Ecologie Systematique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, 91198 Gif-sur-Yvette, France
| | - Hanna Johannesson
- Systematic Biology, Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden
- The Royal Swedish Academy of Sciences, 114 18 Stockholm, Sweden
- Department of Ecology, Environmental and Plant Sciences, Stockholm University, 106 91 Stockholm, Sweden
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Wang Z, Kim W, Wang YW, Yakubovich E, Dong C, Trail F, Townsend JP, Yarden O. The Sordariomycetes: an expanding resource with Big Data for mining in evolutionary genomics and transcriptomics. FRONTIERS IN FUNGAL BIOLOGY 2023; 4:1214537. [PMID: 37746130 PMCID: PMC10512317 DOI: 10.3389/ffunb.2023.1214537] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 06/06/2023] [Indexed: 09/26/2023]
Abstract
Advances in genomics and transcriptomics accompanying the rapid accumulation of omics data have provided new tools that have transformed and expanded the traditional concepts of model fungi. Evolutionary genomics and transcriptomics have flourished with the use of classical and newer fungal models that facilitate the study of diverse topics encompassing fungal biology and development. Technological advances have also created the opportunity to obtain and mine large datasets. One such continuously growing dataset is that of the Sordariomycetes, which exhibit a richness of species, ecological diversity, economic importance, and a profound research history on amenable models. Currently, 3,574 species of this class have been sequenced, comprising nearly one-third of the available ascomycete genomes. Among these genomes, multiple representatives of the model genera Fusarium, Neurospora, and Trichoderma are present. In this review, we examine recently published studies and data on the Sordariomycetes that have contributed novel insights to the field of fungal evolution via integrative analyses of the genetic, pathogenic, and other biological characteristics of the fungi. Some of these studies applied ancestral state analysis of gene expression among divergent lineages to infer regulatory network models, identify key genetic elements in fungal sexual development, and investigate the regulation of conidial germination and secondary metabolism. Such multispecies investigations address challenges in the study of fungal evolutionary genomics derived from studies that are often based on limited model genomes and that primarily focus on the aspects of biology driven by knowledge drawn from a few model species. Rapidly accumulating information and expanding capabilities for systems biological analysis of Big Data are setting the stage for the expansion of the concept of model systems from unitary taxonomic species/genera to inclusive clusters of well-studied models that can facilitate both the in-depth study of specific lineages and also investigation of trait diversity across lineages. The Sordariomycetes class, in particular, offers abundant omics data and a large and active global research community. As such, the Sordariomycetes can form a core omics clade, providing a blueprint for the expansion of our knowledge of evolution at the genomic scale in the exciting era of Big Data and artificial intelligence, and serving as a reference for the future analysis of different taxonomic levels within the fungal kingdom.
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Affiliation(s)
- Zheng Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, United States
| | - Wonyong Kim
- Korean Lichen Research Institute, Sunchon National University, Suncheon, Republic of Korea
| | - Yen-Wen Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, United States
| | - Elizabeta Yakubovich
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Caihong Dong
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Frances Trail
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | - Jeffrey P. Townsend
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, United States
- Department of Ecology and Evolutionary Biology, Program in Microbiology, and Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, United States
| | - Oded Yarden
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
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Lelandais G, Remy D, Malagnac F, Grognet P. New insights into genome annotation in Podospora anserina through re-exploiting multiple RNA-seq data. BMC Genomics 2022; 23:859. [PMID: 36581831 PMCID: PMC9801653 DOI: 10.1186/s12864-022-09085-4] [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: 09/16/2022] [Accepted: 12/16/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Publicly available RNA-seq datasets are often underused although being helpful to improve functional annotation of eukaryotic genomes. This is especially true for filamentous fungi genomes which structure differs from most well annotated yeast genomes. Podospora anserina is a filamentous fungal model, which genome has been sequenced and annotated in 2008. Still, the current annotation lacks information about cis-regulatory elements, including promoters, transcription starting sites and terminators, which are instrumental to integrate epigenomic features into global gene regulation strategies. RESULTS Here we took advantage of 37 RNA-seq experiments that were obtained in contrasted developmental and physiological conditions, to complete the functional annotation of P. anserina genome. Out of the 10,800 previously annotated genes, 5'UTR and 3'UTR were defined for 7554, among which, 3328 showed differential transcriptional signal starts and/or transcriptional end sites. In addition, alternative splicing events were detected for 2350 genes, mostly due alternative 3'splice sites and 1732 novel transcriptionally active regions (nTARs) in unannotated regions were identified. CONCLUSIONS Our study provides a comprehensive genome-wide functional annotation of P. anserina genome, including chromatin features, cis-acting elements such as UTRs, alternative splicing events and transcription of non-coding regions. These new findings will likely improve our understanding of gene regulation strategies in compact genomes, such as those of filamentous fungi. Characterization of alternative transcripts and nTARs paves the way to the discovery of putative new genes, alternative peptides or regulatory non-coding RNAs.
