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Ayika MG, Rosano A, Valiente J, Chakrabarti S, Rollins JA, Dhillon B. Characterizing the Palm Pathogenic Thielaviopsis Species from Florida. J Fungi (Basel) 2024; 10:247. [PMID: 38667918 PMCID: PMC11051176 DOI: 10.3390/jof10040247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 03/15/2024] [Accepted: 03/20/2024] [Indexed: 04/28/2024] Open
Abstract
Thielaviopsis paradoxa sensu lato is a soilborne fungal pathogen that causes Thielaviopsis trunk rot and heart rot in palms. The loss of structural integrity resulting from trunk rot can cause the palm trunk to collapse suddenly and poses a serious threat to life and property. Even though rudimentary knowledge about the Thielaviopsis infection process in palms is available, nothing is known about the T. paradoxa species complex in the US. The aim of this study was to characterize T. paradoxa s. lat. isolates collected from diseased palms grown in Florida. Multi-locus phylogeny using three genes, ITS, β-tubulin, and tef1-α, revealed that the isolates separate into two distinct clades with high bootstrap support. The majority of the isolates clustered with the species T. ethacetica, while two isolates formed a separate clade, distinct from T. musarum, and might represent an undescribed Thielaviopsis species. One representative isolate from each clade, when grown on three distinct media and at four different temperatures, showed differences in gross colony morphology, as well as growth rates. The T. ethacetica isolate TP5448 and the Thielaviopsis sp. isolate PLM300 grew better at opposite ends of the temperature spectrum tested in this study, i.e., 35 °C and 10 °C, respectively. In pathogenicity assays on whole plants, the T. ethacetica isolate proved to be more aggressive than Thielaviopsis sp. isolate PLM300, as it produced larger lesions when inoculated on wounded leaflets. An unequal distribution was observed for the mating-type locus of T. ethacetica, as 12 isolates carried the MAT1-1-1 allele, while the status for four isolates remained undefined. Variation in mycelial growth in response to different fungicides was also observed between the two clades. These results demonstrate the existence of two Thielaviopsis clades that can infect palms in Florida and underscore the need for targeted sampling to help uncover the diversity of Thielaviopsis species across palm-growing regions in the US.
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Affiliation(s)
- Marie-Gabrielle Ayika
- Department of Plant Pathology, Fort Lauderdale Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Davie, FL 33314, USA; (M.-G.A.); (S.C.)
| | - Avril Rosano
- Institute of Food and Agricultural Sciences, College of Agricultural and Life Sciences, University of Florida, Gainesville, FL 32611, USA;
| | | | - Seemanti Chakrabarti
- Department of Plant Pathology, Fort Lauderdale Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Davie, FL 33314, USA; (M.-G.A.); (S.C.)
| | - Jeffrey A. Rollins
- Department of Plant Pathology, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA;
| | - Braham Dhillon
- Department of Plant Pathology, Fort Lauderdale Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Davie, FL 33314, USA; (M.-G.A.); (S.C.)
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Wilken PM, Lane FA, Steenkamp ET, Wingfield MJ, Wingfield BD. Unidirectional mating-type switching is underpinned by a conserved MAT1 locus architecture. Fungal Genet Biol 2024; 170:103859. [PMID: 38114017 DOI: 10.1016/j.fgb.2023.103859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 12/11/2023] [Accepted: 12/14/2023] [Indexed: 12/21/2023]
Abstract
Unidirectional mating-type switching is a form of homothallic reproduction known only in a small number of filamentous ascomycetes. Their ascospores can give rise to either self-sterile isolates that require compatible partners for subsequent sexual reproduction, or self-fertile individuals capable of completing this process in isolation. The limited studies previously conducted in these fungi suggest that the differences in mating specificity are determined by the architecture of the MAT1 locus. In self-fertile isolates that have not undergone unidirectional mating-type switching, the locus contains both MAT1-1 and MAT1-2 mating-type genes, typical of primary homothallism. In the self-sterile isolates produced after a switching event, the MAT1-2 genes are lacking from the locus, likely due to a recombination-mediated deletion of the MAT1-2 gene information. To determine whether these arrangements of the MAT1 locus support unidirectional mating-type switching in the Ceratocystidaceae, the largest known fungal assemblage capable of this reproduction strategy, a combination of genetic and genomic approaches were used. The MAT1 locus was annotated in representative species of Ceratocystis, Endoconidiophora, and Davidsoniella. In all cases, MAT1-2 genes interrupted the MAT1-1-1 gene in self-fertile isolates. The MAT1-2 genes were flanked by two copies of a direct repeat that accurately predicted the boundaries of the deletion event that would yield the MAT1 locus of self-sterile isolates. Although the relative position of the MAT1-2 gene region differed among species, it always disrupted the MAT1-1-1 gene and/or its expression in the self-fertile MAT1 locus. Following switching, this gene and/or its expression was restored in the self-sterile arrangement of the locus. This mirrors what has been reported in other species capable of unidirectional mating-type switching, providing the strongest support for a conserved MAT1 locus structure that is associated with this process. This study contributes to our understanding of the evolution of unidirectional mating-type switching.
