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Jay P, Jeffries D, Hartmann FE, Véber A, Giraud T. Why do sex chromosomes progressively lose recombination? Trends Genet 2024:S0168-9525(24)00067-2. [PMID: 38677904 DOI: 10.1016/j.tig.2024.03.005] [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: 10/17/2023] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 04/29/2024]
Abstract
Progressive recombination loss is a common feature of sex chromosomes. Yet, the evolutionary drivers of this phenomenon remain a mystery. For decades, differences in trait optima between sexes (sexual antagonism) have been the favoured hypothesis, but convincing evidence is lacking. Recent years have seen a surge of alternative hypotheses to explain progressive extensions and maintenance of recombination suppression: neutral accumulation of sequence divergence, selection of nonrecombining fragments with fewer deleterious mutations than average, sheltering of recessive deleterious mutations by linkage to heterozygous alleles, early evolution of dosage compensation, and constraints on recombination restoration. Here, we explain these recent hypotheses and dissect their assumptions, mechanisms, and predictions. We also review empirical studies that have brought support to the various hypotheses.
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Affiliation(s)
- Paul Jay
- Center for GeoGenetics, University of Copenhagen, Copenhagen, Denmark; Université Paris-Saclay, CNRS, AgroParisTech, Laboratoire Ecologie Systématique et Evolution, UMR 8079, Bâtiment 680, 12 route RD128, 91190 Gif-sur-Yvette, France.
| | - Daniel Jeffries
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Fanny E Hartmann
- Université Paris-Saclay, CNRS, AgroParisTech, Laboratoire Ecologie Systématique et Evolution, UMR 8079, Bâtiment 680, 12 route RD128, 91190 Gif-sur-Yvette, France
| | - Amandine Véber
- Université Paris Cité, CNRS, MAP5, F-75006 Paris, France
| | - Tatiana Giraud
- Université Paris-Saclay, CNRS, AgroParisTech, Laboratoire Ecologie Systématique et Evolution, UMR 8079, Bâtiment 680, 12 route RD128, 91190 Gif-sur-Yvette, France
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2
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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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3
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Luo Z, McTaggart A, Schwessinger B. Genome biology and evolution of mating-type loci in four cereal rust fungi. PLoS Genet 2024; 20:e1011207. [PMID: 38498573 PMCID: PMC10977897 DOI: 10.1371/journal.pgen.1011207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 03/28/2024] [Accepted: 03/04/2024] [Indexed: 03/20/2024] Open
Abstract
Permanent heterozygous loci, such as sex- or mating-compatibility regions, often display suppression of recombination and signals of genomic degeneration. In Basidiomycota, two distinct loci confer mating compatibility. These loci encode homeodomain (HD) transcription factors and pheromone receptor (Pra)-ligand allele pairs. To date, an analysis of genome level mating-type (MAT) loci is lacking for obligate biotrophic basidiomycetes in the Pucciniales, an order containing serious agricultural plant pathogens. Here, we focus on four species of Puccinia that infect oat and wheat, including P. coronata f. sp. avenae, P. graminis f. sp. tritici, P. triticina and P. striiformis f. sp. tritici. MAT loci are located on two separate chromosomes supporting previous hypotheses of a tetrapolar mating compatibility system in the Pucciniales. The HD genes are multiallelic in all four species while the PR locus appears biallelic, except for P. graminis f. sp. tritici, which potentially has multiple alleles. HD loci are largely conserved in their macrosynteny, both within and between species, without strong signals of recombination suppression. Regions proximal to the PR locus, however, displayed signs of recombination suppression and genomic degeneration in the three species with a biallelic PR locus. Our observations support a link between recombination suppression, genomic degeneration, and allele diversity of MAT loci that is consistent with recent mathematical modelling and simulations. Finally, we confirm that MAT genes are expressed during the asexual infection cycle, and we propose that this may support regulating nuclear maintenance and pairing during infection and spore formation. Our study provides insights into the evolution of MAT loci of key pathogenic Puccinia species. Understanding mating compatibility can help predict possible combinations of nuclear pairs, generated by sexual reproduction or somatic recombination, and the potential evolution of new virulent isolates of these important plant pathogens.