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Affiliation(s)
- Gaëlle Lelandais
- grid.457334.20000 0001 0667 2738Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Damien Remy
- grid.457334.20000 0001 0667 2738Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Fabienne Malagnac
- grid.457334.20000 0001 0667 2738Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Pierre Grognet
- grid.457334.20000 0001 0667 2738Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
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ATP-Binding Cassette (ABC) Transporters in Fusarium Specific Mycoparasite Sphaerodes mycoparasitica during Biotrophic Mycoparasitism. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12157641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Recent transcriptomic profiling has revealed importance membrane transporters such as ATP-binding cassette (ABC) transporters in fungal necrotrophic mycoparasites. In this study, RNA-Seq allowed rapid detection of ABC transcripts involved in biotrophic mycoparasitism of Sphaerodes mycoparasitica against the phytopathogenic and mycotoxigenic Fusarium graminearum host, the causal agent of Fusarium head blight (FHB). Transcriptomic analyses of highly expressed S. mycoparasitica genes, and their phylogenetic relationships with other eukaryotic fungi, portrayed the ABC transporters’ evolutionary paths towards biotrophic mycoparasitism. Prior to the in silico phylogenetic analyses, transmission electron microscopy (TEM) was used to confirm the formation of appressorium/haustorium infection structures in S. mycoparasitica during early (1.5 d and 3.5 d) stages of mycoparasitism. Transcripts encoding biotrophy-associated secreted proteins did uncover the enrolment of ABC transporter genes in this specific biocontrol mode of action, while tandem ABC and BUB2 (non-ABC) transcripts seemed to be proper for appressorium development. The next-generation HiSeq transcriptomic profiling of the mycoparasitic hypha samples, revealed 81 transcripts annotated to ABC transporters consisting of a variety of ABC-B (14%), ABC-C (22%), and ABC-G (23%), and to ABC-A, ABC-F, aliphatic sulfonates importer (TC 3.A.1.17.2), BtuF, ribose importer (TC 3.A.1.2.1), and unknown families. The most abundant transcripts belonged to the multidrug resistance exporter (TC 3.A.1.201) subfamily of the ABC-B family, the conjugate transporter (TC 3.A.1.208) subfamily of the ABC-C family, and the pleiotropic drug resistance (PDR) (TC 3.A.1.205) subfamily of the ABC-G family. These findings highlight the significance of ABC transporter genes that control cellular detoxification against toxic substances (e.g., chemical pesticides and mycotoxins) in sustaining a virulence of S. mycoparasitica for effective biotrophic mycoparasitism on the F. graminearum host. The findings of this study provide clues to better understand the biotrophic mycoparasitism of S. mycoparasitica interacting with the Fusarium host, which implies that the ABC transporter group of key proteins is involved in the mycoparasite’s virulence and multidrug resistance to toxic substances including cellular detoxification.