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Affiliation(s)
- P Markus Wilken
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, Private Bag X20, Pretoria 0028, South Africa.
| | - Frances A Lane
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, Private Bag X20, Pretoria 0028, South Africa
| | - Emma T Steenkamp
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, Private Bag X20, Pretoria 0028, South Africa
| | - Michael J Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, Private Bag X20, Pretoria 0028, South Africa
| | - Brenda D Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, Private Bag X20, Pretoria 0028, South Africa
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Maseko NN, Steenkamp ET, Wingfield BD, Wilken PM. An in Silico Approach to Identifying TF Binding Sites: Analysis of the Regulatory Regions of BUSCO Genes from Fungal Species in the Ceratocystidaceae Family. Genes (Basel) 2023; 14:genes14040848. [PMID: 37107606 PMCID: PMC10137650 DOI: 10.3390/genes14040848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
Transcriptional regulation controls gene expression through regulatory promoter regions that contain conserved sequence motifs. These motifs, also known as regulatory elements, are critically important to expression, which is driving research efforts to identify and characterize them. Yeasts have been the focus of such studies in fungi, including in several in silico approaches. This study aimed to determine whether in silico approaches could be used to identify motifs in the Ceratocystidaceae family, and if present, to evaluate whether these correspond to known transcription factors. This study targeted the 1000 base-pair region upstream of the start codon of 20 single-copy genes from the BUSCO dataset for motif discovery. Using the MEME and Tomtom analysis tools, conserved motifs at the family level were identified. The results show that such in silico approaches could identify known regulatory motifs in the Ceratocystidaceae and other unrelated species. This study provides support to ongoing efforts to use in silico analyses for motif discovery.
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Wilson AM, Wingfield MJ, Wingfield BD. Truncation of MAT1-2-7 Deregulates Developmental Pathways Associated with Sexual Reproduction in Huntiella omanensis. Microbiol Spectr 2022; 10:e0142522. [PMID: 36154282 PMCID: PMC9602353 DOI: 10.1128/spectrum.01425-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 09/07/2022] [Indexed: 12/30/2022] Open
Abstract
The MAT1-1-1 and MAT1-2-1 genes are thought to be the master regulators of sexual development in most ascomycete fungi, and they are often essential for this process. In contrast, it has been suggested that the secondary mating-type genes act to calibrate the sexual cycle and can be dispensable. Recent functional characterization of genes such as Aspergillus fumigatus MAT1-2-4, Huntiella omanensis MAT1-2-7, and Botrytis cinerea MAT1-1-5 has, however, shown that these secondary genes may play more central roles in the sexual pathway and are essential for the production of mature fruiting structures. We used a comparative transcriptome sequencing (RNA-seq) experiment to show that the truncation of MAT1-2-7 in the wood inhabiting H. omanensis residing in the Ceratocystidaceae is associated with the differential expression of approximately 25% of all the genes present in the genome, including the transcriptional regulators ste12, wc-2, sub1, VeA, HMG8, and pro1. This suggests that MAT1-2-7 may act as a transcription factor and that ΔMAT1-2-7 mutant sterility is the result of layered deregulation of a variety of signaling and developmental pathways. This study is one of only a few that details the functional characterization of a secondary MAT gene in a nonmodel species. Given that this gene is present in other Ceratocystidaceae species and that there are diverse secondary MAT genes present throughout the Pezizomycotina, further investigation into this gene and others like it will provide a clearer understanding of sexual development in these eukaryotes. IMPORTANCE Secondary mating-type genes are being described almost as quickly as new fungal genomes are being sequenced. Understanding the functions of these genes has lagged behind their description, in part due to limited taxonomic distribution, lack of conserved functional domains, and difficulties with regard to genetic manipulation protocols. This study aimed to address this by investigating a novel mating-type gene, MAT1-2-7, for which two independent mutant strains were generated in a previous study. We characterized the molecular response to the truncation of this gene in a nonmodel, wood-infecting fungus and showed that it resulted in widespread differential expression throughout the transcriptome of this fungus. This suggests that secondary MAT genes may play a more important role than previously thought. This study also emphasizes the need for further research into the life cycles of nonmodel fungi, which often exhibit unique features that are very different from the systems understood from model species.
