1
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Holden S, Bakkeren G, Hubensky J, Bamrah R, Abbasi M, Qutob D, de Graaf ML, Kim SH, Kutcher HR, McCallum BD, Randhawa HS, Iqbal M, Uloth K, Burlakoti RR, Brar GS. Uncovering the history of recombination and population structure in western Canadian stripe rust populations through mating type alleles. BMC Biol 2023; 21:233. [PMID: 37880702 PMCID: PMC10601111 DOI: 10.1186/s12915-023-01717-9] [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: 04/26/2023] [Accepted: 09/27/2023] [Indexed: 10/27/2023] Open
Abstract
BACKGROUND The population structure of crop pathogens such as Puccinia striiformis f. sp. tritici (Pst), the cause of wheat stripe rust, is of interest to researchers looking to understand these pathogens on a molecular level as well as those with an applied focus such as disease epidemiology. Cereal rusts can reproduce sexually or asexually, and the emergence of novel lineages has the potential to cause serious epidemics such as the one caused by the 'Warrior' lineage in Europe. In a global context, Pst lineages in Canada were not well-characterized and the origin of foreign incursions was not known. Additionally, while some Pst mating type genes have been identified in published genomes, there has been no rigorous assessment of mating type diversity and distribution across the species. RESULTS We used a whole-genome/transcriptome sequencing approach for the Canadian Pst population to identify lineages in their global context and evidence tracing foreign incursions. More importantly: for the first time ever, we identified nine alleles of the homeodomain mating type locus in the worldwide Pst population and show that previously identified lineages exhibit a single pair of these alleles. Consistently with the literature, we find only two pheromone receptor mating type alleles. We show that the recent population shift from the 'PstS1' lineage to the 'PstS1-related' lineage is also associated with the introduction of a novel mating type allele (Pst-b3-HD) to the Canadian population. We also show evidence for high levels of mating type diversity in samples associated with the Himalayan center of diversity for Pst, including a single Canadian race previously identified as 'PstPr' (probable recombinant) which we identify as a foreign incursion, most closely related to isolates sampled from China circa 2015. CONCLUSIONS These data describe a recent shift in the population of Canadian Pst field isolates and characterize homeodomain-locus mating type alleles in the global Pst population which can now be utilized in testing several research questions and hypotheses around sexuality and hybridization in rust fungi.
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Affiliation(s)
- Samuel Holden
- Faculty of Land and Food Systems, The University of British Columbia (UBC), Vancouver, BC, Canada.
| | - Guus Bakkeren
- Agriculture and Agri-Food Canada (AAFC), Summerland Research and Development Center, Summerland, BC, Canada
| | - John Hubensky
- Faculty of Land and Food Systems, The University of British Columbia (UBC), Vancouver, BC, Canada
| | - Ramandeep Bamrah
- Faculty of Land and Food Systems, The University of British Columbia (UBC), Vancouver, BC, Canada
| | - Mehrdad Abbasi
- Faculty of Land and Food Systems, The University of British Columbia (UBC), Vancouver, BC, Canada
| | - Dinah Qutob
- Kent State University, Stark Campus, North Canton, OH, USA
| | - Mei-Lan de Graaf
- Agriculture and Agri-Food Canada (AAFC), Summerland Research and Development Center, Summerland, BC, Canada
| | - Sang Hu Kim
- Agriculture and Agri-Food Canada (AAFC), Summerland Research and Development Center, Summerland, BC, Canada
| | - Hadley R Kutcher
- Department of Plant Science/Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Brent D McCallum
- Agriculture and Agri-Food Canada (AAFC), Brandon Research and Development Center, Brandon, MB, Canada
| | - Harpinder S Randhawa
- Agriculture and Agri-Food Canada (AAFC), Lethbridge Research and Development Center, Lethbridge, AB, Canada
| | - Muhammad Iqbal
- Faculty of Agricultural, Life & Environmental Sciences, University of Alberta, Edmonton, AB, Canada
| | - Keith Uloth
- British Columbia Pest Monitoring Network, Dawson Creek, BC, Canada
| | - Rishi R Burlakoti
- Agriculture and Agri-Food Canada (AAFC), Agassiz Research and Development Center, Agassiz, BC, Canada
| | - Gurcharn S Brar
- Faculty of Land and Food Systems, The University of British Columbia (UBC), Vancouver, BC, Canada.