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A gene cluster with positive and negative elements controls bistability and hysteresis of the Crippled versus Normal growth in the fungus Podospora anserina. Fungal Genet Biol 2022; 161:103711. [PMID: 35597448 DOI: 10.1016/j.fgb.2022.103711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/06/2022] [Accepted: 05/15/2022] [Indexed: 11/23/2022]
Abstract
The Crippled Growth (CG) cell degeneration of the model ascomycete Podospora anserina (strain S) is controlled by a prion-like element and has been linked to the self-activation of the PaMpk1 MAP kinase cascade. Here, we report on the identification of the "86-11" locus containing twelve genes, ten of which are involved either in setting up the self-activation loop of CG or in inhibiting this loop, as demonstrated by targeted gene deletion. Interestingly, deletion of the whole locus results only in the elimination of CG and in no detectable additional physiological defect. Sequence comparison shows that these ten genes belong to four different families, each one endowed with a specific activity: two encode factors activating the loop, a third one encodes a factor crucial for inhibition of the loop and the fourth one participates in inhibiting the loop in a pathway parallel to the one controlled by the previously described PDC1 gene. Intriguingly, a very distant homologue of this "86-11" locus is present at the syntenic position in Podospora comata (strain T) that do not present Crippled Growth. Introgression of the P. comata strain T locus in P. anserina strain S and the P. anserina strain S in P. comata strain T showed that both drive CG in the P. anserina strain S genetic background, but not in the genetic background of strain P. comata T, indicating that genetic determinants outside the twelve-gene locus are responsible for lack of CG in P. comata strain T. Our data question the role of this twelve-gene locus in the physiology of P. anserina.
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Hartmann FE, Ament-Velásquez SL, Vogan AA, Gautier V, Le Prieur S, Berramdane M, Snirc A, Johannesson H, Grognet P, Malagnac F, Silar P, Giraud T. Size Variation of the Nonrecombining Region on the Mating-Type Chromosomes in the Fungal Podospora anserina Species Complex. Mol Biol Evol 2021; 38:2475-2492. [PMID: 33555341 PMCID: PMC8136517 DOI: 10.1093/molbev/msab040] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Sex chromosomes often carry large nonrecombining regions that can extend progressively over time, generating evolutionary strata of sequence divergence. However, some sex chromosomes display an incomplete suppression of recombination. Large genomic regions without recombination and evolutionary strata have also been documented around fungal mating-type loci, but have been studied in only a few fungal systems. In the model fungus Podospora anserina (Ascomycota, Sordariomycetes), the reference S strain lacks recombination across a 0.8-Mb region around the mating-type locus. The lack of recombination in this region ensures that nuclei of opposite mating types are packaged into a single ascospore (pseudohomothallic lifecycle). We found evidence for a lack of recombination around the mating-type locus in the genomes of ten P. anserina strains and six closely related pseudohomothallic Podospora species. Importantly, the size of the nonrecombining region differed between strains and species, as indicated by the heterozygosity levels around the mating-type locus and experimental selfing. The nonrecombining region is probably labile and polymorphic, differing in size and precise location within and between species, resulting in occasional, but infrequent, recombination at a given base pair. This view is also supported by the low divergence between mating types, and the lack of strong linkage disequilibrium, chromosomal rearrangements, transspecific polymorphism and genomic degeneration. We found a pattern suggestive of evolutionary strata in P. pseudocomata. The observed heterozygosity levels indicate low but nonnull outcrossing rates in nature in these pseudohomothallic fungi. This study adds to our understanding of mating-type chromosome evolution and its relationship to mating systems.
