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Sun W, Liu W, Cai Y, Shi X, Wu L, Zhang J, Er L, Huang Q, Yin Q, Zhao Z, He P, Yu F. Structure of the Mating-Type Genes and Mating Systems of Verpa bohemica and Verpa conica (Ascomycota, Pezizomycotina). J Fungi (Basel) 2023; 9:1202. [PMID: 38132802 PMCID: PMC10745113 DOI: 10.3390/jof9121202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/06/2023] [Accepted: 12/12/2023] [Indexed: 12/23/2023] Open
Abstract
Verpa spp. are potentially important economic fungi within Morchellaceae. However, fundamental research on their mating systems, the key aspects of their life cycle, remains scarce. Fungal sexual reproduction is chiefly governed by mating-type genes, where the configuration of these genes plays a pivotal role in facilitating the reproductive process. For this study, de novo assembly methodologies based on genomic data from Verpa spp. were employed to extract precise information on the mating-type genes, which were then precisely identified in silico and by amplifying their single-ascospore populations using MAT-specific primers. The results suggest that the MAT loci of the three tested strains of V. bohemica encompassed both the MAT1-1-1 and MAT1-2-1 genes, implying homothallism. On the other hand, amongst the three V. conica isolates, only the MAT1-1-1 or MAT1-2-1 genes were present in their MAT loci, suggesting that V. conica is heterothallic. Moreover, bioinformatic analysis reveals that the three tested V. bohemica strains and one V. conica No. 21110 strain include a MAT1-1-10 gene in their MAT loci, while the other two V. conica strains contained MAT1-1-11, exhibiting high amino acid identities with those from corresponding Morchella species. In addition, MEME analysis shows that a total of 17 conserved protein motifs are present among the MAT1-1-10 encoded protein, while the MAT1-1-11 protein contained 10. Finally, the mating type genes were successfully amplified in corresponding single-ascospore populations of V. bohemica and V. conica, further confirming their life-cycle type. This is the first report on the mating-type genes and mating systems of Verpa spp., and the presented results are expected to benefit further exploitation of these potentially important economic fungi.
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Affiliation(s)
- Wenhua Sun
- School of Food and Biological Engineering, Zhengzhou University of Light Industry, Zhengzhou 450002, China; (W.S.); (Q.Y.)
| | - Wei Liu
- Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (W.L.); (X.S.); (L.W.); (J.Z.); (L.E.); (Q.H.)
| | - Yingli Cai
- Institute of Agro-Products Processing, Yunnan Academy of Agricultural Sciences, Kunming 650221, China;
| | - Xiaofei Shi
- Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (W.L.); (X.S.); (L.W.); (J.Z.); (L.E.); (Q.H.)
| | - Liyuan Wu
- Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (W.L.); (X.S.); (L.W.); (J.Z.); (L.E.); (Q.H.)
| | - Jin Zhang
- Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (W.L.); (X.S.); (L.W.); (J.Z.); (L.E.); (Q.H.)
- College of Resource and Environment, Yunnan Agricultural University, Kunming 650100, China
| | - Lingfang Er
- Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (W.L.); (X.S.); (L.W.); (J.Z.); (L.E.); (Q.H.)
- College of Resource and Environment, Yunnan Agricultural University, Kunming 650100, China
| | - Qiuchen Huang
- Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (W.L.); (X.S.); (L.W.); (J.Z.); (L.E.); (Q.H.)
- School of Biodiversity Conservation, Southwest Forestry University, Kunming 650224, China
| | - Qi Yin
- School of Food and Biological Engineering, Zhengzhou University of Light Industry, Zhengzhou 450002, China; (W.S.); (Q.Y.)
| | - Zhiqiang Zhao
- Agricultural Technology Promotion Station in Zhuoni County, Gannan 747600, China;
| | - Peixin He
- School of Food and Biological Engineering, Zhengzhou University of Light Industry, Zhengzhou 450002, China; (W.S.); (Q.Y.)
| | - Fuqiang Yu
- Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (W.L.); (X.S.); (L.W.); (J.Z.); (L.E.); (Q.H.)
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Abstract
Meiosis is critical for germ cell development in multicellular organisms. Initiation of meiosis coincides with pre-meiotic S phase, which is followed by meiotic prophase, a prolonged G2 phase that ensures numerous meiosis-specific chromosome events. Meiotic prophase is accompanied by robust alterations of gene expression. In mouse germ cells, MEIOSIN and STRA8 direct cell cycle switch from mitosis to meiosis. MEIOSIN and STRA8 coordinate meiotic initiation with cell cycle, by activating the meiotic genes to have meiotic prophase program installed at S phase. This review mainly focuses on the mechanism of meiotic initiation in mouse germ cells from the viewpoint of the transcription of meiotic genes. Furthermore, signaling pathways that regulate meiotic initiation will be discussed in the context of germ cell development, pointing out the sexual differences in the mode of meiotic initiation.
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Affiliation(s)
- Kei-Ichiro Ishiguro
- Department of Chromosome Biology, Institute of Molecular Embryology and Genetics (IMEG), Kumamoto University, Kumamoto, Japan.
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Abstract
True morels (Morchella spp., Morchellaceae, Ascomycota) are widely regarded as a highly prized delicacy and are of great economic and scientific value. Recently, the rapid development of cultivation technology and expansion of areas for artificial morel cultivation have propelled morel research into a hot topic. Many studies have been conducted in various aspects of morel biology, but despite this, cultivation sites still frequently report failure to fruit or only low production of fruiting bodies. Key problems include the gap between cultivation practices and basic knowledge of morel biology. In this review, in an effort to highlight the mating systems, evolution, and life cycle of morels, we summarize the current state of knowledge of morel sexual reproduction, the structure and evolution of mating-type genes, the sexual process itself, and the influence of mating-type genes on the asexual stages and conidium production. Understanding of these processes is critical for improving technology for the cultivation of morels and for scaling up their commercial production. Morel species may well be good candidates as model species for improving sexual development research in ascomycetes in the future.
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Sharanabasav H, Pramesh D, Prasannakumar MK, Chidanandappa E, Yadav MK, Ngangkham U, Parivallal B, Raghavendra BT, Manjunatha C, Sharma SK, Karthik N. Morpho-molecular and mating-type locus diversity of Ustilaginoidea virens: an incitant of false smut of rice from Southern parts of India. J Appl Microbiol 2021; 131:2372-2386. [PMID: 33772985 DOI: 10.1111/jam.15087] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 02/17/2021] [Accepted: 03/21/2021] [Indexed: 11/30/2022]
Abstract
AIMS To characterize the geo-distinct isolates of Ustilaginoidea virens for morpho-molecular and mating-type locus diversity. METHODS AND RESULTS Sixty-one isolates of U. virens collected from Southern India exhibited significant diversity in mycelial width (3·45-5·50 µm), colony colour (yellow, pale yellow, and white), and growth pattern (thick leather mat, raised-fluffy, flat-fluffy, and raised). Field-borne chlamydospores of each isolate were significantly smaller in size (3·34-5·26 µm2 ) compared to those formed on culture media (18·6-100·89 µm2 ). The phylogenetic study based on internal transcribed sequences revealed two clusters; however, most isolates (n = 54) were grouped in cluster-I, indicating common ancestral origin. We also identified 42 haplotypes; among them, Hap_3 has the highest number of isolates (n = 19). Mating-type locus (MAT1) analysis revealed all sixty-one isolates as heterothallic, wherein 37 and 24 isolates belonging to MAT1-1-1 and MAT1-2-1 heterothallic mating types, respectively. The microsynteny analysis of MAT1 loci of one of the Indian strain (Uv-Gvt) along with Uv-8b (China) strain revealed synteny conservation at MAT1 locus, which is flanked by conserved genes SLA2 and a hypothetical protein in the upstream and APN2, COX12 and APC5 in the downstream of the locus. CONCLUSIONS Morpho-molecular study revealed the significant diversity among geo-distinct isolates, and MAT1 loci analysis indicated the distribution of heterothallic mating types in south Indian paddy fields. And also, complete synteny conservation between Indian and Chinese strain was observed at the MAT1 locus. SIGNIFICANCE AND IMPACT OF THE STUDY This is the first report describing the sexuality of Indian strains of the U. virens, which would help better understand the genetic diversity of the U. virens prevailing in Southern India and aid in developing resistant rice cultivars against this pathogen population.
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Affiliation(s)
- H Sharanabasav
- Rice Pathology Laboratory, All India Coordinated Rice Improvement Programme, University of Agricultural Sciences, Raichur, India
| | - D Pramesh
- Rice Pathology Laboratory, All India Coordinated Rice Improvement Programme, University of Agricultural Sciences, Raichur, India
| | - M K Prasannakumar
- Department of Plant Pathology, University of Agricultural Sciences, Bangalore, India
| | - E Chidanandappa
- Rice Pathology Laboratory, All India Coordinated Rice Improvement Programme, University of Agricultural Sciences, Raichur, India
| | - M K Yadav
- ICAR-National Rice Research Institute, Cuttack, India
| | - U Ngangkham
- ICAR-Research Complex for NEH Region Umia, Meghalaya, India
| | - B Parivallal
- Department of Plant Pathology, University of Agricultural Sciences, Bangalore, India
| | - B T Raghavendra
- Department of Plant Pathology, University of Agricultural Sciences, Raichur, India
| | - C Manjunatha
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington, India
| | - S K Sharma
- ICAR-Research Complex for NEH Region, Imphal Center, Manipur, India
| | - N Karthik
- University of Madras, Chennai, India
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Krämer D, Lane FA, Steenkamp ET, Wingfield BD, Wilken PM. Unidirectional mating-type switching confers self-fertility to Thielaviopsis cerberus, the only homothallic species in the genus. Fungal Biol 2021; 125:427-434. [PMID: 34024590 DOI: 10.1016/j.funbio.2020.12.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 12/28/2020] [Accepted: 12/30/2020] [Indexed: 11/29/2022]
Abstract
Sexual reproduction is ubiquitous in nature, and nowhere is this more so than in the fungi. Heterothallic behaviour is observed when there is a strict requirement of contact between two individuals of opposite mating type for sexual reproduction to occur. In contrast, a homothallic species can complete the entire sexual cycle in isolation, although several genetic mechanisms underpin this self-fertility. These can be inferred by characterising the structure and gene-content of the mating-type locus, which contains genes that are involved in the regulation of sexual reproduction. In this study, the genetic basis of homothallism in Thielaviopsis cerberus was investigated, the only known self-fertile species within this genus. Using genome sequencing and conventional molecular techniques, two versions of the mating-type locus were identified in this species. This is typical of species that have a unidirectional mating-type switching reproductive strategy. The first version was a self-fertile locus that contained four known mating-type genes, while the second was a self-sterile version with a single mating-type gene. The conversion from a self-fertile to a self-sterile locus is likely mediated by a homologous recombination event at two direct repeats present in the self-fertile locus, resulting in the deletion of three mating-type genes and one of the repeats. Both locus versions were present in isolates that were self-fertile, while self-sterility was caused by the presence of only a switched locus. This study provides a clear example of the architectural fluidity in the mating-type loci that is common among even closely related fungal species.