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Affiliation(s)
- Zhenyan Luo
- Research Biology School, Australian National University, Canberra, ACT, Australia
| | - Alistair McTaggart
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Ecosciences Precinct, Dutton Park, Queensland, Australia
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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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Vittorelli N, Rodríguez de la Vega RC, Snirc A, Levert E, Gautier V, Lalanne C, De Filippo E, Gladieux P, Guillou S, Zhang Y, Tejomurthula S, Grigoriev IV, Debuchy R, Silar P, Giraud T, Hartmann FE. Stepwise recombination suppression around the mating-type locus in an ascomycete fungus with self-fertile spores. PLoS Genet 2023; 19:e1010347. [PMID: 36763677 PMCID: PMC9949647 DOI: 10.1371/journal.pgen.1010347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 02/23/2023] [Accepted: 01/17/2023] [Indexed: 02/12/2023] Open
Abstract
Recombination is often suppressed at sex-determining loci in plants and animals, and at self-incompatibility or mating-type loci in plants and fungi. In fungal ascomycetes, recombination suppression around the mating-type locus is associated with pseudo-homothallism, i.e. the production of self-fertile dikaryotic sexual spores carrying the two opposite mating types. This has been well studied in two species complexes from different families of Sordariales: Podospora anserina and Neurospora tetrasperma. However, it is unclear whether this intriguing association holds in other species. We show here that Schizothecium tetrasporum, a fungus from a third family in the order Sordariales, also produces mostly self-fertile dikaryotic spores carrying the two opposite mating types. This was due to a high frequency of second meiotic division segregation at the mating-type locus, indicating the occurrence of a single and systematic crossing-over event between the mating-type locus and the centromere, as in P. anserina. The mating-type locus has the typical Sordariales organization, plus a MAT1-1-1 pseudogene in the MAT1-2 haplotype. High-quality genome assemblies of opposite mating types and segregation analyses revealed a suppression of recombination in a region of 1.47 Mb around the mating-type locus. We detected three evolutionary strata, indicating a stepwise extension of recombination suppression. The three strata displayed no rearrangement or transposable element accumulation but gene losses and gene disruptions were present, and precisely at the strata margins. Our findings indicate a convergent evolution of self-fertile dikaryotic sexual spores across multiple ascomycete fungi. The particular pattern of meiotic segregation at the mating-type locus was associated with recombination suppression around this locus, that had extended stepwise. This association between pseudo-homothallism and recombination suppression across lineages and the presence of gene disruption at the strata limits are consistent with a recently proposed mechanism of sheltering deleterious alleles to explain stepwise recombination suppression.
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Affiliation(s)
- Nina Vittorelli
- Ecologie Systematique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
- Laboratoire Interdisciplinaire des Energies de Demain, Université Paris Cité, Paris, France
- Département de Biologie, École Normale Supérieure, PSL Université Paris, Paris, France
| | | | - Alodie Snirc
- Ecologie Systematique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
| | - Emilie Levert
- Ecologie Systematique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
- Laboratoire Interdisciplinaire des Energies de Demain, Université Paris Cité, Paris, France
| | - Valérie Gautier
- Laboratoire Interdisciplinaire des Energies de Demain, Université Paris Cité, Paris, France
| | - Christophe Lalanne
- Laboratoire Interdisciplinaire des Energies de Demain, Université Paris Cité, Paris, France
| | - Elsa De Filippo
- Ecologie Systematique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
- Laboratoire Interdisciplinaire des Energies de Demain, Université Paris Cité, Paris, France
| | - Pierre Gladieux
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Sonia Guillou
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Yu Zhang
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Sravanthi Tejomurthula
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Igor V. Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Robert Debuchy
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Philippe Silar
- Laboratoire Interdisciplinaire des Energies de Demain, Université Paris Cité, Paris, France
| | - Tatiana Giraud
- Ecologie Systematique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
| | - Fanny E. Hartmann
- Ecologie Systematique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
- * E-mail:
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6
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Martinossi-Allibert I, Ament-Velásquez SL, Saupe SJ, Johannesson H. To self or not to self? Absence of mate choice despite costly outcrossing in the fungus Podospora anserina. J Evol Biol 2023; 36:238-250. [PMID: 36263943 PMCID: PMC10092876 DOI: 10.1111/jeb.14108] [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: 03/10/2022] [Revised: 09/16/2022] [Accepted: 09/20/2022] [Indexed: 01/11/2023]
Abstract
Fungi have a large potential for flexibility in their mode of sexual reproduction, resulting in mating systems ranging from haploid selfing to outcrossing. However, we know little about which mating strategies are used in nature, and why, even in well-studied model organisms. Here, we explored the fitness consequences of alternative mating strategies in the ascomycete fungus Podospora anserina. We measured and compared fitness proxies of nine genotypes in either diploid selfing or outcrossing events, over two generations, and with or without environmental stress. We showed that fitness was consistently lower in outcrossing events, irrespective of the environment. The cost of outcrossing was partly attributed to non-self recognition genes with pleiotropic effects on fertility. We then predicted that when presented with options to either self or outcross, individuals would perform mate choice in favour of the reproductive strategy that yields higher fitness. Contrary to our prediction, individuals did not seem to avoid outcrossing when a choice was offered, in spite of the fitness cost incurred. Our results suggest that, although functionally diploid, P. anserina does not benefit from outcrossing in most cases. We outline different explanations for the apparent lack of mate choice in face of high fitness costs associated with outcrossing, including a new perspective on the pleiotropic effect of non-self recognition genes.