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Affiliation(s)
- Fanny E Hartmann
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | | | - Aaron A Vogan
- Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Valérie Gautier
- Laboratoire Interdisciplinaire des Energies de Demain, Université de Paris, Paris, France
| | - Stephanie Le Prieur
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Myriam Berramdane
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Alodie Snirc
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | | | - Pierre Grognet
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Gif-sur-Yvette, France
| | - Fabienne Malagnac
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Gif-sur-Yvette, France
| | - Philippe Silar
- Laboratoire Interdisciplinaire des Energies de Demain, Université de Paris, Paris, France
| | - Tatiana Giraud
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
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7
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Carlier F, Li M, Maroc L, Debuchy R, Souaid C, Noordermeer D, Grognet P, Malagnac F. Loss of EZH2-like or SU(VAR)3-9-like proteins causes simultaneous perturbations in H3K27 and H3K9 tri-methylation and associated developmental defects in the fungus Podospora anserina. Epigenetics Chromatin 2021; 14:22. [PMID: 33962663 PMCID: PMC8105982 DOI: 10.1186/s13072-021-00395-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 04/19/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Selective gene silencing is key to development. It is generally accepted that H3K27me3-enriched heterochromatin maintains transcriptional repression established during early development and regulates cell fate. Conversely, H3K9me3-enriched heterochromatin prevents differentiation but constitutes protection against transposable elements. We exploited the fungus Podospora anserina, a valuable alternative to higher eukaryote models, to question the biological relevance and functional interplay of these two distinct heterochromatin conformations. RESULTS We established genome-wide patterns of H3K27me3 and H3K9me3 modifications, and found these marks mutually exclusive within gene-rich regions but not within repeats. We generated the corresponding histone methyltransferase null mutants and showed an interdependence of H3K9me3 and H3K27me3 marks. Indeed, removal of the PaKmt6 EZH2-like enzyme resulted not only in loss of H3K27me3 but also in significant H3K9me3 reduction. Similarly, removal of PaKmt1 SU(VAR)3-9-like enzyme caused loss of H3K9me3 and substantial decrease of H3K27me3. Removal of the H3K9me binding protein PaHP1 provided further support to the notion that each type of heterochromatin requires the presence of the other. We also established that P. anserina developmental programs require H3K27me3-mediated silencing, since loss of the PaKmt6 EZH2-like enzyme caused severe defects in most aspects of the life cycle including growth, differentiation processes and sexual reproduction, whereas loss of the PaKmt1 SU(VAR)3-9-like enzyme resulted only in marginal defects, similar to loss of PaHP1. CONCLUSIONS Our findings support a conserved function of the PRC2 complex in fungal development. However, we uncovered an intriguing evolutionary fluidity in the repressive histone deposition machinery, which challenges canonical definitions of constitutive and facultative heterochromatin.
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Affiliation(s)
- F Carlier
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198, Gif-sur-Yvette, France
- Group Fungal Epigenomics, Department of Mycology, Institut Pasteur, Paris, France
| | - M Li
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198, Gif-sur-Yvette, France
| | - L Maroc
- Génétique Quantitative et Évolution-Le Moulon, INRA-Université Paris-Saclay-CNRS-AgroParisTech, Batiment 400, UFR Des Sciences, 91405, Orsay CEDEX, France
| | - R Debuchy
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198, Gif-sur-Yvette, France
| | - C Souaid
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198, Gif-sur-Yvette, France
- Inserm, Theories and Approaches of Genomic Complexity (TAGC), UMR1090, Aix-Marseille University, 13288, Marseille, France
| | - D Noordermeer
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198, Gif-sur-Yvette, France
| | - P Grognet
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198, Gif-sur-Yvette, France.
| | - F Malagnac
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198, Gif-sur-Yvette, France.