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Affiliation(s)
- Daniella Krämer
- Department of Biochemistry, Genetics and Microbiology; Forestry and Agricultural Biotechnology Institute, University of Pretoria, Private Bag X20, Hatfield, Pretoria, 0028, South Africa
| | - Frances A Lane
- Department of Biochemistry, Genetics and Microbiology; Forestry and Agricultural Biotechnology Institute, University of Pretoria, Private Bag X20, Hatfield, Pretoria, 0028, South Africa
| | - Emma T Steenkamp
- Department of Biochemistry, Genetics and Microbiology; Forestry and Agricultural Biotechnology Institute, University of Pretoria, Private Bag X20, Hatfield, Pretoria, 0028, South Africa
| | - Brenda D Wingfield
- Department of Biochemistry, Genetics and Microbiology; Forestry and Agricultural Biotechnology Institute, University of Pretoria, Private Bag X20, Hatfield, Pretoria, 0028, South Africa
| | - P Markus Wilken
- Department of Biochemistry, Genetics and Microbiology; Forestry and Agricultural Biotechnology Institute, University of Pretoria, Private Bag X20, Hatfield, Pretoria, 0028, South Africa. http://
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Yong M, Yu J, Pan X, Yu M, Cao H, Qi Z, Du Y, Zhang R, Song T, Yin X, Chen Z, Liu W, Liu Y. MAT1-1-3, a Mating Type Gene in the Villosiclava virens, Is Required for Fruiting Bodies and Sclerotia Formation, Asexual Development and Pathogenicity. Front Microbiol 2020; 11:1337. [PMID: 32714294 PMCID: PMC7344243 DOI: 10.3389/fmicb.2020.01337] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 05/25/2020] [Indexed: 12/29/2022] Open
Abstract
Villosiclava virens is the prevalent causative pathogen of rice false smut, a destructive rice disease. Mating-type genes play a vital role in the evolution of mating systems in fungi. Some fungi have lost MAT1-1-3, one of the mating-type genes, during evolution, whereas others still retain MAT1-1-3. However, how MAT1-1-3 regulates the sexual development of heterothallic V. virens remains unknown. Here, we generated the MAT1-1-3 mutants, which exhibited defects in vegetative growth, stress response, pathogenicity, sclerotia formation and fruiting body maturation. An artificial outcrossing inoculation assay showed that the Δmat1-1-3 mutant was unable to produce sclerotia. Unexpectedly, the Δmat1-1-3 mutant could form immature fruiting bodies without mating on potato sucrose agar medium (PSA) compared with the wild-type strain, most likely by activating the truncated MAT1-2-1 transcription to regulate the sexual development. Moreover, RNA-seq data showed that knockout of MAT1-1-3 results in misregulation of a subset of genes involved in sexual development, MAPK signaling, cell wall integrity, autophagy, epigenetic modification, and transcriptional regulation. Collectively, this study reveals that MAT1-1-3 is required for asexual and sexual development, and pathogenicity of V. virens, thereby provides new insights into the function of mating-type genes in the fungi life cycle and infection process.
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Affiliation(s)
- Mingli Yong
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Junjie Yu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xiayan Pan
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Mina Yu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Huijuan Cao
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Zhongqiang Qi
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Yan Du
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Rongsheng Zhang
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Tianqiao Song
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xiaole Yin
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Zhiyi Chen
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Wende Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yongfeng Liu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
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MEIOSIN Directs the Switch from Mitosis to Meiosis in Mammalian Germ Cells. Dev Cell 2020; 52:429-445.e10. [DOI: 10.1016/j.devcel.2020.01.010] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 10/10/2019] [Accepted: 01/09/2020] [Indexed: 01/12/2023]
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Pizarro D, Dal Grande F, Leavitt SD, Dyer PS, Schmitt I, Crespo A, Thorsten Lumbsch H, Divakar PK. Whole-Genome Sequence Data Uncover Widespread Heterothallism in the Largest Group of Lichen-Forming Fungi. Genome Biol Evol 2019; 11:721-730. [PMID: 30715356 PMCID: PMC6414310 DOI: 10.1093/gbe/evz027] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/31/2019] [Indexed: 12/20/2022] Open
Abstract
Fungal reproduction is regulated by the mating-type (MAT1) locus, which typically comprises two idiomorphic genes. The presence of one or both allelic variants at the locus determines the reproductive strategy in fungi—homothallism versus heterothallism. It has been hypothesized that self-fertility via homothallism is widespread in lichen-forming fungi. To test this hypothesis, we characterized the MAT1 locus of 41 genomes of lichen-forming fungi representing a wide range of growth forms and reproductive strategies in the class Lecanoromycetes, the largest group of lichen-forming fungi. Our results show the complete lack of genetic homothallism suggesting that lichens evolved from a heterothallic ancestor. We argue that this may be related to the symbiotic lifestyle of these fungi, and may be a key innovation that has contributed to the accelerated diversification rates in this fungal group.
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Affiliation(s)
- David Pizarro
- Departamento de Farmacología, Farmacognosia y Botánica, Facultad de Farmacia, Universidad Complutense de Madrid, Spain
| | - Francesco Dal Grande
- Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe Universität and Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany
| | - Steven Don Leavitt
- Department of Biology and M.L. Bean Life Science Museum, Brigham Young University, Provo, Utah
| | | | - Imke Schmitt
- Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe Universität and Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany
| | - Ana Crespo
- Departamento de Farmacología, Farmacognosia y Botánica, Facultad de Farmacia, Universidad Complutense de Madrid, Spain
| | | | - Pradeep Kumar Divakar
- Departamento de Farmacología, Farmacognosia y Botánica, Facultad de Farmacia, Universidad Complutense de Madrid, Spain
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Affiliation(s)
- Lisa J. Vaillancourt
- Department of Plant Pathology, S-305 Agricultural Science Building-North, University of Kentucky, Lexington, Kentucky 40506-0091
| | - Robert M. Hanau
- Department of Botany and Plant Pathology, Agricultural Research Building, Purdue University, West Lafayette, Indiana 47907-1155
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10
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Simpson MC, Coetzee MPA, van der Nest MA, Wingfield MJ, Wingfield BD. Ceratocystidaceae exhibit high levels of recombination at the mating-type (MAT) locus. Fungal Biol 2018; 122:1184-1191. [PMID: 30449356 DOI: 10.1016/j.funbio.2018.09.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 07/11/2018] [Accepted: 09/12/2018] [Indexed: 12/29/2022]
Abstract
Mating is central to many fungal life cycles and is controlled by genes at the mating-type (MAT) locus. These genes determine whether the fungus will be self-sterile (heterothallic) or self-fertile (homothallic). Species in the ascomycete family Ceratocystidaceae have different mating strategies, making them interesting to consider with regards to their MAT loci. The aim of this study was to compare the composition of the MAT locus flanking regions in 11 species of Ceratocystidaceae representing four genera. Genome assemblies for each species were examined to identify the MAT locus and determine the structure of the flanking regions. Large contigs containing the MAT locus were then functionally annotated and analysed for the presence of transposable elements. Genes typically flanking the MAT locus in sordariomycetes were found to be highly conserved in the Ceratocystidaceae. The different genera in the Ceratocystidaceae displayed little synteny outside of the immediate MAT locus flanking genes. Even though species ofCeratocystis did not show much synteny outside of the immediate MAT locus flanking genes, species of Huntiella and Endoconidiophora were comparatively syntenic. Due to the high number of transposable elements present in Ceratocystis MAT flanking regions, we hypothesise that Ceratocystis species may have undergone recombination in this region.
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Affiliation(s)
- Melissa C Simpson
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, 0002, South Africa.
| | - Martin P A Coetzee
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, 0002, South Africa.
| | - Magriet A van der Nest
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, 0002, South Africa.
| | - Michael J Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, 0002, South Africa.
| | - Brenda D Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, 0002, South Africa.
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Li HX, Gottilla TM, Brewer MT. Organization and evolution of mating-type genes in three Stagonosporopsis species causing gummy stem blight of cucurbits and leaf spot and dry rot of papaya. Fungal Biol 2017; 121:849-857. [PMID: 28889909 DOI: 10.1016/j.funbio.2017.06.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 06/12/2017] [Accepted: 06/13/2017] [Indexed: 11/25/2022]
Abstract
Population divergence and speciation of closely related lineages can result from reproductive differences leading to genetic isolation. An increasing number of fungal diseases of plants and animals have been determined to be caused by morphologically indistinguishable species that are genetically distinct, thereby representing cryptic species. We were interested in identifying if mating systems among three Stagonosporopsis species (S. citrulli, S. cucurbitacearum, and S. caricae) causing gummy stem blight (GSB) of cucurbits or leaf spot and dry rot of papaya differed, possibly underlying species divergence. Additionally, we were interested in identifying evolutionary pressures acting on the genes controlling mating in these fungi. The mating-type loci (MAT1) of three isolates from each of the three species were identified in draft genome sequences. For the three species, MAT1 was structurally identical and contained both mating-type genes necessary for sexual reproduction, which suggests that all three species are homothallic. However, both MAT1-1-1 and MAT1-2-1 were divergent among species showing rapid evolution with a much greater number of amino acid-changing substitutions detected for the reproductive genes compared with genes flanking MAT1. Positive selection was detected in MAT1-2-1, especially in the highly conserved high mobility group (MATA_HMG-box) domain. Thus, the mating-type genes are rapidly evolving in GSB fungi, but a difference in mating systems among the three species does not underlie their divergence.