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2
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Raudaskoski M, Butler-Hallissey C. Nuclear-Localized Fluorescent Proteins Enable Visualization of Nuclear Behavior in the Basidiomycete Schizophyllum commune Early Mating Interactions. J Fungi (Basel) 2023; 9:1043. [PMID: 37998849 PMCID: PMC10671879 DOI: 10.3390/jof9111043] [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: 09/12/2023] [Revised: 10/12/2023] [Accepted: 10/21/2023] [Indexed: 11/25/2023] Open
Abstract
Spinning disc confocal microscopical research was conducted on living mating hyphae of the tetrapolar basidiomycete Schizophyllum commune. Haploid strains with either the same or different A and B mating-type genes and expressing differently labelled histone 2B were confronted. In the haploid hyphae histone 2B mCherry and histone 2B EGFP were visualized as red and green nuclei, respectively. In hyphae with the same A but different B genes, the red and green nuclei were observed next to each other. This indicated that nuclear migration between strains, regulated by the B mating type, had taken place. The compatible mating with different A and B genes produced a high number of mixed EFGP/mCherry, yellow nuclei. The mixed nuclei resulted from nearby divisions of nuclei encoding different histones and mating-type genes. During this process, the histones with the different labels were incorporated in the same nuclei, along with the heterodimerized transcription factors encoded by the different A mating-type genes and present around the nuclei. This led to the activation of the A-regulated pathway and indicated that different A genes are important to the cell cycle activation of a compatible mating. Consequently, a yellow nuclear pair stuck together, divided synchronously and proceeded in the migration hyphae towards the colony periphery, where the dikaryotization was promoted by branch formation from the migration hyphae.
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Affiliation(s)
- Marjatta Raudaskoski
- Molecular Plant Biology, Department of Life Technologies, University of Turku, FIN-20014 Turku, Finland
| | - Ciarán Butler-Hallissey
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FIN-20014 Turku, Finland;
- Aix-Marseille Université, CNRS, INP UMR7051, NeuroCyto, 13005 Marseille, France
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3
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Kahmann R. My Personal Journey from the Fascination for Phages to a Tumor-Inducing Fungal Pathogen of Corn. Annu Rev Microbiol 2022; 76:1-19. [PMID: 35395169 DOI: 10.1146/annurev-micro-121721-111032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
My path in science began with a fascination for microbiology and phages and later involved a switch of subjects to the fungus Ustilago maydis and how it causes disease in maize. I will not provide a review of my work but rather focus on decisive findings, serendipitous, lucky moments when major advances made the U. maydis-maize system what it is now-a well-established model for biotrophic fungi. I also want to share with you the joy of finding the needle in a haystack at the very end of my scientific career, a fungal structure likely used for effector delivery, and how we were able to translate this into a potential application in agriculture. Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Regine Kahmann
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany;
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4
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Wang G, Wang Y, Chen L, Wang H, Guo L, Zhou X, Dou M, Wang B, Lin J, Liu L, Wang Z, Deng Y, Zhang J. Genetic structure and evolutionary diversity of mating-type (MAT) loci in Hypsizygus marmoreus. IMA Fungus 2021; 12:35. [PMID: 34930496 PMCID: PMC8686365 DOI: 10.1186/s43008-021-00086-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 12/15/2021] [Indexed: 11/12/2022] Open
Abstract
The mating compatibility in fungi is generally governed by genes located within a single or two unlinked mating type (MAT) loci. Hypsizygus marmoreus is an edible mushroom in the order Agaricales with a tetrapolar system, which contains two unlinked MAT loci-homeodomain (HD) transcription factor genes and pheromone/pheromone receptor genes (P/R). In this study, we analyzed the genetic structure and diversity of MAT loci in tetrapolar system of H. marmoreus through sequencing of 54 heterokaryon and 8 homokaryon strains. Although within the HD loci, the gene order was conserved, the gene contents were variable, and the HD loci haplotypes were further classified into four types. By analyzing the structure, phylogeny, and the HD transmissibility based on the progeny of these four HD mating-type loci