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8
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Vogan AA, Ament-Velásquez SL, Bastiaans E, Wallerman O, Saupe SJ, Suh A, Johannesson H. The Enterprise, a massive transposon carrying Spok meiotic drive genes. Genome Res 2021; 31:789-798. [PMID: 33875482 PMCID: PMC8092012 DOI: 10.1101/gr.267609.120] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 03/05/2021] [Indexed: 12/19/2022]
Abstract
The genomes of eukaryotes are full of parasitic sequences known as transposable elements (TEs). Here, we report the discovery of a putative giant tyrosine-recombinase-mobilized DNA transposon, Enterprise, from the model fungus Podospora anserina Previously, we described a large genomic feature called the Spok block which is notable due to the presence of meiotic drive genes of the Spok gene family. The Spok block ranges from 110 kb to 247 kb and can be present in at least four different genomic locations within P. anserina, despite what is an otherwise highly conserved genome structure. We propose that the reason for its varying positions is that the Spok block is not only capable of meiotic drive but is also capable of transposition. More precisely, the Spok block represents a unique case where the Enterprise has captured the Spoks, thereby parasitizing a resident genomic parasite to become a genomic hyperparasite. Furthermore, we demonstrate that Enterprise (without the Spoks) is found in other fungal lineages, where it can be as large as 70 kb. Lastly, we provide experimental evidence that the Spok block is deleterious, with detrimental effects on spore production in strains which carry it. This union of meiotic drivers and a transposon has created a selfish element of impressive size in Podospora, challenging our perception of how TEs influence genome evolution and broadening the horizons in terms of what the upper limit of transposition may be.
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Affiliation(s)
- Aaron A Vogan
- Systematic Biology, Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden
| | - S Lorena Ament-Velásquez
- Systematic Biology, Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden
| | - Eric Bastiaans
- Systematic Biology, Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden
- Laboratory of Genetics, Wageningen University, 6703 BD, Wageningen, The Netherlands
| | - Ola Wallerman
- Department of Medical Biochemistry and Microbiology, Comparative Genetics and Functional Genomics; Uppsala University, 752 37 Uppsala, Sweden
| | - Sven J Saupe
- IBGC, UMR 5095, CNRS Université de Bordeaux, 33077 Bordeaux Cedex, France
| | - Alexander Suh
- Systematic Biology, Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden
| | - Hanna Johannesson
- Systematic Biology, Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden
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9
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Ament-Velásquez SL, Johannesson H, Giraud T, Debuchy R, Saupe SJ, Debets AJ, Bastiaans E, Malagnac F, Grognet P, Peraza-Reyes L, Gladieux P, Kruys Å, Silar P, Huhndorf SM, Miller AN, Vogan AA. The taxonomy of the model filamentous fungus Podospora anserina. MycoKeys 2020; 75:51-69. [PMID: 33281477 PMCID: PMC7710671 DOI: 10.3897/mycokeys.75.55968] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 08/11/2020] [Indexed: 11/17/2022] Open
Abstract
The filamentous fungus Podospora anserina has been used as a model organism for more than 100 years and has proved to be an invaluable resource in numerous areas of research. Throughout this period, P. anserina has been embroiled in a number of taxonomic controversies regarding the proper name under which it should be called. The most recent taxonomic treatment proposed to change the name of this important species to Triangularia anserina. The results of past name changes of this species indicate that the broader research community is unlikely to accept this change, which will lead to nomenclatural instability and confusion in literature. Here, we review the phylogeny of the species closely related to P. anserina and provide evidence that currently available marker information is insufficient to resolve the relationships amongst many of the lineages. We argue that it is not only premature to propose a new name for P. anserina based on current data, but also that every effort should be made to retain P. anserina as the current name to ensure stability and to minimise confusion in scientific literature. Therefore, we synonymise Triangularia with Podospora and suggest that either the type species of Podospora be moved to P. anserina from P. fimiseda or that all species within the Podosporaceae be placed in the genus Podospora.