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Affiliation(s)
- Hao-Xi Li
- Department of Plant Pathology, University of Georgia, Athens 30602, USA
| | - Thomas M Gottilla
- Department of Plant Pathology, University of Georgia, Athens 30602, USA
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12
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Yun SH, Kim HK, Lee T, Turgeon BG. Self-fertility in Chromocrea spinulosa is a consequence of direct repeat-mediated loss of MAT1-2, subsequent imbalance of nuclei differing in mating type, and recognition between unlike nuclei in a common cytoplasm. PLoS Genet 2017; 13:e1006981. [PMID: 28892488 PMCID: PMC5608430 DOI: 10.1371/journal.pgen.1006981] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Revised: 09/21/2017] [Accepted: 08/17/2017] [Indexed: 11/18/2022] Open
Abstract
The filamentous fungus Chromocrea spinulosa (Trichoderma spinulosum) exhibits both self-fertile (homothallic) and self-sterile (heterothallic) sexual reproductive behavior. Self-fertile strains produce progeny cohorts that are 50% homothallic, 50% heterothallic. Heterothallic progeny can mate only with homothallic strains, and progeny also segregate 50% homothallic, 50% heterothallic. Sequencing of the mating type (MAT) region of homothallic and heterothallic strains revealed that both carry an intact MAT1-1 locus with three MAT1-1 genes (MAT1-1-1, MAT1-1-2, MAT1-1-3), as previously described for the Sordariomycete group of filamentous fungi. Homothallic strains, however, have a second version of MAT with the MAT1-2 locus genetically linked to MAT1-1. In this version, the MAT1-1-1 open reading frame is split into a large and small fragment and the truncated ends are bordered by 115bp direct repeats (DR). The MAT1-2-1 gene and additional sequences are inserted between the repeats. To understand the mechanism whereby C. spinulosa can exhibit both homothallic and heterothallic behavior, we utilized molecular manipulation to delete one of the DRs from a homothallic strain and insert MAT1-2 into a heterothallic strain. Mating assays indicated that: i) the DRs are key to homothallic behavior, ii) looping out of MAT1-2-1 via intra-molecular homologous recombination between the DRs in self-fertile strains results in two nuclear types in an individual (one carrying both MAT1-1 and MAT1-2 and one carrying MAT1-1 only), iii) self-fertility is achieved by inter-nuclear recognition between these two nuclear types before meiosis, iv) the two types of nuclei are in unequal proportion, v) having both an intact MAT1-1-1 and MAT1-2-1 gene in a single nucleus is not sufficient for self-fertility, and vi) the large truncated MAT1-1-1 fragment is expressed. Comparisons with MAT regions of Trichoderma reesei and Trichoderma virens suggest that several crossovers between misaligned parental MAT chromosomes may have led to the MAT architecture of homothallic C. spinulosa. Fungi employ one of two mating tactics for sexual reproduction: self-sterile/heterothallic species can mate only with a genetically distinct partner while self-fertile/homothallic species do not require a partner. In ascomycetes, sexual reproduction is controlled by master regulators encoded by the mating-type (MAT) locus. The architecture of MAT differs in heterothallic versus homothallic species; heterothallics carry one of two forms (MAT1-1 or MAT1-2) per nucleus, whereas most homothallics carry both MAT forms in a single nucleus. There are intriguing exceptions. For example, the yeast models, Saccharomyces cerevisiae, and Schizosaccharomyces pombe undergo reversible MAT switching, not demonstrated in filamentous fungi. Here, we describe the mating mechanism in Chromocrea spinulosa (Trichoderma spinulosum), a filamentous ascomycete that exhibits both homothallic and heterothallic behavior. Self-fertile strains produce progeny cohorts that are 50% homothallic, 50% heterothallic. Self-sterile strains can mate only with homothallic strains, and when this occurs, homothallic and heterothallic progeny are also produced in a 1:1 ratio. By MAT sequencing and manipulation, we discovered unique MAT architecture and determined that self-fertility is achieved by deletion of MAT1-2 from most homothallic nuclei and subsequent inter-nuclear recognition between the resulting two, unevenly present, nuclear types in a common cytoplasm.
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Affiliation(s)
- Sung-Hwan Yun
- Department of Medical Biotechnology, Soonchunhyang University, Asan, Chungnam, Republic of Korea
- * E-mail: (SHY); (BGT)
| | - Hee-Kyoung Kim
- Department of Medical Biotechnology, Soonchunhyang University, Asan, Chungnam, Republic of Korea
| | - Theresa Lee
- Microbial Safety Team, National Institute of Agricultural Science, Rural Development Administration, Wanju, Jeonbuk, Republic of Korea
| | - B. Gillian Turgeon
- Plant Pathology & Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States of America
- * E-mail: (SHY); (BGT)
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13
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Chai H, Chen L, Chen W, Zhao Q, Zhang X, Su K, Zhao Y. Characterization of mating-type idiomorphs suggests that Morchella importuna, Mel-20 and M. sextelata are heterothallic. Mycol Prog 2017. [DOI: 10.1007/s11557-017-1309-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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14
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De la Varga H, Le Tacon F, Lagoguet M, Todesco F, Varga T, Miquel I, Barry-Etienne D, Robin C, Halkett F, Martin F, Murat C. Five years investigation of female and male genotypes in périgord black truffle (Tuber melanosporum
Vittad.) revealed contrasted reproduction strategies. Environ Microbiol 2017; 19:2604-2615. [DOI: 10.1111/1462-2920.13735] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 03/17/2017] [Accepted: 03/17/2017] [Indexed: 11/27/2022]
Affiliation(s)
- Herminia De la Varga
- UMR1136 Interactions Arbres-Microorganismes, Laboratoire d'Excellence ARBRE; INRA, Université de Lorraine; Champenoux F-54280 France
| | - François Le Tacon
- UMR1136 Interactions Arbres-Microorganismes, Laboratoire d'Excellence ARBRE; INRA, Université de Lorraine; Champenoux F-54280 France
| | - Mélanie Lagoguet
- UMR1136 Interactions Arbres-Microorganismes, Laboratoire d'Excellence ARBRE; INRA, Université de Lorraine; Champenoux F-54280 France
| | - Flora Todesco
- UMR1136 Interactions Arbres-Microorganismes, Laboratoire d'Excellence ARBRE; INRA, Université de Lorraine; Champenoux F-54280 France
| | - Torda Varga
- UMR1136 Interactions Arbres-Microorganismes, Laboratoire d'Excellence ARBRE; INRA, Université de Lorraine; Champenoux F-54280 France
| | - Igor Miquel
- UMR1136 Interactions Arbres-Microorganismes, Laboratoire d'Excellence ARBRE; INRA, Université de Lorraine; Champenoux F-54280 France
| | | | - Christophe Robin
- UMR 1121 Laboratoire Agronomie-Environnement, Nancy-Colmar; INRA, Université de Lorraine; Vandoeuvre-les-Nancy 54518 France
| | - Fabien Halkett
- UMR1136 Interactions Arbres-Microorganismes, Laboratoire d'Excellence ARBRE; INRA, Université de Lorraine; Champenoux F-54280 France
| | - Francis Martin
- UMR1136 Interactions Arbres-Microorganismes, Laboratoire d'Excellence ARBRE; INRA, Université de Lorraine; Champenoux F-54280 France
| | - Claude Murat
- UMR1136 Interactions Arbres-Microorganismes, Laboratoire d'Excellence ARBRE; INRA, Université de Lorraine; Champenoux F-54280 France
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15
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Sex and diversity: The mutualistic and parasitic fungi of a fungus-growing termite differ in genetic diversity and reproductive strategy. FUNGAL ECOL 2017. [DOI: 10.1016/j.funeco.2016.11.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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16
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Barman A, Tamuli R. The pleiotropic vegetative and sexual development phenotypes of Neurospora crassa arise from double mutants of the calcium signaling genes plc-1, splA2, and cpe-1. Curr Genet 2017; 63:861-875. [PMID: 28265741 DOI: 10.1007/s00294-017-0682-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 01/30/2017] [Accepted: 02/07/2017] [Indexed: 11/25/2022]
Abstract
We investigated phenotypes of the double mutants of the calcium (Ca2+) signaling genes plc-1, splA2, and cpe-1 encoding for a phospholipase C1 (PLC-1), a secretory phospholipase A2 (sPLA2), and a Ca2+/H+ exchanger (CPE-1), respectively, to understand the cell functions regulated by their genetic interactions. Mutants lacking plc-1 and either splA2 or cpe-1 exhibited numerous defects including reduced colonial growth, stunted aerial hyphae, premature conidiation on plates with delayed germination, inappropriate conidiation in submerged culture, and lesser mycelial pigmentation. Moreover, the ∆plc-1; ∆splA2 and ∆plc-1; ∆cpe-1 double mutants were female-sterile when crossed with wild type as the male parent. In addition, ∆plc-1, ∆splA2, and ∆cpe-1 single mutants displayed higher carotenoid accumulation and an increased level of intracellular reactive oxygen species (ROS). Therefore, the pleiotropic phenotype of the double mutants of plc-1, splA2, and cpe-1 suggested that the genetic interaction of these genes plays a critical role for normal vegetative and sexual development in N. crassa.
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Affiliation(s)
- Ananya Barman
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781 039, India
| | - Ranjan Tamuli
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781 039, India.