types, we found that they were heritable and tightly linked at the HD loci. The P/R loci genes were found to comprise three pheromone receptors, three pheromones, and two pheromone receptor-like genes. Intra- and inter-specific phylogenetic analyses of pheromone receptors revealed that the STE3 genes were divided into three groups, and we thus theorize that they diverged before speciation. Comparative analysis of the MAT regions among 73 Basidiomycete species indicated that the diversity of HD and P/R loci in Agaricales and Boletales may contribute to mating compatibility. The number of HD genes were not correlated with the tetrapolar or bipolar systems. In H. marmoreus, the expression levels of these genes at HD and P/R loci of compatible strains were found higher than in those of homonuclear/homokaryotic strains, indicating that these mating genes acted as switches for mating processes. Further collinear analysis of HD loci in interspecific species found that HD loci contains conserved recombination hotspots showing major rearrangements in Coprinopsis cinerea and Schizophyllum commune, suggesting different mechanisms for evolution of physically linked MAT loci in these groups. It seems likely that gene rearrangements are common in Agaricales fungi around HD loci. Together, our study provides insights into the genomic basis of mating compatibility in H. marmoreus.
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Affiliation(s)
- Gang Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, Yancheng Teachers University, Yancheng, 224002 China
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Yuanyuan Wang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Lianfu Chen
- College of Plant Sciences and Technology, Huazhong Agricultural University, Wuhan, 430000 China
| | - Hongbo Wang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Lin Guo
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Xuan Zhou
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Meijie Dou
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Baiyu Wang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Jingxian Lin
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Lei Liu
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Zhengchao Wang
- Provincial Key Laboratory for Developmental Biology and Neurosciences, College of Life Sciences, Fujian Normal University, Fuzhou, 350002 China
| | - Youjin Deng
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Jisen Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
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Guerreiro MA, Ahrendt S, Pangilinan J, Chen C, Yan M, Lipzen A, Barry K, Grigoriev IV, Begerow D, Nowrousian M. Draft genome sequences of strains CBS6241 and CBS6242 of the basidiomycetous yeast Filobasidium floriforme. G3-GENES GENOMES GENETICS 2021; 12:6428540. [PMID: 34791213 PMCID: PMC9210288 DOI: 10.1093/g3journal/jkab398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 11/08/2021] [Indexed: 12/03/2022]
Abstract
The Tremellomycetes are a species-rich group within the basidiomycete fungi; however, most analyses of this group to date have focused on pathogenic Cryptococcus species within the order Tremellales. Recent genome-assisted studies of other Tremellomycetes have identified interesting features with respect to biotechnological applications as well as the evolution of genes involved in mating and sexual development. Here, we report genome sequences of two strains of Filobasidium floriforme, a species from the order Filobasidiales, which branches basally to the Tremellales, Trichosporonales, and Holtermanniales. The assembled genomes of strains CBS6241 and CBS6242 are 27.4 Mb and 26.4 Mb in size, respectively, with 8314 and 7695 predicted protein-coding genes. Overall sequence identity at nucleic acid level between the strains is 97%. Among the predicted genes are pheromone precursor and pheromone receptor genes as well as two genes encoding homedomain (HD) transcription factors, which are predicted to be part of the mating type (MAT) locus. Sequence analysis indicates that CBS6241 and CBS6242 carry different alleles for both the pheromone/receptor genes as well as the HD transcription factors. Orthology inference identified 1482 orthogroups exclusively found in F. floriforme, some of which were involved in carbohydrate transport and metabolism. Subsequent CAZyme repertoire characterization identified 267 and 247 enzymes for CBS6241 and CBS6242, respectively, the second highest number of CAZymes among the analyzed Tremellomycete species. In addition, F. floriforme contains five CAZymes absent in other species and several plant-cell-wall degrading CAZymes with the highest copy number in Tremellomycota, indicating the biotechnological potential of this species.