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Affiliation(s)
- S. Lorena Ament-Velásquez
- Systematic Biology, Department of Organismal Biology, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, SwedenUppsala UniveristyUppsalaSweden
| | - Hanna Johannesson
- Systematic Biology, Department of Organismal Biology, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, SwedenUppsala UniveristyUppsalaSweden
| | - Tatiana Giraud
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, 91400, Orsay, FranceUniversité Paris-SaclayOrsayFrance
| | - Robert Debuchy
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, FranceUniversité Paris-SaclayGif-sur-YvetteFrance
| | - Sven J. Saupe
- IBGC, UMR 5095, CNRS Université de Bordeaux, 1 rue Camille Saint Saëns, 33077, Bordeaux, FranceUniversité de BordeauxBordeauxFrance
| | - Alfons J.M. Debets
- Laboratory of Genetics, Wageningen University, Arboretumlaan 4, 6703 BD, Wageningen, NetherlandsWageningen UniversityWageningenNetherlands
| | - Eric Bastiaans
- Laboratory of Genetics, Wageningen University, Arboretumlaan 4, 6703 BD, Wageningen, NetherlandsWageningen UniversityWageningenNetherlands
| | - Fabienne Malagnac
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, FranceUniversité Paris-SaclayGif-sur-YvetteFrance
| | - Pierre Grognet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, FranceUniversité Paris-SaclayGif-sur-YvetteFrance
| | - Leonardo Peraza-Reyes
- Instituto de Fisiología Celular, Departamento de Bioquímica y Biología Estructural, Universidad Nacional Autónoma de México, Mexico City, MexicoUniversidad Nacional Autónoma de MéxicoMexico CityMexico
| | - Pierre Gladieux
- UMR BGPI, Université de Montpellier, INRAE, CIRAD, Institut Agro, F-34398, Montpellier, FranceUniversité de MontpellierMontpellierFrance
| | - Åsa Kruys
- Museum of Evolution, Botany, Uppsala University, Norbyvägen 18, 752 36, Uppsala, SwedenUppsala UniversityUppsalaSweden
| | - Philippe Silar
- Université de Paris, Laboratoire Interdisciplinaire des Energies de Demain (LIED), F-75006, Paris, FranceUniversité de ParisParisFrance
| | - Sabine M. Huhndorf
- Botany Department, The Field Museum, Chicago, Illinois 60605, USAThe Field MuseumChicagoUnited States of America
| | - Andrew N. Miller
- Illinois Natural History Survey, University of Illinois, Champaign, IL 61820, USAUniversity of IllinoisChampaignUnited States of America
| | - Aaron A. Vogan
- Systematic Biology, Department of Organismal Biology, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, SwedenUppsala UniveristyUppsalaSweden
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Li Y, Yan P, Lu X, Qiu Y, Liang S, Liu G, Li S, Mou L, Xie N. Involvement of PaSNF1 in Fungal Development, Sterigmatocystin Biosynthesis, and Lignocellulosic Degradation in the Filamentous Fungus Podospora anserina. Front Microbiol 2020; 11:1038. [PMID: 32587577 PMCID: PMC7299030 DOI: 10.3389/fmicb.2020.01038] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Accepted: 04/27/2020] [Indexed: 02/05/2023] Open
Abstract
The sucrose non-fermenting 1/AMP-activated protein kinase (SNF1/AMPK) is a central regulator of carbon metabolism and energy production in the eukaryotes. In this study, the functions of the Podospora anserina SNF1 (PaSNF1) ortholog were investigated. The ΔPaSNF1 mutant displays a delayed development of mycelium and fruiting bodies and fails to form ascospores. The expression of the PaSNF1 gene in the strain providing female organs in a cross is sufficient to ensure fertility, indicating a maternal effect. Results of environmental stress showed that ΔPaSNF1 was hypersensitive to stress, such as osmotic pressure and heat shock, and resistant to fluconazole. Interestingly, the knockout of PaSNF1 significantly promoted sterigmatocystin (ST) synthesis but suppressed cellulase [filter paperase (FPA), endoglucanase (EG), and β-glucosidase (BG)] activity. Further, transcriptome analysis indicated that PaSNF1 made positive regulatory effects on the expression of genes encoding cellulolytic enzymes. These results suggested that PaSNF1 may function in balancing the operation of primary and secondary metabolism. This study suggested that SNF1 was a key regulator concerting vegetative growth, sexual development, and stress tolerance. Our study provided the first genetic evidence that SNF1 was involved in the ST biosynthesis and that it may also be a major actor of lignocellulose degradation in P. anserina.