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17
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Aylward J, Steenkamp ET, Dreyer LL, Roets F, Wingfield MJ, Wingfield BD. Genetic basis for high population diversity in Protea-associated Knoxdaviesia. Fungal Genet Biol 2016; 96:47-57. [DOI: 10.1016/j.fgb.2016.10.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 09/12/2016] [Accepted: 10/04/2016] [Indexed: 11/25/2022]
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18
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Stieha C, García-Ramos G, Nicholas McLetchie D, Crowley P. Maintenance of the sexes and persistence of a clonal organism in spatially complex metapopulations. Evol Ecol 2016. [DOI: 10.1007/s10682-016-9841-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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19
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Maharachchikumbura SSN, Hyde KD, Jones EBG, McKenzie EHC, Bhat JD, Dayarathne MC, Huang SK, Norphanphoun C, Senanayake IC, Perera RH, Shang QJ, Xiao Y, D’souza MJ, Hongsanan S, Jayawardena RS, Daranagama DA, Konta S, Goonasekara ID, Zhuang WY, Jeewon R, Phillips AJL, Abdel-Wahab MA, Al-Sadi AM, Bahkali AH, Boonmee S, Boonyuen N, Cheewangkoon R, Dissanayake AJ, Kang J, Li QR, Liu JK, Liu XZ, Liu ZY, Luangsa-ard JJ, Pang KL, Phookamsak R, Promputtha I, Suetrong S, Stadler M, Wen T, Wijayawardene NN. Families of Sordariomycetes. FUNGAL DIVERS 2016. [DOI: 10.1007/s13225-016-0369-6] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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20
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Xu L, Jardini TM, Chen W. Direct repeat-mediated DNA deletion of the mating type MAT1-2 genes results in unidirectional mating type switching in Sclerotinia trifoliorum. Sci Rep 2016; 6:27083. [PMID: 27255676 PMCID: PMC4891775 DOI: 10.1038/srep27083] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 05/13/2016] [Indexed: 11/18/2022] Open
Abstract
The necrotrophic fungal pathogen Sclerotinia trifoliorum exhibits ascospore dimorphism and unidirectional mating type switching - self-fertile strains derived from large ascospores produce both self-fertile (large-spores) and self-sterile (small-spores) offsprings in a 4:4 ratio. The present study, comparing DNA sequences at MAT locus of both self-fertile and self-sterile strains, found four mating type genes (MAT1-1-1, MAT1-1-5, MAT1-2-1 and MAT1-2-4) in the self-fertile strain. However, a 2891-bp region including the entire MAT1-2-1 and MAT1-2-4 genes had been completely deleted from the MAT locus in the self-sterile strain. Meanwhile, two copies of a 146-bp direct repeat motif flanking the deleted region were found in the self-fertile strain, but only one copy of this 146-bp motif (a part of the MAT1-1-1 gene) was present in the self-sterile strain. The two direct repeats were believed to be responsible for the deletion through homologous intra-molecular recombination in meiosis. Tetrad analyses showed that all small ascospore-derived strains lacked the missing DNA between the two direct repeats that was found in all large ascospore-derived strains. In addition, heterokaryons at the MAT locus were observed in field isolates as well as in laboratory derived isolates.
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MESH Headings
- Ascomycota/genetics
- Ascomycota/growth & development
- Ascomycota/metabolism
- Base Sequence
- DNA, Fungal/genetics
- DNA, Fungal/metabolism
- DNA, Intergenic/genetics
- DNA, Intergenic/metabolism
- Genes, Mating Type, Fungal
- Genetic Loci
- Genome, Fungal
- Homologous Recombination
- Meiosis
- Repetitive Sequences, Nucleic Acid
- Sequence Alignment
- Sequence Deletion
- Spores, Fungal/genetics
- Spores, Fungal/growth & development
- Spores, Fungal/metabolism
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Affiliation(s)
- Liangsheng Xu
- Department of Plant Pathology, Washington State University, Pullman, WA 99164, USA
| | - Teresa M. Jardini
- Department of Plant Pathology, Washington State University, Pullman, WA 99164, USA
| | - Weidong Chen
- Department of Plant Pathology, Washington State University, Pullman, WA 99164, USA
- USDA-ARS, Grain Legume Genetics and Physiology Research Unit, Washington State University, Pullman, WA 99164, USA
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21
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The Renaissance of Neurospora crassa: How a Classical Model System is Used for Applied Research. Fungal Biol 2016. [DOI: 10.1007/978-3-319-27951-0_3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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22
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Global Analysis of Predicted G Protein-Coupled Receptor Genes in the Filamentous Fungus, Neurospora crassa. G3-GENES GENOMES GENETICS 2015; 5:2729-43. [PMID: 26464358 PMCID: PMC4683645 DOI: 10.1534/g3.115.020974] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
G protein−coupled receptors (GPCRs) regulate facets of growth, development, and environmental sensing in eukaryotes, including filamentous fungi. The largest predicted GPCR class in these organisms is the Pth11-related, with members similar to a protein required for disease in the plant pathogen Magnaporthe oryzae. However, the Pth11-related class has not been functionally studied in any filamentous fungal species. Here, we analyze phenotypes in available mutants for 36 GPCR genes, including 20 Pth11-related, in the model filamentous fungus Neurospora crassa. We also investigate patterns of gene expression for all 43 predicted GPCR genes in available datasets. A total of 17 mutants (47%) possessed at least one growth or developmental phenotype. We identified 18 mutants (56%) with chemical sensitivity or nutritional phenotypes (11 uniquely), bringing the total number of mutants with at least one defect to 28 (78%), including 15 mutants (75%) in the Pth11-related class. Gene expression trends for GPCR genes correlated with the phenotypes observed for many mutants and also suggested overlapping functions for several groups of co-transcribed genes. Several members of the Pth11-related class have phenotypes and/or are differentially expressed on cellulose, suggesting a possible role for this gene family in plant cell wall sensing or utilization.
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23
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Böhm J, Dahlmann TA, Gümüşer H, Kück U. A MAT1-2 wild-type strain from Penicillium chrysogenum: functional mating-type locus characterization, genome sequencing and mating with an industrial penicillin-producing strain. Mol Microbiol 2015; 95:859-74. [PMID: 25521009 PMCID: PMC4357460 DOI: 10.1111/mmi.12909] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/12/2014] [Indexed: 01/07/2023]
Abstract
In heterothallic ascomycetes, mating is controlled by two nonallelic idiomorphs that determine the 'sex' of the corresponding strains. We recently discovered mating-type loci and a sexual life cycle in the penicillin-producing fungus, Penicillium chrysogenum. All industrial penicillin production strains worldwide are derived from a MAT1-1 isolate. No MAT1-2 strain has been investigated in detail until now. Here, we provide the first functional analysis of a MAT1-2 locus from a wild-type strain. Similar to MAT1-1, the MAT1-2 locus has functions beyond sexual development. Unlike MAT1-1, the MAT1-2 locus affects germination and surface properties of conidiospores and controls light-dependent asexual sporulation. Mating of the MAT1-2 wild type with a MAT1-1 high penicillin producer generated sexual spores. We determined the genomic sequences of parental and progeny strains using next-generation sequencing and found evidence for genome-wide recombination. SNP calling showed that derived industrial strains had an uneven distribution of point mutations compared with the wild type. We found evidence for meiotic recombination in all chromosomes. Our results point to a strategy combining the use of mating-type genes, genetics, and next-generation sequencing to optimize conventional strain improvement methods.
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Affiliation(s)
- Julia Böhm
- Christian Doppler Laboratory for Fungal Biotechnology, Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universität BochumUniversitätsstr. 150, D-44780, Bochum, Germany
| | - Tim A Dahlmann
- Christian Doppler Laboratory for Fungal Biotechnology, Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universität BochumUniversitätsstr. 150, D-44780, Bochum, Germany
| | - Hendrik Gümüşer
- Christian Doppler Laboratory for Fungal Biotechnology, Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universität BochumUniversitätsstr. 150, D-44780, Bochum, Germany
| | - Ulrich Kück
- Christian Doppler Laboratory for Fungal Biotechnology, Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universität BochumUniversitätsstr. 150, D-44780, Bochum, Germany
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24
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Yu JJ, Sun WX, Yu MN, Yin XL, Meng XK, Zhao J, Huang L, Huang L, Liu YF. Characterization of mating-type loci in rice false smut fungus Villosiclava virens. FEMS Microbiol Lett 2015; 362:fnv014. [DOI: 10.1093/femsle/fnv014] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/29/2015] [Indexed: 11/12/2022] Open
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25
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Wilken PM, Steenkamp ET, Wingfield MJ, de Beer ZW, Wingfield BD. DNA loss at the Ceratocystis fimbriata mating locus results in self-sterility. PLoS One 2014; 9:e92180. [PMID: 24651494 PMCID: PMC3961304 DOI: 10.1371/journal.pone.0092180] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 02/20/2014] [Indexed: 12/15/2022] Open
Abstract
Fungi have evolved a remarkable diversity of reproductive strategies. Some of these, most notably those of the model fungi, have been well studied but others are poorly understood. The latter is also true for uni-directional mating type switching, which has been reported in only five fungal genera, including Ceratocystis. Mating type switching allows a self-fertile fungal isolate to produce both self-fertile and self-sterile offspring. This study considered the molecular nature of uni-directional mating type switching in the type species of Ceratocystis, C. fimbriata. To do this, the genome of C. fimbriata was first examined for the presence of mating type genes. Three mating genes (MAT1-1-1, MAT1-2-1 and MAT1-1-2) were found in an atypical organisation of the mating type locus. To study the effect that uni-directional switching has on this locus, several self-sterile offspring were analysed. Using a combination of next generation and conventional Sanger sequencing, it was shown that a 3581 base pair (bp) region had been completely deleted from the MAT locus. This deletion, which includes the entire MAT1-2-1 gene, results in the permanent loss of self-fertility, rendering these isolates exclusively self-sterile. Our data also suggest that the deletion mechanism is tightly controlled and that it always occurs at the same genomic position. Two 260 bp direct repeats flanking the deleted region are strongly implicated in the process, although the exact mechanism behind the switching remains unclear.