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Affiliation(s)
- Ivain Martinossi-Allibert
- Systematic Biology, Department of Organismal Biology, Uppsala University, Uppsala, Sweden.,Institut de Biochimie et de Génétique Cellulaire, UMR 5095 CNRS, Université de Bordeaux, Bordeaux CEDEX, France.,Department of Biology, Realfagbygget, Norwegian University of Science and Technology, Trondheim, Norway
| | | | - Sven J Saupe
- Institut de Biochimie et de Génétique Cellulaire, UMR 5095 CNRS, Université de Bordeaux, Bordeaux CEDEX, France
| | - Hanna Johannesson
- Systematic Biology, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
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7
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Duhamel M, Carpentier F, Begerow D, Hood ME, Rodríguez de la Vega RC, Giraud T. Onset and stepwise extensions of recombination suppression are common in mating-type chromosomes of Microbotryum anther-smut fungi. J Evol Biol 2022; 35:1619-1634. [PMID: 35271741 PMCID: PMC10078771 DOI: 10.1111/jeb.13991] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/21/2021] [Accepted: 02/07/2022] [Indexed: 12/16/2022]
Abstract
Sex chromosomes and mating-type chromosomes can display large genomic regions without recombination. Recombination suppression often extended stepwise with time away from the sex- or mating-type-determining genes, generating evolutionary strata of differentiation between alternative sex or mating-type chromosomes. In anther-smut fungi of the Microbotryum genus, recombination suppression evolved repeatedly, linking the two mating-type loci and extended multiple times in regions distal to the mating-type genes. Here, we obtained high-quality genome assemblies of alternative mating types for four Microbotryum fungi. We found an additional event of independent chromosomal rearrangements bringing the two mating-type loci on the same chromosome followed by recombination suppression linking them. We also found, in a new clade analysed here, that recombination suppression between the two mating-type loci occurred in several steps, with first an ancestral recombination suppression between one of the mating-type locus and its centromere; later, completion of recombination suppression up to the second mating-type locus occurred independently in three species. The estimated dates of recombination suppression between the mating-type loci ranged from 0.15 to 3.58 million years ago. In total, this makes at least nine independent events of linkage between the mating-type loci across the Microbotryum genus. Several mating-type locus linkage events occurred through the same types of chromosomal rearrangements, where similar chromosome fissions at centromeres represent convergence in the genomic changes leading to the phenotypic convergence. These findings further highlight Microbotryum fungi as excellent models to study the evolution of recombination suppression.
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Affiliation(s)
- Marine Duhamel
- Ecologie Systématique Evolution, Bâtiment 360CNRSAgroParisTechUniversité Paris‐SaclayOrsayFrance
- Evolution der Pflanzen und PilzeRuhr‐Universität BochumBochumGermany
| | - Fantin Carpentier
- Ecologie Systématique Evolution, Bâtiment 360CNRSAgroParisTechUniversité Paris‐SaclayOrsayFrance
| | - Dominik Begerow
- Evolution der Pflanzen und PilzeRuhr‐Universität BochumBochumGermany
| | | | | | - Tatiana Giraud
- Ecologie Systématique Evolution, Bâtiment 360CNRSAgroParisTechUniversité Paris‐SaclayOrsayFrance
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8
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Ament-Velásquez SL, Vogan AA, Granger-Farbos A, Bastiaans E, Martinossi-Allibert I, Saupe SJ, de Groot S, Lascoux M, Debets AJM, Clavé C, Johannesson H. Allorecognition genes drive reproductive isolation in Podospora anserina. Nat Ecol Evol 2022; 6:910-923. [PMID: 35551248 PMCID: PMC9262711 DOI: 10.1038/s41559-022-01734-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 03/15/2022] [Indexed: 11/09/2022]
Abstract
Allorecognition, the capacity to discriminate self from conspecific non-self, is a ubiquitous organismal feature typically governed by genes evolving under balancing selection. Here, we show that in the fungus Podospora anserina, allorecognition loci controlling vegetative incompatibility (het genes), define two reproductively isolated groups through pleiotropic effects on sexual compatibility. These two groups emerge from the antagonistic interactions of the unlinked loci het-r (encoding a NOD-like receptor) and het-v (encoding a methyltransferase and an MLKL/HeLo domain protein). Using a combination of genetic and ecological data, supported by simulations, we provide a concrete and molecularly defined example whereby the origin and coexistence of reproductively isolated groups in sympatry is driven by pleiotropic genes under balancing selection.