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Affiliation(s)
- Yuanjing Li
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Pengfei Yan
- Key Laboratory of Functional Inorganic Material Chemistry (MOE), School of Chemistry and Materials Science, Heilongjiang University, Harbin, China
| | - Xiaojie Lu
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Yanling Qiu
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Shang Liang
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Gang Liu
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Shuangfei Li
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Lin Mou
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Ning Xie
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
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Grognet P, Timpano H, Carlier F, Aït-Benkhali J, Berteaux-Lecellier V, Debuchy R, Bidard F, Malagnac F. A RID-like putative cytosine methyltransferase homologue controls sexual development in the fungus Podospora anserina. PLoS Genet 2019; 15:e1008086. [PMID: 31412020 PMCID: PMC6709928 DOI: 10.1371/journal.pgen.1008086] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 08/26/2019] [Accepted: 07/15/2019] [Indexed: 11/18/2022] Open
Abstract
DNA methyltransferases are ubiquitous enzymes conserved in bacteria, plants and opisthokonta. These enzymes, which methylate cytosines, are involved in numerous biological processes, notably development. In mammals and higher plants, methylation patterns established and maintained by the cytosine DNA methyltransferases (DMTs) are essential to zygotic development. In fungi, some members of an extensively conserved fungal-specific DNA methyltransferase class are both mediators of the Repeat Induced Point mutation (RIP) genome defense system and key players of sexual reproduction. Yet, no DNA methyltransferase activity of these purified RID (RIP deficient) proteins could be detected in vitro. These observations led us to explore how RID-like DNA methyltransferase encoding genes would play a role during sexual development of fungi showing very little genomic DNA methylation, if any. To do so, we used the model ascomycete fungus Podospora anserina. We identified the PaRid gene, encoding a RID-like DNA methyltransferase and constructed knocked-out ΔPaRid defective mutants. Crosses involving P. anserina ΔPaRid mutants are sterile. Our results show that, although gametes are readily formed and fertilization occurs in a ΔPaRid background, sexual development is blocked just before the individualization of the dikaryotic cells leading to meiocytes. Complementation of ΔPaRid mutants with ectopic alleles of PaRid, including GFP-tagged, point-mutated and chimeric alleles, demonstrated that the catalytic motif of the putative PaRid methyltransferase is essential to ensure proper sexual development and that the expression of PaRid is spatially and temporally restricted. A transcriptomic analysis performed on mutant crosses revealed an overlap of the PaRid-controlled genetic network with the well-known mating-types gene developmental pathway common to an important group of fungi, the Pezizomycotina.