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Affiliation(s)
- P. Markus Wilken
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Emma T. Steenkamp
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Michael J. Wingfield
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Z. Wilhelm de Beer
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Brenda D. Wingfield
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
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26
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Kothe E. Solving a Puzzle Piece by Piece: Sexual Development in the Basidiomycetous FungusSchizophyllum commune. ACTA ACUST UNITED AC 2014. [DOI: 10.1111/j.1438-8677.1997.tb00630.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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27
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Bolton MD, de Jonge R, Inderbitzin P, Liu Z, Birla K, Van de Peer Y, Subbarao KV, Thomma BPHJ, Secor GA. The heterothallic sugarbeet pathogen Cercospora beticola contains exon fragments of both MAT genes that are homogenized by concerted evolution. Fungal Genet Biol 2013; 62:43-54. [PMID: 24216224 DOI: 10.1016/j.fgb.2013.10.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 10/24/2013] [Accepted: 10/28/2013] [Indexed: 12/23/2022]
Abstract
Dothideomycetes is one of the most ecologically diverse and economically important classes of fungi. Sexual reproduction in this group is governed by mating type (MAT) genes at the MAT1 locus. Self-sterile (heterothallic) species contain one of two genes at MAT1 (MAT1-1-1 or MAT1-2-1) and only isolates of opposite mating type are sexually compatible. In contrast, self-fertile (homothallic) species contain both MAT genes at MAT1. Knowledge of the reproductive capacities of plant pathogens are of particular interest because recombining populations tend to be more difficult to manage in agricultural settings. In this study, we sequenced MAT1 in the heterothallic Dothideomycete fungus Cercospora beticola to gain insight into the reproductive capabilities of this important plant pathogen. In addition to the expected MAT gene at MAT1, each isolate contained fragments of both MAT1-1-1 and MAT1-2-1 at ostensibly random loci across the genome. When MAT fragments from each locus were manually assembled, they reconstituted MAT1-1-1 and MAT1-2-1 exons with high identity, suggesting a retroposition event occurred in a homothallic ancestor in which both MAT genes were fused. The genome sequences of related taxa revealed that MAT gene fragment pattern of Cercospora zeae-maydis was analogous to C. beticola. In contrast, the genome of more distantly related Mycosphaerella graminicola did not contain MAT fragments. Although fragments occurred in syntenic regions of the C. beticola and C. zeae-maydis genomes, each MAT fragment was more closely related to the intact MAT gene of the same species. Taken together, these data suggest MAT genes fragmented after divergence of M. graminicola from the remaining taxa, and concerted evolution functioned to homogenize MAT fragments and MAT genes in each species.
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Affiliation(s)
- Melvin D Bolton
- Northern Crop Science Laboratory, United States Department of Agriculture, Agricultural Research Service, Fargo, ND, United States.
| | - Ronnie de Jonge
- Department of Plant Systems Biology, VIB, Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Patrik Inderbitzin
- Department of Plant Pathology, University of California, Davis, CA, United States
| | - Zhaohui Liu
- Department of Plant Pathology, North Dakota State University, Fargo, ND, United States
| | - Keshav Birla
- Northern Crop Science Laboratory, United States Department of Agriculture, Agricultural Research Service, Fargo, ND, United States; Department of Phytopathology, Wageningen University, Wageningen, The Netherlands
| | - Yves Van de Peer
- Department of Plant Systems Biology, VIB, Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Krishna V Subbarao
- Department of Plant Pathology, University of California, Davis, CA, United States
| | - Bart P H J Thomma
- Department of Phytopathology, Wageningen University, Wageningen, The Netherlands
| | - Gary A Secor
- Department of Plant Pathology, North Dakota State University, Fargo, ND, United States
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28
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Duong TA, de Beer ZW, Wingfield BD, Wingfield MJ. Characterization of the mating-type genes in Leptographium procerum and Leptographium profanum. Fungal Biol 2013; 117:411-21. [PMID: 23809651 DOI: 10.1016/j.funbio.2013.04.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Revised: 04/11/2013] [Accepted: 04/12/2013] [Indexed: 11/20/2022]
Abstract
Leptographium procerum and the closely related species Leptographium profanum, are ascomycetes associated with root-infesting beetles on pines and hardwood trees, respectively. Both species occur in North America where they are apparently native. L. procerum has also been found in Europe, China New Zealand, and South Africa where it has most probably been introduced. As is true for many other Leptographium species, sexual states have never been observed in L. procerum or L. profanum. The objectives of this study were to clone and characterize the mating type loci of these fungi, and to develop markers to determine the mating types of individual isolates. To achieve this, a partial sequence of MAT1-2-1 was amplified using degenerate primers targeting the high mobility group (HMG) sequence. A complete MAT1-2 idiomorph of L. profanum was subsequently obtained by screening a genomic library using the HMG sequence as a probe. Long range PCR was used to amplify the complete MAT1-1 idiomorph of L. profanum and both the MAT1-1 and MAT1-2 idiomorphs of L. procerum. Characterization of the MAT idiomorphs suggests that the MAT genes are fully functional and that individuals of both these species are self-sterile in nature with a heterothallic mating system. Mating type markers were developed and tested on a population of L. procerum isolates from the USA, the assumed center of origin for this species. The results suggest that cryptic sexual reproduction is occurring or has recently taken place within this population.
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Affiliation(s)
- Tuan A Duong
- Department of Genetics, Forestry and Agricultural Biotechnology Institute-FABI, University of Pretoria, Pretoria 0002, South Africa.
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29
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Zörgö E, Chwialkowska K, Gjuvsland AB, Garré E, Sunnerhagen P, Liti G, Blomberg A, Omholt SW, Warringer J. Ancient evolutionary trade-offs between yeast ploidy states. PLoS Genet 2013; 9:e1003388. [PMID: 23555297 PMCID: PMC3605057 DOI: 10.1371/journal.pgen.1003388] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Accepted: 01/31/2013] [Indexed: 11/18/2022] Open
Abstract
The number of chromosome sets contained within the nucleus of eukaryotic organisms is a fundamental yet evolutionarily poorly characterized genetic variable of life. Here, we mapped the impact of ploidy on the mitotic fitness of baker's yeast and its never domesticated relative Saccharomyces paradoxus across wide swaths of their natural genotypic and phenotypic space. Surprisingly, environment-specific influences of ploidy on reproduction were found to be the rule rather than the exception. These ploidy–environment interactions were well conserved across the 2 billion generations separating the two species, suggesting that they are the products of strong selection. Previous hypotheses of generalizable advantages of haploidy or diploidy in ecological contexts imposing nutrient restriction, toxin exposure, and elevated mutational loads were rejected in favor of more fine-grained models of the interplay between ecology and ploidy. On a molecular level, cell size and mating type locus composition had equal, but limited, explanatory power, each explaining 12.5%–17% of ploidy–environment interactions. The mechanism of the cell size–based superior reproductive efficiency of haploids during Li+ exposure was traced to the Li+ exporter ENA. Removal of the Ena transporters, forcing dependence on the Nha1 extrusion system, completely altered the effects of ploidy on Li+ tolerance and evoked a strong diploid superiority, demonstrating how genetic variation at a single locus can completely reverse the relative merits of haploidy and diploidy. Taken together, our findings unmasked a dynamic interplay between ploidy and ecology that was of unpredicted evolutionary importance and had multiple molecular roots. Organisms vary in the number of chromosome sets contained within the nucleus of each cell, but neither the reasons nor the consequences of this variation are well understood. We designed yeasts that differed in the number of chromosome sets but were otherwise identical and mapped the consequences of such ploidy variations during exposure to a large palette of environments. Contrary to commonly held assumptions, we found ploidy effects on the mitotic reproductive capacity of yeast to be the rule rather than the exception and to be highly evolutionarily conserved. Furthermore, our data rejected previously contemplated hypotheses of generalizable advantages of haploidy or diploidy when cells face nutrient starvation or are exposed to toxins or increased mutation rates. We also mapped the molecular processes mediating ploidy–environment interactions, showing that cell size and mating type locus composition had equal explanatory power. Finally we show that ploidy effects can be mechanistically very subtle, as a designed shift from one plasma membrane Li+ transporter to another completely altered the relative merits of having one or two chromosome sets when exposed to high Li+ concentrations. This complex and dynamic interplay between the number of chromosomes sets and the fluctuating environment must be taken into account when considering organismal form and behavior.
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Affiliation(s)
- Enikö Zörgö
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences (UMB), Ås, Norway
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Karolina Chwialkowska
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Arne B. Gjuvsland
- Centre for Integrative Genetics (CIGENE), Department of Mathematical Sciences and Technology, Norwegian University of Life Sciences (UMB), Ås, Norway
| | - Elena Garré
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Per Sunnerhagen
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Gianni Liti
- IRCAN, CNRS UMR 6267, INSERM U998, University of Nice, Nice, France
| | - Anders Blomberg
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Stig W. Omholt
- NTNU Norwegian University of Science and Technology, Faculty of Natural Sciences and Technology, Department of Biotechnology, Trondheim, Norway
| | - Jonas Warringer
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences (UMB), Ås, Norway
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
- * E-mail:
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Singh G, Dal Grande F, Cornejo C, Schmitt I, Scheidegger C. Genetic basis of self-incompatibility in the lichen-forming fungus Lobaria pulmonaria and skewed frequency distribution of mating-type idiomorphs: implications for conservation. PLoS One 2012; 7:e51402. [PMID: 23236495 PMCID: PMC3517546 DOI: 10.1371/journal.pone.0051402] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Accepted: 11/02/2012] [Indexed: 12/14/2022] Open
Abstract
Fungal populations that reproduce sexually are likely to be genetically more diverse and have a higher adaptive potential than asexually reproducing populations. Mating systems of fungal species can be self-incompatible, requiring the presence of isolates of different mating-type genes for sexual reproduction to occur, or self-compatible, requiring only one. Understanding the distribution of mating-type genes in populations can help to assess the potential of self-incompatible species to reproduce sexually. In the locally threatened epiphytic lichen-forming fungus Lobaria pulmonaria (L.) Hoffm., low frequency of sexual reproduction is likely to limit the potential of populations to adapt to changing environmental conditions. Our study provides direct evidence of self-incompatibility (heterothallism) in L. pulmonaria. It can thus be hypothesized that sexual reproduction in small populations might be limited by an unbalanced distribution of mating-type genes. We therefore assessed neutral genetic diversity (using microsatellites) and mating-type ratio in 27 lichen populations (933 individuals). We found significant differences in the frequency of the two mating types in 13 populations, indicating a lower likelihood of sexual reproduction in these populations. This suggests that conservation translocation activities aiming at maximizing genetic heterogeneity in threatened and declining populations should take into account not only presence of fruiting bodies in transplanted individuals, but also the identity and balanced representation of mating-type genes.