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Affiliation(s)
| | - Steven Ahrendt
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Jasmyn Pangilinan
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Cindy Chen
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Mi Yan
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Anna Lipzen
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Kerrie Barry
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California 94720, USA
| | - Dominik Begerow
- Lehrstuhl für Evolution der Pflanzen und Pilze, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Minou Nowrousian
- Lehrstuhl für Molekulare und Zelluläre Botanik, Ruhr-Universität Bochum, 44801 Bochum, Germany
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6
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Boekhout T, Aime MC, Begerow D, Gabaldón T, Heitman J, Kemler M, Khayhan K, Lachance MA, Louis EJ, Sun S, Vu D, Yurkov A. The evolving species concepts used for yeasts: from phenotypes and genomes to speciation networks. FUNGAL DIVERS 2021; 109:27-55. [PMID: 34720775 PMCID: PMC8550739 DOI: 10.1007/s13225-021-00475-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 05/31/2021] [Indexed: 12/12/2022]
Abstract
Here we review how evolving species concepts have been applied to understand yeast diversity. Initially, a phenotypic species concept was utilized taking into consideration morphological aspects of colonies and cells, and growth profiles. Later the biological species concept was added, which applied data from mating experiments. Biophysical measurements of DNA similarity between isolates were an early measure that became more broadly applied with the advent of sequencing technology, leading to a sequence-based species concept using comparisons of parts of the ribosomal DNA. At present phylogenetic species concepts that employ sequence data of rDNA and other genes are universally applied in fungal taxonomy, including yeasts, because various studies revealed a relatively good correlation between the biological species concept and sequence divergence. The application of genome information is becoming increasingly common, and we strongly recommend the use of complete, rather than draft genomes to improve our understanding of species and their genome and genetic dynamics. Complete genomes allow in-depth comparisons on the evolvability of genomes and, consequently, of the species to which they belong. Hybridization seems a relatively common phenomenon and has been observed in all major fungal lineages that contain yeasts. Note that hybrids may greatly differ in their post-hybridization development. Future in-depth studies, initially using some model species or complexes may shift the traditional species concept as isolated clusters of genetically compatible isolates to a cohesive speciation network in which such clusters are interconnected by genetic processes, such as hybridization.
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Affiliation(s)
- Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
- Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - M. Catherine Aime
- Dept Botany and Plant Pathology, College of Agriculture, Purdue University, West Lafayette, IN 47907 USA
| | - Dominik Begerow
- Evolution of Plants and Fungi, Ruhr-University Bochum, 44801 Bochum, Germany
| | - Toni Gabaldón
- Barcelona Supercomputing Centre (BSC–CNS), Jordi Girona, 29, 08034 Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710 USA
| | - Martin Kemler
- Evolution of Plants and Fungi, Ruhr-University Bochum, 44801 Bochum, Germany
| | - Kantarawee Khayhan
- Department of Microbiology and Parasitology, Faculty of Medical Sciences, University of Phayao, Phayao, 56000 Thailand
| | - Marc-André Lachance
- Department of Biology, University of Western Ontario, London, ON N6A 5B7 Canada
| | - Edward J. Louis
- Department of Genetics and Genome Biology, Genetic Architecture of Complex Traits, University of Leicester, Leicester, LE1 7RH UK
| | - Sheng Sun
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710 USA
| | - Duong Vu
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Andrey Yurkov
- German Collection of Microorganisms and Cell Cultures, Leibniz Institute DSMZ, Brunswick, Germany
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7
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Auxier B, Scholtmeijer K, van Peer AF, Baars JJP, Debets AJM, Aanen DK. Cytoplasmic Mixing, Not Nuclear Coexistence, Can Explain Somatic Incompatibility in Basidiomycetes. Microorganisms 2021; 9:1248. [PMID: 34201361 PMCID: PMC8229728 DOI: 10.3390/microorganisms9061248] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/03/2021] [Accepted: 06/04/2021] [Indexed: 12/03/2022] Open
Abstract