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Affiliation(s)
- S Lorena Ament-Velásquez
- Systematic Biology, Department of Organismal Biology, Uppsala University, Uppsala, Sweden. .,Department of Zoology, Stockholm University, Stockholm, Sweden.
| | - Aaron A Vogan
- Systematic Biology, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Alexandra Granger-Farbos
- Institut de Biochimie et de Génétique Cellulaires, UMR 5095, CNRS, Université de Bordeaux, Bordeaux, France
| | - Eric Bastiaans
- Systematic Biology, Department of Organismal Biology, Uppsala University, Uppsala, Sweden.,Laboratory of Genetics, Wageningen University & Research, Wageningen, the Netherlands
| | - Ivain Martinossi-Allibert
- Systematic Biology, Department of Organismal Biology, Uppsala University, Uppsala, Sweden.,Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Sven J Saupe
- Institut de Biochimie et de Génétique Cellulaires, UMR 5095, CNRS, Université de Bordeaux, Bordeaux, France
| | - Suzette de Groot
- Laboratory of Genetics, Wageningen University & Research, Wageningen, the Netherlands
| | - Martin Lascoux
- Plant Ecology and Evolution, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Alfons J M Debets
- Laboratory of Genetics, Wageningen University & Research, Wageningen, the Netherlands
| | - Corinne Clavé
- Institut de Biochimie et de Génétique Cellulaires, UMR 5095, CNRS, Université de Bordeaux, Bordeaux, France
| | - Hanna Johannesson
- Systematic Biology, Department of Organismal Biology, Uppsala University, Uppsala, Sweden.
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9
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Foulongne-Oriol M, Taskent O, Kües U, Sonnenberg ASM, van Peer AF, Giraud T. Mating-Type Locus Organization and Mating-Type Chromosome Differentiation in the Bipolar Edible Button Mushroom Agaricus bisporus. Genes (Basel) 2021; 12:1079. [PMID: 34356095 PMCID: PMC8305134 DOI: 10.3390/genes12071079] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/06/2021] [Accepted: 07/09/2021] [Indexed: 12/20/2022] Open
Abstract
In heterothallic basidiomycete fungi, sexual compatibility is restricted by mating types, typically controlled by two loci: PR, encoding pheromone precursors and pheromone receptors, and HD, encoding two types of homeodomain transcription factors. We analysed the single mating-type locus of the commercial button mushroom variety, Agaricus bisporus var. bisporus, and of the related variety burnettii. We identified the location of the mating-type locus using genetic map and genome information, corresponding to the HD locus, the PR locus having lost its mating-type role. We found the mip1 and β-fg genes flanking the HD genes as in several Agaricomycetes, two copies of the β-fg gene, an additional HD2 copy in the reference genome of A. bisporus var. bisporus and an additional HD1 copy in the reference genome of A. bisporus var. burnettii. We detected a 140 kb-long inversion between mating types in an A. bisporus var. burnettii heterokaryon, trapping the HD genes, the mip1 gene and fragments of additional genes. The two varieties had islands of transposable elements at the mating-type locus, spanning 35 kb in the A. bisporus var. burnettii reference genome. Linkage analyses showed a region with low recombination in the mating-type locus region in the A. bisporus var. burnettii variety. We found high differentiation between β-fg alleles in both varieties, indicating an ancient event of recombination suppression, followed more recently by a suppression of recombination at the mip1 gene through the inversion in A. bisporus var. burnettii and a suppression of recombination across whole chromosomes in A. bisporus var. bisporus, constituting stepwise recombination suppression as in many other mating-type chromosomes and sex chromosomes.
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Affiliation(s)
| | - Ozgur Taskent
- Ecologie Systématique Evolution, Bâtiment 360, CNRS, AgroParisTech, Université Paris-Saclay, 91400 Orsay, France;
| | - Ursula Kües
- Molecular Wood Biotechnology and Technical Mycology, Goettingen Center for Molecular Biosciences (GZMB), Büsgen-Institute, University of Goettingen, Büsgenweg 2, 37077 Goettingen, Germany;
| | - Anton S. M. Sonnenberg
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands; (A.S.M.S.); (A.F.v.P.)
| | - Arend F. van Peer
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands; (A.S.M.S.); (A.F.v.P.)
| | - Tatiana Giraud
- Ecologie Systématique Evolution, Bâtiment 360, CNRS, AgroParisTech, Université Paris-Saclay, 91400 Orsay, France;
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