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Affiliation(s)
- Garima Singh
- Biodiversity and Conservation Biology, WSL Swiss Federal Research Institute, Birmensdorf, Switzerland
| | - Francesco Dal Grande
- Biodiversity and Conservation Biology, WSL Swiss Federal Research Institute, Birmensdorf, Switzerland
- Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
| | - Carolina Cornejo
- Biodiversity and Conservation Biology, WSL Swiss Federal Research Institute, Birmensdorf, Switzerland
| | - Imke Schmitt
- Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
- Institute of Ecology, Evolution and Diversity, Goethe Universität, Frankfurt, Germany
| | - Christoph Scheidegger
- Biodiversity and Conservation Biology, WSL Swiss Federal Research Institute, Birmensdorf, Switzerland
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31
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Wilken PM, Steenkamp ET, Hall TA, de Beer ZW, Wingfield MJ, Wingfield BD. Both mating types in the heterothallic fungus Ophiostoma quercus contain MAT1-1 and MAT1-2 genes. Fungal Biol 2012; 116:427-37. [DOI: 10.1016/j.funbio.2012.01.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Revised: 01/02/2012] [Accepted: 01/05/2012] [Indexed: 10/14/2022]
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32
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Morita A, Saitoh Y, Izumitsu K, Tanaka C. Molecular organization of the mating type (Mat) locus of Exserohilum monoceras (Setosphaeria monoceras), a bioherbicide agent for Echinochloa weeds. MYCOSCIENCE 2012. [DOI: 10.1007/s10267-011-0141-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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33
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Neurospora crassa Light Signal Transduction Is Affected by ROS. JOURNAL OF SIGNAL TRANSDUCTION 2011; 2012:791963. [PMID: 22046507 PMCID: PMC3199206 DOI: 10.1155/2012/791963] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Accepted: 06/23/2011] [Indexed: 11/17/2022]
Abstract
In the ascomycete fungus Neurospora crassa blue-violet light controls the expression of genes responsible for differentiation of reproductive structures, synthesis of secondary metabolites, and the circadian oscillator activity. A major photoreceptor in Neurospora cells is WCC, a heterodimeric complex formed by the PAS-domain-containing polypeptides WC-1 and WC-2, the products of genes white collar-1 and white collar-2. The photosignal transduction is started by photochemical activity of an excited FAD molecule noncovalently bound by the LOV domain (a specialized variant of the PAS domain). The presence of zinc fingers (the GATA-recognizing sequences) in both WC-1 and WC-2 proteins suggests that they might function as transcription factors. However, a critical analysis of the phototransduction mechanism considers the existence of residual light responses upon absence of WCC or its homologs in fungi. The data presented
point at endogenous ROS generated by a photon stimulus as an alternative input to pass on light signals to downstream targets.
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34
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Complex mechanisms regulate developmental expression of the matA (HMG) mating type gene in homothallic Aspergillus nidulans. Genetics 2011; 189:795-808. [PMID: 21868608 DOI: 10.1534/genetics.111.131458] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Sexual reproduction is a fundamental developmental process that allows for genetic diversity through the control of zygote formation, recombination, and gametogenesis. The correct regulation of these events is paramount. Sexual reproduction in filamentous fungi, including mating strategy (self-fertilization/homothallism or outcrossing/heterothallism), is determined by the expression of mating type genes at mat loci. Aspergillus nidulans matA encodes a critical regulator that is a fungal ortholog of the hSRY/SOX9 HMG box proteins. In contrast to well-studied outcrossing systems, the molecular basis of homothallism and role of mating type genes during a self-fertile sexual cycle remain largely unknown. In this study the genetic model organism, A. nidulans, has been used to investigate the regulation and molecular functions of the matA mating type gene in a homothallic system. Our data demonstrate that complex regulatory mechanisms underlie functional matA expression during self-fertilization and sexual reproduction in A. nidulans. matA expression is suppressed in vegetative hyphae and is progressively derepressed during the sexual cycle. Elevated levels of matA transcript are required for differentiation of fruiting bodies, karyogamy, meiosis, and efficient formation of meiotic progeny. matA expression is driven from both initiator (Inr) and novel promoter elements that are tightly developmentally regulated by position-dependent and position-independent mechanisms. Deletion of an upstream silencing element, matA SE, results in derepressed expression from wild-type (wt) promoter elements and activation of an additional promoter. These studies provide novel insights into the molecular basis of homothallism in fungi and genetic regulation of sexual reproduction in eukaryotes.
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35
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Deka R, Kumar R, Tamuli R. Neurospora crassa homologue of Neuronal Calcium Sensor-1 has a role in growth, calcium stress tolerance, and ultraviolet survival. Genetica 2011; 139:885-94. [DOI: 10.1007/s10709-011-9592-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2010] [Accepted: 06/22/2011] [Indexed: 10/18/2022]
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36
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Characterization of the mating type (MAT) locus in the Phialocephala fortinii s.l. – Acephala applanata species complex. Fungal Genet Biol 2010; 47:761-72. [DOI: 10.1016/j.fgb.2010.06.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2010] [Revised: 06/01/2010] [Accepted: 06/01/2010] [Indexed: 11/18/2022]
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37
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Primers for mating-type diagnosis in Diaporthe and Phomopsis: their use in teleomorph induction in vitro and biological species definition. Fungal Biol 2010; 114:255-70. [PMID: 20943136 DOI: 10.1016/j.funbio.2010.01.007] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2009] [Revised: 01/07/2010] [Accepted: 01/23/2010] [Indexed: 11/20/2022]
Abstract
Sexual reproduction in ascomycete fungi is governed by the mating-type (MAT) locus. The MAT loci of Diaporthe and its Phomopsis anamorphs differ in only one gene: MAT1-1-1 in mating-type MAT1-1 and MAT1-2-1 in mating-type MAT1-2. In order to diagnose mating-types in Diaporthe and Phomopsis and evaluate their usefulness in teleomorph induction in vitro and biological species delimitation, we designed primers that amplify part of the MAT1-1-1 and MAT1-2-1 genes. MAT phylogenies were generated and compared with ITS and EF1-α phylograms. Species recognised in the EF1-α phylogeny corresponded directly with those determined in the MAT phylogenies. ITS was shown to be highly variable resulting in a large number of phylogenetic species that were discordant with MAT and EF1-α species. Mating experiments were conducted to evaluate the existence of reproductive barriers between some isolates, and their anamorphic morphologies were compared. The primers proved to be useful in the mating-type diagnosis of isolates, selection of compatible mating pairs, and in the assessment of biological species boundaries.
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38
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Covert SF, Aoki T, O'Donnell K, Starkey D, Holliday A, Geiser DM, Cheung F, Town C, Strom A, Juba J, Scandiani M, Yang XB. Sexual reproduction in the soybean sudden death syndrome pathogen Fusarium tucumaniae. Fungal Genet Biol 2007; 44:799-807. [PMID: 17300967 DOI: 10.1016/j.fgb.2006.12.009] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2006] [Revised: 12/07/2006] [Accepted: 12/22/2006] [Indexed: 11/16/2022]
Abstract
We investigated the sexual reproductive mode of the two most important etiological agents of soybean sudden death syndrome, Fusarium tucumaniae and Fusarium virguliforme. F. tucumaniae sexual crosses often were highly fertile, making it possible to assign mating type and assess female fertility in 24 South American isolates. These crosses produced red perithecia and oblong-elliptical ascospores, as is typical for sexual members of the F. solani species complex. Genotyping of progeny from three F. tucumaniae crosses confirmed that sexual recombination had occurred. In contrast, pairings among 17 U.S. F. virguliforme isolates never produced perithecia. Inter-species crosses between F. tucumaniae and F. virguliforme, in which infertile perithecia were induced only in one of the two F. tucumaniae mating types, suggest that all U.S. F. virguliforme isolates are of a single mating type. We conclude that the F. tucumaniae life cycle in S. America includes a sexual reproductive mode, and thus this species has greater potential for rapid evolution than the F. virguliforme population in the U.S., which may be exclusively asexual.
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Affiliation(s)
- S F Covert
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA 30602, USA.