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Affiliation(s)
- Pierre Grognet
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris‐Saclay, France
| | - Hélène Timpano
- Université Paris-Sud, Institut de Génétique et Microbiologie UMR8621, Orsay, France, CNRS, Institut de Génétique et Microbiologie UMR8621, Orsay, France
| | - Florian Carlier
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris‐Saclay, France
| | - Jinane Aït-Benkhali
- Université Paris-Sud, Institut de Génétique et Microbiologie UMR8621, Orsay, France, CNRS, Institut de Génétique et Microbiologie UMR8621, Orsay, France
| | | | - Robert Debuchy
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris‐Saclay, France
| | - Frédérique Bidard
- Université Paris-Sud, Institut de Génétique et Microbiologie UMR8621, Orsay, France, CNRS, Institut de Génétique et Microbiologie UMR8621, Orsay, France
| | - Fabienne Malagnac
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris‐Saclay, France
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Vogan AA, Ament-Velásquez SL, Granger-Farbos A, Svedberg J, Bastiaans E, Debets AJ, Coustou V, Yvanne H, Clavé C, Saupe SJ, Johannesson H. Combinations of Spok genes create multiple meiotic drivers in Podospora. eLife 2019; 8:46454. [PMID: 31347500 PMCID: PMC6660238 DOI: 10.7554/elife.46454] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 06/09/2019] [Indexed: 11/13/2022] Open
Abstract
Meiotic drive is the preferential transmission of a particular allele during sexual reproduction. The phenomenon is observed as spore killing in multiple fungi. In natural populations of Podospora anserina, seven spore killer types (Psks) have been identified through classical genetic analyses. Here we show that the Spok gene family underlies the Psks. The combination of Spok genes at different chromosomal locations defines the spore killer types and creates a killing hierarchy within a population. We identify two novel Spok homologs located within a large (74–167 kbp) region (the Spok block) that resides in different chromosomal locations in different strains. We confirm that the SPOK protein performs both killing and resistance functions and show that these activities are dependent on distinct domains, a predicted nuclease and kinase domain. Genomic and phylogenetic analyses across ascomycetes suggest that the Spok genes disperse through cross-species transfer, and evolve by duplication and diversification within lineages. In many organisms, most cells carry two versions of a given gene, one coming from the mother and the other from the father. An exception is sexual cells such as eggs, sperm, pollen or spores, which should only contain one variant of a gene. During their formation, these cells usually have an equal chance of inheriting one of the two gene versions. However, a certain class of gene variants called meiotic drivers can cheat this process and end up in more than half of the sexual cells; often, the cells that contain the drivers can kill sibling cells that do not carry these variants. This results in the selfish genetic elements spreading through populations at a higher rate, sometimes with severe consequences such as shifting the ratio of males to females. Meiotic drivers have been discovered in a wide range of organisms, from corn to mice to fruit flies and bread mold. They also exist in the fungus Podospora anserina, where they are called ‘spore killers’. Fungi are often used to study complex genetic processes, yet the identity and mode of action of spore killers in P. anserina were still unknown. Vogan, Ament-Velásquez et al. used a combination of genetic methods to identify three genes from the Spok family which are responsible for certain spores being able to kill their siblings. Two of these were previously unknown, and they could be found in different locations throughout the genome as part of a larger genetic region. Depending on the combination of Spok genes it carries, a spore can kill or be protected against other spores that contain different permutations of the genes. Copies of these genes were also shown to be present in other fungi, including species that are a threat to crops. Scientists have already started to create synthetic meiotic drivers to manipulate how certain traits are inherited within a population. This could be useful to control or eradicate pests and insects that transmit dangerous diseases. The results by Vogan, Ament-Velásquez et al. shine a light on the complex ways that natural meiotic drivers work, including how they can be shared between species; this knowledge could inform how to safely deploy synthetic drivers in the wild.
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Affiliation(s)
- Aaron A Vogan
- Organismal biology, Uppsala University, Uppsala, Sweden
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Abstract
Fungi are prone to phenotypic instability, that is, the vegetative phase of these organisms, be they yeasts or molds, undergoes frequent switching between two or more behaviors, often with different morphologies, but also sometime having different physiologies without any obvious morphological outcome. In the context of industrial utilization of fungi, this can have a negative impact on the maintenance of strains and/or on their productivity. Instabilities have been shown to result from various mechanisms, either genetic or epigenetic. This chapter will review different types of instabilities and discuss some lesser-known ones, mostly in filamentous fungi, while it will direct readers to additional literature in the case of well-known phenomena such as the amyloid prions or fungal senescence. It will present in depth the "white/opaque" switch of Candida albicans and the "crippled growth" degeneration of the model fungus Podospora anserina. These are two of the most thoroughly studied epigenetic phenotypic switches. I will also discuss the "sectors" presented by many filamentous ascomycetes, for which a prion-based model exists but is not demonstrated. Finally, I will also describe intriguing examples of phenotypic instability for which an explanation has yet to be provided.
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