Nonself recognition leading to somatic incompatibility (SI) is commonly used by mycologists to distinguish fungal individuals. Despite this, the process remains poorly understood in basidiomycetes as all current models of SI are based on genetic and molecular research in ascomycete fungi. Ascomycete fungi are mainly found in a monokaryotic stage, with a single type of haploid nuclei, and only briefly during mating do two genomes coexist in heterokaryotic cells. The sister phylum, Basidiomycota, differs in several relevant aspects. Basidiomycete fungi have an extended heterokaryotic stage, and SI is generally observed between heterokaryons instead of between homokaryons. Additionally, considerable nuclear migration occurs during a basidiomycete mating reaction, introducing a nucleus into a resident homokaryon with cytoplasmic mixing limited to the fused or neighboring cells. To accommodate these differences, we describe a basidiomycete model for nonself recognition using post-translational modification, based on a reader-writer system as found in other organisms. This post-translational modification combined with nuclear migration allows for the coexistence of two genomes in one individual while maintaining nonself recognition during all life stages. Somewhat surprisingly, this model predicts localized cell death during mating, which is consistent with previous observations but differs from the general assumptions of basidiomycete mating. This model will help guide future research into the mechanisms behind basidiomycete nonself recognition.
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Affiliation(s)
- Ben Auxier
- Laboratory of Genetics, Wageningen University and Research, 6708 PB Wageningen, The Netherlands;
| | - Karin Scholtmeijer
- Mushroom Group, Plant Breeding Department, Wageningen University and Research, 6708 PB Wageningen, The Netherlands; (K.S.); (A.F.v.P.); (J.J.P.B.)
| | - Arend F. van Peer
- Mushroom Group, Plant Breeding Department, Wageningen University and Research, 6708 PB Wageningen, The Netherlands; (K.S.); (A.F.v.P.); (J.J.P.B.)
| | - Johan J. P. Baars
- Mushroom Group, Plant Breeding Department, Wageningen University and Research, 6708 PB Wageningen, The Netherlands; (K.S.); (A.F.v.P.); (J.J.P.B.)
- CNC Grondstoffen, P.O. Box 13, 6590 AA Gennep, The Netherlands
| | - Alfons J. M. Debets
- Laboratory of Genetics, Wageningen University and Research, 6708 PB Wageningen, The Netherlands;
| | - Duur K. Aanen
- Laboratory of Genetics, Wageningen University and Research, 6708 PB Wageningen, The Netherlands;
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8
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Schweizer G, Haider MB, Barroso GV, Rössel N, Münch K, Kahmann R, Dutheil JY. Population Genomics of the Maize Pathogen Ustilago maydis: Demographic History and Role of Virulence Clusters in Adaptation. Genome Biol Evol 2021; 13:evab073. [PMID: 33837781 PMCID: PMC8120014 DOI: 10.1093/gbe/evab073] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/06/2021] [Indexed: 11/14/2022] Open
Abstract
The tight interaction between pathogens and their hosts results in reciprocal selective forces that impact the genetic diversity of the interacting species. The footprints of this selection differ between pathosystems because of distinct life-history traits, demographic histories, or genome architectures. Here, we studied the genome-wide patterns of genetic diversity of 22 isolates of the causative agent of the corn smut disease, Ustilago maydis, originating from five locations in Mexico, the presumed center of origin of this species. In this species, many genes encoding secreted effector proteins reside in so-called virulence clusters in the genome, an arrangement that is so far not found in other filamentous plant pathogens. Using a combination of population genomic statistical analyses, we assessed the geographical, historical, and genome-wide variation of genetic diversity in this fungal pathogen. We report evidence of two partially admixed subpopulations that are only loosely associated with geographic origin. Using the multiple sequentially Markov coalescent model, we inferred the demographic history of the two pathogen subpopulations over the last 0.5 Myr. We show that both populations experienced a recent strong bottleneck starting around 10,000 years ago, coinciding with the assumed time of maize domestication. Although the genome average genetic diversity is low compared with other fungal pathogens, we estimated that the rate of nonsynonymous adaptive substitutions is three times higher in genes located within virulence clusters compared with nonclustered genes, including nonclustered effector genes. These results highlight the role that these singular genomic regions play in the evolution of this pathogen.