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39
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Lim YW, Sturrock R, Leal I, Pellow K, Yamaguchi T, Breuil C. Distinguishing homokaryons and heterokaryons in Phellinus sulphurascens using pairing tests and ITS polymorphisms. Antonie van Leeuwenhoek 2007; 93:99-110. [PMID: 17610140 DOI: 10.1007/s10482-007-9184-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2007] [Accepted: 06/14/2007] [Indexed: 01/21/2023]
Abstract
Phellinus sulphurascens Pilát causes laminated root rot of coniferous species in both western North America (WNA) and Asia. Accurate somatic incompatibility tests for mapping population structures have been difficult to conduct for P. sulphurascens because no single, unambiguous criterion has allowed differentiation of homokaryotic and heterokaryotic isolates. In a population study of P. sulphurascens in WNA, two types of ITS sequences were found in the single spore and vegetative isolates. All single spore isolates (SSIs) had either ITS type-1 or type-2 whereas some vegetative isolates had both ITS types. The segregation pattern for inheritance of ITS, which we observed in SSIs from eight basidiocarps, suggested that each ITS type occurred in a different nucleus and that each basidiospore inherited only one ITS type. In four SSIs from Russia and eight heterokaryotic isolates from Japan, nine different ITS types, referred to as type-3 to -11, were detected. A variety of pairing tests conducted between known Asian and WNA homokaryon and heterokaryon isolates did not always give consistent results with respect to fungal mat morphologies and formation of demarcation lines. However, the ITS types that occurred after pairing tests did follow consistent patterns. Thus, using ITS polymorphisms and pairing tests between Asian tester isolates and 49 vegetative isolates from WNA, we were able to accurately distinguish between homokaryotic and heterokaryotic isolates.
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Affiliation(s)
- Young Woon Lim
- Institute of Molecular Biology and Genetics, Seoul National University, 56-1 Shillim-dong, Kwanak-gu, Seoul, 151-742, Korea.
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40
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Powell AJ, Jacobson DJ, Natvig DO. Ancestral polymorphism and linkage disequilibrium at the het-6 region in pseudohomothallic Neurospora tetrasperma. Fungal Genet Biol 2007; 44:896-904. [PMID: 17576083 DOI: 10.1016/j.fgb.2007.04.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2006] [Revised: 03/26/2007] [Accepted: 04/10/2007] [Indexed: 11/29/2022]
Abstract
In species of Neurospora, non-self recognition is mediated by at least 11 heterokaryon (het) incompatibility loci. Previously, we identified ancient allelic variation at het-c in pseudohomothallic N. tetrasperma, which confirmed outcrossing in this species. Here, we report distinct ancestral alleles at het-6 and un-24, two closely linked genes with het incompatibility function in N. crassa. The pattern of variation at het-6 and un-24 in N. tetrasperma is similar to that observed for N. crassa, where two ancestral allele specificities exist for each locus, Oak Ridge (het-6(OR), un-24(OR)) and Panama (het-6(PA), un-24(PA)). Only het-6(OR)/un-24(OR) and het-6(PA)/un-24(PA) allele combinations have been observed. The absence of recombinant haplotypes (e.g., het-6(OR)/un-24(PA)) appears to derive from an ancestral chromosomal rearrangement that limits recombination. Allelic variation at het-6 and un-24 in N. tetrasperma provides further evidence of outcrossing in this predominantly selfing species and indicates that selection maintains ancient allelic diversity at het loci.
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Affiliation(s)
- Amy J Powell
- Department of Plant Pathology, North Carolina State University, Campus Box 7244, Raleigh, NC 27695-7244, USA.
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41
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Keszthelyi A, Jeney A, Kerényi Z, Mendes O, Waalwijk C, Hornok L. Tagging target genes of the MAT1-2-1 transcription factor in Fusarium verticillioides (Gibberella fujikuroi MP-A). Antonie van Leeuwenhoek 2006; 91:373-91. [PMID: 17124547 DOI: 10.1007/s10482-006-9123-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2006] [Accepted: 10/09/2006] [Indexed: 11/27/2022]
Abstract
Mating type in filamentous ascomycetes is controlled by idiomorphic alleles, named MAT1-1 and MAT1-2, which contain 1-3 genes. Of these genes MAT1-1-1 and MAT1-2-1 encode putative transcription factors and are thus considered to be the major regulators of sexual communication and mating. Fungi with no known sexual stage may also have fully functional mating type genes and therefore it was plausible to hypothesize that the MAT products may also regulate other types of genes not involved directly in the mating process. To identify putative target genes of these transcription factors in Fusarium verticillioides, DeltaMAT1-2-1 knock out mutants were produced and transcript profiles of mutant and wild type were compared by means of differential cDNA hybridization. Clones, either up- or down-regulated in the DeltaMAT1-2-1 mutant were sequenced and a total of 248 sequences were blasted against the NCBI database as well as the Gibberella zeae and Gibberella moniliformis genomes. Fifty-five percent of the clones were down-regulated in the mutant, indicating that the MAT1-2-1 product positively affected these tagged sequences. On the other hand, 45% were found to be up-regulated in the mutant, suggesting that the MAT1-2-1 product also exerted a negative regulatory function on this set of genes. Sequences involved in protein synthesis and metabolism occurred more frequently among the clones up-regulated in the mutant, whereas genes belonging to cell signalling and communication were especially frequently tagged among the sequences down-regulated in the mutant.
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Affiliation(s)
- Anita Keszthelyi
- Agricultural Biotechnology Center, Szent-Györgyi A. u. 4, H-2100, Gödöllo, Hungary
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42
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Lee SH, Lee S, Choi D, Lee YW, Yun SH. Identification of the down-regulated genes in a mat1-2-deleted strain of Gibberella zeae, using cDNA subtraction and microarray analysis. Fungal Genet Biol 2006; 43:295-310. [PMID: 16504554 DOI: 10.1016/j.fgb.2005.12.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2005] [Revised: 12/08/2005] [Accepted: 12/27/2005] [Indexed: 10/25/2022]
Abstract
Gibberella zeae (anamorph: Fusarium graminearum), a self-fertile ascomycete, is an important pathogen of cereal crops. Here, we have focused on the genes specifically controlled by the mating type (MAT) locus, a master regulator of sexual developmental process in G. zeae. To identify these genes, we employed suppression subtractive hybridization between a G. zeae wild-type strain Z03643 and the isogenic self-sterile mat1-2 strain T43deltaM2-2. Both reverse Northern and cDNA microarray analyses using 291 subtractive unigenes confirmed that 58.8% (171 genes) were significantly down-regulated in T43deltaM2-2. Among these, 98 could be either manually or automatically annotated based on known functions of their possible homologs. Northern blot analysis revealed that all of the genes examined were differentially regulated by MAT1-2 during sexual development. This study is the first report on the set of genes that are transcriptionally altered by the deletion of MAT1-2 during sexual reproduction in G. zeae.
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Affiliation(s)
- Seung-Ho Lee
- School of Agricultural Biotechnology and Center for Agricultural Biomaterials, Seoul National University, Seoul 151-921, Republic of Korea
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43
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Cai L, Jeewon R, Hyde KD. Phylogenetic investigations of Sordariaceae based on multiple gene sequences and morphology. ACTA ACUST UNITED AC 2006; 110:137-50. [PMID: 16378718 DOI: 10.1016/j.mycres.2005.09.014] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2005] [Revised: 08/19/2005] [Accepted: 09/29/2005] [Indexed: 11/29/2022]
Abstract
The family Sordariaceae incorporates a number of fungi that are excellent model organisms for various biological, biochemical, ecological, genetic and evolutionary studies. To determine the evolutionary relationships within this group and their respective phylogenetic placements, multiple-gene sequences (partial nuclear 28S ribosomal DNA, nuclear ITS ribosomal DNA and partial nuclear beta-tubulin) were analysed using maximum parsimony and Bayesian analyses. Analyses of different gene datasets were performed individually and then combined to generate phylogenies. We report that Sordariaceae, with the exclusion Apodus and Diplogelasinospora, is a monophyletic group. Apodus and Diplogelasinospora are related to Lasiosphaeriaceae. Multiple gene analyses suggest that the spore sheath is not a phylogenetically significant character to segregate Asordaria from Sordaria. Smooth-spored Sordaria species (including so-called Asordaria species) constitute a natural group. Asordaria is therefore congeneric with Sordaria. Anixiella species nested among Gelasinospora species, providing further evidence that non-ostiolate ascomata have evolved from ostiolate ascomata on several independent occasions. This study agrees with previous studies that show heterothallic Neurospora species to be monophyletic, but that homothallic ones may have a multiple origins. Although Gelasinospora and Neurospora are closely related and not resolved as monophyletic groups, there is insufficient evidence to place currently accepted Gelasinospora and Neurospora species into the same genus.
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Affiliation(s)
- Lei Cai
- Centre for Research in Fungal Diversity, Department of Ecology & Biodiversity, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, PR China.
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44
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Mello A, Murat C, Vizzini A, Gavazza V, Bonfante P. Tuber magnatum Pico, a species of limited geographical distribution: its genetic diversity inside and outside a truffle ground. Environ Microbiol 2005; 7:55-65. [PMID: 15643936 DOI: 10.1111/j.1462-2920.2004.00678.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The aim of this work was to clarify the genetic structure of the ectomycorrhizal fungus, Tuber magnatum Pico, in a natural truffle ground located in north Italy. Ascomata of this population of T. magnatum were collected over a period of up to 5 years. For comparative analysis, T. magnatum fruit bodies of different geographical origin were also considered. We used single locus markers, such as the variable region of ribosomal genes (ITS), the beta-tubulin gene and sequence-characterized amplified regions (SCAR), as tools to identify single-nucleotide polymorphisms (SNPs). On the basis of the molecular results, which were indirectly supported by a karyological analysis, a self-fertilization mechanism is suggested. A SCAR region was polymorphic within the samples of the truffle ground, leading to the identification of two genotypes. In addition, both the SCAR and the ITS proved to be polymorphic among samples coming from different geographical regions, revealing a genetic differentiation in T. magnatum.
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Affiliation(s)
- Antonietta Mello
- Istituto per la Protezione delle Piante del CNR, Sezione di Torino, Torino, Italy.