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Affiliation(s)
- A. M. Wilson
- Forestry & Agricultural Biotechnology Institute (FABI), Department of Biochemistry, Genetics & Microbiology, University of Pretoria, Pretoria, South Africa
| | - M. J. Wingfield
- Forestry & Agricultural Biotechnology Institute (FABI), Department of Biochemistry, Genetics & Microbiology, University of Pretoria, Pretoria, South Africa
| | - B. D. Wingfield
- Forestry & Agricultural Biotechnology Institute (FABI), Department of Biochemistry, Genetics & Microbiology, University of Pretoria, Pretoria, South Africa
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Aylward J, Havenga M, Wingfield BD, Wingfield MJ, Dreyer LL, Roets F, Steenkamp ET. Novel mating-type-associated genes and gene fragments in the genomes of Mycosphaerellaceae and Teratosphaeriaceae fungi. Mol Phylogenet Evol 2022; 171:107456. [DOI: 10.1016/j.ympev.2022.107456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 03/02/2022] [Accepted: 03/21/2022] [Indexed: 11/27/2022]
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Wingfield BD, De Vos L, Wilson AM, Duong TA, Vaghefi N, Botes A, Kharwar RN, Chand R, Poudel B, Aliyu H, Barbetti MJ, Chen S, de Maayer P, Liu F, Navathe S, Sinha S, Steenkamp ET, Suzuki H, Tshisekedi KA, van der Nest MA, Wingfield MJ. IMA Genome - F16 : Draft genome assemblies of Fusarium marasasianum, Huntiella abstrusa, two Immersiporthe knoxdaviesiana isolates, Macrophomina pseudophaseolina, Macrophomina phaseolina, Naganishia randhawae, and Pseudocercospora cruenta. IMA Fungus 2022; 13:3. [PMID: 35197126 PMCID: PMC8867778 DOI: 10.1186/s43008-022-00089-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Brenda D Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, 0028, South Africa.
| | - Lieschen De Vos
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, 0028, South Africa
| | - Andi M Wilson
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, 0028, South Africa
| | - Tuan A Duong
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, 0028, South Africa
| | - Niloofar Vaghefi
- Centre for Crop Health, University of Southern Queensland, Toowoomba, Australia
| | - Angela Botes
- School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, South Africa
| | - Ravindra Nath Kharwar
- Center of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Ramesh Chand
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India
| | - Barsha Poudel
- Centre for Crop Health, University of Southern Queensland, Toowoomba, Australia
| | - Habibu Aliyu
- Institute of Process Engineering in Life Science, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Martin J Barbetti
- School of Agriculture and Environment and the UWA Institute of Agriculture, University of Western Australia, Perth, Australia
| | - ShuaiFei Chen
- China Eucalypt Research Centre, Chinese Academy of Forestry, Zhanjiang, Guangdong Province, China
| | - Pieter de Maayer
- School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, South Africa
| | - FeiFei Liu
- China Eucalypt Research Centre, Chinese Academy of Forestry, Zhanjiang, Guangdong Province, China
| | | | - Shagun Sinha
- Center of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, India
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India
| | - Emma T Steenkamp
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, 0028, South Africa
| | - Hiroyuki Suzuki
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, 0028, South Africa
| | - Kalonji A Tshisekedi
- School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, South Africa
| | - Magriet A van der Nest
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, 0028, South Africa
- Biotechnology Platform, Agricultural Research Council, Pretoria, South Africa
| | - Michael J Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, 0028, South Africa
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Abstract
Sexual development in filamentous fungi is a complex process that relies on the precise control of and interaction between a variety of genetic networks and pathways. The mating-type (MAT) genes are the master regulators of this process and typically act as transcription factors, which control the expression of genes involved at all stages of the sexual cycle. In many fungi, the sexual cycle typically begins when the mating pheromones of one mating type are recognized by a compatible partner, followed by physical interaction and fertilization. Subsequently, highly specialized sexual structures are formed, within which the sexual spores develop after rounds of meiosis and mitosis. These spores are then released and germinate, forming new individuals that initiate new cycles of growth. This review provides an overview of the known genetic networks and pathways that are involved in each major stage of the sexual cycle in filamentous ascomycete fungi.