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Affiliation(s)
- Gabriel Schweizer
- Department of Organismic Interactions, Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany
| | - Muhammad Bilal Haider
- Max-Planck-Institute for Evolutionary Biology, Research Group Molecular Systems Evolution, Plön, Germany
| | - Gustavo V Barroso
- Max-Planck-Institute for Evolutionary Biology, Research Group Molecular Systems Evolution, Plön, Germany
| | - Nicole Rössel
- Department of Organismic Interactions, Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany
| | - Karin Münch
- Department of Organismic Interactions, Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany
| | - Regine Kahmann
- Department of Organismic Interactions, Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany
| | - Julien Y Dutheil
- Department of Organismic Interactions, Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany
- Max-Planck-Institute for Evolutionary Biology, Research Group Molecular Systems Evolution, Plön, Germany
- Institute of Evolutionary Sciences of Montpellier, University of Montpellier 2, France
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9
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Wallen RM, Richardson K, Furnish M, Mendoza H, Dentinger A, Khanal S, Perlin MH. Hungry for Sex: Differential Roles for Ustilago maydisb Locus Components in Haploid Cells vis à vis Nutritional Availability. J Fungi (Basel) 2021; 7:jof7020135. [PMID: 33673296 PMCID: PMC7918651 DOI: 10.3390/jof7020135] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 01/29/2021] [Accepted: 02/08/2021] [Indexed: 12/25/2022] Open
Abstract
Mating-types allow single-celled eukaryotic organisms to distinguish self from non-self in preparation for sexual reproduction. The components of mating-type loci provide initial self/non-self-recognition through pheromone and receptor interactions that control early cell fusion events. However, they may also provide a second level of scrutiny that requires differences in alleles leading to production of a transcription factor required for successful downstream developmental pathways after initial cell fusion. Interestingly, the protein subunits of these transcription factors have not been thoroughly examined for their roles, if any, in the haploid cells themselves. In Ustilago maydis, the causative agent of galls in maize plants, the b locus, encoding bEast (bE) and bWest (bW), components of the eventual requisite transcription factor, has been extensively studied for its role in formation of the stable dikaryon after mating and subsequent pathogenic program. Little is known, however, about any roles for bE or bW in haploid cells. Since mating in fungi is often induced under conditions of nitrogen starvation, we have explored connections between the b locus and the nitrogen-sensing and response pathways in U. maydis. We previously identified a connection in haploid cells between the b locus and Ump2, the high-affinity transceptor, a protein that both transports ammonium and triggers filamentous growth as a response to nitrogen starvation. Deletion of the entire b locus abrogates the filamentous response to low ammonium, a phenotype that is rescued by overexpression of Ump2. Here we further investigated the individual roles of bE and bW in haploid cells. We show that bE and bW are expressed differentially in haploid cells starved for ammonium. Their respective deletion elicits different effects on transcription of mating and pathogenic-related genes and, importantly, on the degree of pathogenic development in host plants. This is the first demonstration of a role for these mating locus components on haploid development and the first to demonstrate a connection to the ammonium transceptors.
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10
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Perlin MH. Governing diversity: mechanistic insights on the evolution of self/nonself determination. THE NEW PHYTOLOGIST 2020; 228:799-801. [PMID: 32860712 DOI: 10.1111/nph.16847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Affiliation(s)
- Michael H Perlin
- Department of Biology, University of Louisville, Louisville, KY, 40292, USA
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