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45
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Johnson LJ, Koufopanou V, Goddard MR, Hetherington R, Schäfer SM, Burt A. Population genetics of the wild yeast Saccharomyces paradoxus. Genetics 2004; 166:43-52. [PMID: 15020405 PMCID: PMC1470673 DOI: 10.1534/genetics.166.1.43] [Citation(s) in RCA: 131] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Saccharomyces paradoxus is the closest known relative of the well-known S. cerevisiae and an attractive model organism for population genetic and genomic studies. Here we characterize a set of 28 wild isolates from a 10-km(2) sampling area in southern England. All 28 isolates are homothallic (capable of mating-type switching) and wild type with respect to nutrient requirements. Nine wild isolates and two lab strains of S. paradoxus were surveyed for sequence variation at six loci totaling 7 kb, and all 28 wild isolates were then genotyped at seven polymorphic loci. These data were used to calculate nucleotide diversity and number of segregating sites in S. paradoxus and to investigate geographic differentiation, population structure, and linkage disequilibrium. Synonymous site diversity is approximately 0.3%. Extensive incompatibilities between gene genealogies indicate frequent recombination between unlinked loci, but there is no evidence of recombination within genes. Some localized clonal growth is apparent. The frequency of outcrossing relative to inbreeding is estimated at 1.1% on the basis of heterozygosity. Thus, all three modes of reproduction known in the lab (clonal replication, inbreeding, and outcrossing) have been important in molding genetic variation in this species.
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Affiliation(s)
- Louise J Johnson
- Department of Biological Sciences, Imperial College at Silwood Park, Ascot SL5 7PY, United Kingdom.
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46
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Borkovich KA, Alex LA, Yarden O, Freitag M, Turner GE, Read ND, Seiler S, Bell-Pedersen D, Paietta J, Plesofsky N, Plamann M, Goodrich-Tanrikulu M, Schulte U, Mannhaupt G, Nargang FE, Radford A, Selitrennikoff C, Galagan JE, Dunlap JC, Loros JJ, Catcheside D, Inoue H, Aramayo R, Polymenis M, Selker EU, Sachs MS, Marzluf GA, Paulsen I, Davis R, Ebbole DJ, Zelter A, Kalkman ER, O'Rourke R, Bowring F, Yeadon J, Ishii C, Suzuki K, Sakai W, Pratt R. Lessons from the genome sequence of Neurospora crassa: tracing the path from genomic blueprint to multicellular organism. Microbiol Mol Biol Rev 2004; 68:1-108. [PMID: 15007097 PMCID: PMC362109 DOI: 10.1128/mmbr.68.1.1-108.2004] [Citation(s) in RCA: 434] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We present an analysis of over 1,100 of the approximately 10,000 predicted proteins encoded by the genome sequence of the filamentous fungus Neurospora crassa. Seven major areas of Neurospora genomics and biology are covered. First, the basic features of the genome, including the automated assembly, gene calls, and global gene analyses are summarized. The second section covers components of the centromere and kinetochore complexes, chromatin assembly and modification, and transcription and translation initiation factors. The third area discusses genome defense mechanisms, including repeat induced point mutation, quelling and meiotic silencing, and DNA repair and recombination. In the fourth section, topics relevant to metabolism and transport include extracellular digestion; membrane transporters; aspects of carbon, sulfur, nitrogen, and lipid metabolism; the mitochondrion and energy metabolism; the proteasome; and protein glycosylation, secretion, and endocytosis. Environmental sensing is the focus of the fifth section with a treatment of two-component systems; GTP-binding proteins; mitogen-activated protein, p21-activated, and germinal center kinases; calcium signaling; protein phosphatases; photobiology; circadian rhythms; and heat shock and stress responses. The sixth area of analysis is growth and development; it encompasses cell wall synthesis, proteins important for hyphal polarity, cytoskeletal components, the cyclin/cyclin-dependent kinase machinery, macroconidiation, meiosis, and the sexual cycle. The seventh section covers topics relevant to animal and plant pathogenesis and human disease. The results demonstrate that a large proportion of Neurospora genes do not have homologues in the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe. The group of unshared genes includes potential new targets for antifungals as well as loci implicated in human and plant physiology and disease.
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Affiliation(s)
- Katherine A Borkovich
- Department of Plant Pathology, University of California, Riverside, California 92521, USA. Katherine/
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47
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McGuire IC, Marra RE, Milgroom MG. Mating-type heterokaryosis and selfing in Cryphonectria parasitica. Fungal Genet Biol 2004; 41:521-33. [PMID: 15050541 DOI: 10.1016/j.fgb.2003.12.007] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2003] [Accepted: 12/17/2003] [Indexed: 11/28/2022]
Abstract
Selfing in the chestnut blight fungus, Cryphonectria parasitica, occurs by two different genetic mechanisms. Most self-fertile isolates of C. parasitica are heterokaryotic for mating type, and the progeny from selfing segregate for mating type. Further, we resolved mating-type (MAT) heterokaryons into homokaryons of both mating types by isolating uninucleate asexual spores (conidia). However, because ascospore progeny, with rare exceptions, are not MAT heterokaryons, C. parasitica must lack a regular mechanism to maintain heterokaryosis by selfing. We hypothesize that heterokaryon formation may occur either because of recurrent biparental inbreeding, or by mating-type switching, possibly one involving some kind of parasexual process. The second mechanism found for selfing in C. parasitica occurred less frequently. Three single-conidial isolates (MAT-1 and MAT-2) selfed and produced progeny that did not segregate for mating type. It is currently not known if meiosis occurs during ascospore formation by this mechanism.
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Affiliation(s)
- I Cristina McGuire
- Department of Plant Pathology, Cornell University, 334 Plant Science Building, Ithaca, NY 14853, USA
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Turina M, Prodi A, Alfen NKV. Role of the Mf1-1 pheromone precursor gene of the filamentous ascomycete Cryphonectria parasitica. Fungal Genet Biol 2004; 40:242-51. [PMID: 14599892 DOI: 10.1016/s1087-1845(03)00084-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Site-directed recombination was used to obtain a Cryphonectria parasitica strain carrying deletions at the Mf1-1 gene locus. Macroscopic features such as growth rate and conidia production were unaffected by Mf1-1 deletions, but, when a strain containing a complete deletion of Mf1-1 was used as spermatia it was male sterile. The same strain was fully competent as a female parent. Deletion of three of the seven putative pheromone peptide repeats within the gene had no effect on mating. Male fertility of the complete deletion strain was restored when an ectopic copy of the Mf1-1 gene was returned by transformation. Expression of the mating type specific pheromone precursor gene Mf1-1 was stimulated by growth in nutritionally poor liquid media. It was found that age and source of inoculum of liquid cultures influences pheromone precusor gene expression, i.e., conidia did not express Mf1-1 and cultures derived from conidia were significantly delayed in expression of this gene, as were cultures derived from young mycelium. Cultures inoculated with older hyphae, however, expressed Mf1-1 within 1 day after inoculation.
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Affiliation(s)
- Massimo Turina
- Department of Plant Pathology, College of Agricultural and Environmental Sciences, University of California, Davis, 95616-5270, Davis, CA, USA
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Lee J, Lee T, Lee YW, Yun SH, Turgeon BG. Shifting fungal reproductive mode by manipulation of mating type genes: obligatory heterothallism of Gibberella zeae. Mol Microbiol 2003; 50:145-52. [PMID: 14507370 DOI: 10.1046/j.1365-2958.2003.03694.x] [Citation(s) in RCA: 128] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Fungi capable of sexual reproduction use heterothallic (self-sterile) or homothallic (self-fertile) mating strategies. In most ascomycetes, a single mating type locus, MAT, with two alternative forms (MAT1-1 and MAT1-2) called idiomorphs, controls mating ability. In heterothallic ascomycetes, these alternative idiomorphs reside in different nuclei. In contrast, most homothallic ascomycetes carry both MAT1-1 and MAT1-2 in a single nucleus, usually closely linked. An example of the latter is Gibberella zeae, a species that is capable of both selfing and outcrossing. G. zeae is a devastating cereal pathogen of ubiquitous geographical distribution, and also a producer of mycotoxins that threaten human and animal health. We asked whether G. zeae could be made strictly heterothallic by manipulation of MAT. Targeted gene replacement was used to differentially delete MAT1-1 or MAT1-2 from a wild-type haploid MAT1-1; MAT1-2 strain, resulting in MAT1-1; mat1-2, mat1-1; MAT1-2 strains that were self-sterile, yet able to cross to wild-type testers and, more importantly, to each other. These results indicated that differential deletion of MAT idiomorphs eliminates selfing ability of G. zeae, but the ability to outcross is retained. They also indicated that both MAT idiomorphs are required for self-fertility. To our knowledge, this is the first report of complete conversion of fungal reproductive strategy from homothallic to heterothallic by targeted manipulation of MAT. Practically, this approach opens the door to simple and efficient procedures for obtaining sexual recombinants of G. zeae that will be useful for genetic analyses of pathogenicity and other traits, such as the ability to produce mycotoxins.
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Affiliation(s)
- Jungkwan Lee
- School of Agricultural Biotechnology, Seoul National University, Suwon 441-744, Korea.
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Bennett RS, Yun SH, Lee TY, Turgeon BG, Arseniuk E, Cunfer BM, Bergstrom GC. Identity and conservation of mating type genes in geographically diverse isolates of Phaeosphaeria nodorum. Fungal Genet Biol 2003; 40:25-37. [PMID: 12948511 DOI: 10.1016/s1087-1845(03)00062-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Mating type idiomorphs (MAT1-1 and MAT1-2) were identified from the heterothallic loculoascomycete Phaeosphaeria nodorum (wheat biotype) using DNA from a pair of isolates from Poland and Georgia, USA that are known to mate. MAT predicted proteins of P. nodorum are similar in sequence and in phylogenetic relationship to those described for other loculoascomycetes such as Cochliobolus spp., Alternaria alternata, and Didymella zeae-maydis. The organization of the MAT locus of the P. nodorum differs from these species in that its idiomorph begins within an adjacent upstream conserved ORF of unknown function. MAT-specific primers were used to identify isolates of both mating types in field populations, demonstrating that an absence of either mating type is not the reason that the teleomorph has not been found in New York. Portions of MAT1-1 and MAT1-2 were sequenced from geographically diverse isolates, including those from regions where the teleomorph has been reported. MAT was highly conserved and no significant differences in sequence were found.
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Affiliation(s)
- R S Bennett
- Department of Plant Pathology, Cornell University, Ithaca, NY, USA
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