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Affiliation(s)
- Andi M. Wilson
- Forestry and Agricultural Biotechnology Institute, Department of Biochemistry, Genetics, and Microbiology, University of Pretoria, Pretoria, Gauteng, South Africa
| | - P. Markus Wilken
- Forestry and Agricultural Biotechnology Institute, Department of Biochemistry, Genetics, and Microbiology, University of Pretoria, Pretoria, Gauteng, South Africa
| | - Michael J. Wingfield
- Forestry and Agricultural Biotechnology Institute, Department of Biochemistry, Genetics, and Microbiology, University of Pretoria, Pretoria, Gauteng, South Africa
| | - Brenda D. Wingfield
- Forestry and Agricultural Biotechnology Institute, Department of Biochemistry, Genetics, and Microbiology, University of Pretoria, Pretoria, Gauteng, South Africa
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Nagel JH, Wingfield MJ, Slippers B. Next-generation sequencing provides important insights into the biology and evolution of the Botryosphaeriaceae. FUNGAL BIOL REV 2021. [DOI: 10.1016/j.fbr.2021.09.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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van der Nest MA, Chávez R, De Vos L, Duong TA, Gil-Durán C, Ferreira MA, Lane FA, Levicán G, Santana QC, Steenkamp ET, Suzuki H, Tello M, Rakoma JR, Vaca I, Valdés N, Wilken PM, Wingfield MJ, Wingfield BD. IMA genome - F14 : Draft genome sequences of Penicillium roqueforti, Fusarium sororula, Chrysoporthe puriensis, and Chalaropsis populi. IMA Fungus 2021; 12:5. [PMID: 33673862 PMCID: PMC7934431 DOI: 10.1186/s43008-021-00055-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Draft genomes of Penicillium roqueforti, Fusarium sororula, Chalaropsis populi, and Chrysoporthe puriensis are presented. Penicillium roqueforti is a model fungus for genetics, physiological and metabolic studies, as well as for biotechnological applications. Fusarium sororula and Chrysoporthe puriensis are important tree pathogens, and Chalaropsis populi is a soil-borne root-pathogen. The genome sequences presented here thus contribute towards a better understanding of both the pathogenicity and biotechnological potential of these species.
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Affiliation(s)
- Magriet A van der Nest
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria, 0028, South Africa
- Biotechnology Platform, Agricultural Research Council, Onderstepoort, Pretoria, 0110, South Africa
| | - Renato Chávez
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Alameda 3363, Estación Central, 9170022, Santiago, Chile.
| | - Lieschen De Vos
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria, 0028, South Africa.
| | - Tuan A Duong
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria, 0028, South Africa.
| | - Carlos Gil-Durán
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Alameda 3363, Estación Central, 9170022, Santiago, Chile
| | - Maria Alves Ferreira
- Department of Plant Pathology, Universidade Federal de Lavras/UFLA, Lavras, MG, 37200-000, Brazil
| | - Frances A Lane
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria, 0028, South Africa
| | - Gloria Levicán
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Alameda 3363, Estación Central, 9170022, Santiago, Chile
| | - Quentin C Santana
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria, 0028, South Africa
| | - Emma T Steenkamp
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria, 0028, South Africa
| | - Hiroyuki Suzuki
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria, 0028, South Africa
| | - Mario Tello
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Alameda 3363, Estación Central, 9170022, Santiago, Chile
| | - Jostina R Rakoma
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria, 0028, South Africa
| | - Inmaculada Vaca
- Departamento de Química, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago, Chile
| | - Natalia Valdés
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Alameda 3363, Estación Central, 9170022, Santiago, Chile
| | - P Markus Wilken
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria, 0028, South Africa.
| | - Michael J Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria, 0028, South Africa
| | - Brenda D Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria, 0028, South Africa
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Kanzi AM, Steenkamp ET, Van der Merwe NA, Wingfield BD. The mating system of the Eucalyptus canker pathogen Chrysoporthe austroafricana and closely related species. Fungal Genet Biol 2019; 123:41-52. [DOI: 10.1016/j.fgb.2018.12.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 11/29/2018] [Accepted: 12/03/2018] [Indexed: 11/18/2022]
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Nel WJ, Duong TA, Wingfield MJ, Wingfield BD, Hammerbacher A, de Beer ZW. Heterothallism revealed in the root rot fungi Berkeleyomyces basicola and B. rouxiae. Fungal Biol 2018; 122:1031-40. [PMID: 30342619 DOI: 10.1016/j.funbio.2018.08.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Revised: 07/30/2018] [Accepted: 08/10/2018] [Indexed: 11/19/2022]
Abstract
Berkeleyomyces basicola and Berkeleyomyces rouxiae, two sister species previously treated collectively as Thielaviopsis basicola, reside in the Ceratocystidaceae (Microascales, Ascomycota). Both species are important root pathogens of many important agricultural crops and ornamental plants. Although T. basicola has been known for more than 150y, a sexual state has never been found and it has been assumed to be an asexual pathogen. The aim of this study was to determine the mating strategy of the two Berkeleyomyces species. Investigation of the genome sequences of two B. basicola isolates allowed for the complete characterization of the MATlocus, revealing that it has a typical heterothallic mating system with the MAT1-1andMAT1-2 idiomorphs occurring in different isolates. PCR amplification using mating type primers developed in this study, showed that the MAT1-1-1andMAT1-2-1 genes were also present in different isolates of B. rouxiae. Pairing of isolates representing the two mating types of both species,using a variety of techniques failed to produce sexual structures. Although we have found no direct evidence that they reproduce sexually, these fungi are clearly heterothallic with both mating types occurring in some countries suggesting that a cryptic sexual cycle could exist for them.
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Wingfield BD, Bills GF, Dong Y, Huang W, Nel WJ, Swalarsk-Parry BS, Vaghefi N, Wilken PM, An Z, de Beer ZW, De Vos L, Chen L, Duong TA, Gao Y, Hammerbacher A, Kikkert JR, Li Y, Li H, Li K, Li Q, Liu X, Ma X, Naidoo K, Pethybridge SJ, Sun J, Steenkamp ET, van der Nest MA, van Wyk S, Wingfield MJ, Xiong C, Yue Q, Zhang X. IMA Genome-F 9: Draft genome sequence of Annulohypoxylon stygium, Aspergillus mulundensis, Berkeleyomyces basicola (syn. Thielaviopsis basicola), Ceratocystis smalleyi, two Cercospora beticola strains, Coleophoma cylindrospora, Fusarium fracticaudum, Phialophora cf . hyalina, and Morchella septimelata. IMA Fungus 2018; 9:199-223. [PMID: 30018880 PMCID: PMC6048567 DOI: 10.5598/imafungus.2018.09.01.13] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 05/28/2018] [Indexed: 11/05/2022] Open
Abstract
Draft genomes of the species Annulohypoxylon stygium, Aspergillus mulundensis, Berkeleyomyces basicola (syn. Thielaviopsis basicola), Ceratocystis smalleyi, two Cercospora beticola strains, Coleophoma cylindrospora, Fusarium fracticaudum, Phialophora cf. hyalina and Morchella septimelata are presented. Both mating types (MAT1-1 and MAT1-2) of Cercospora beticola are included. Two strains of Coleophoma cylindrospora that produce sulfated homotyrosine echinocandin variants, FR209602, FR220897 and FR220899 are presented. The sequencing of Aspergillus mulundensis, Coleophoma cylindrospora and Phialophora cf. hyalina has enabled mapping of the gene clusters encoding the chemical diversity from the echinocandin pathways, providing data that reveals the complexity of secondary metabolism in these different species. Overall these genomes provide a valuable resource for understanding the molecular processes underlying pathogenicity (in some cases), biology and toxin production of these economically important fungi.
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Affiliation(s)
- Brenda D. Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
| | - Gerald F. Bills
- Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77054, USA
| | - Yang Dong
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
- College of Biological Big Data, Yunnan Agriculture University, Kunming 650504, Yunnan, China
| | - Wenli Huang
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610065, Sichuan, China
| | - Wilma J. Nel
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
| | - Benedicta S. Swalarsk-Parry
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
| | - Niloofar Vaghefi
- School of Integrative Plant Science, Plant Pathology & Plant-Microbe Biology Section, Cornell University, Geneva, NY 14456, USA
| | - P. Markus Wilken
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
| | - Zhiqiang An
- Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77054, USA
| | - Z. Wilhelm de Beer
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
| | - Lieschen De Vos
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
| | - Li Chen
- Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77054, USA
| | - Tuan A. Duong
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
| | - Yun Gao
- Nowbio Biotechnology Company, Kunming, 650201,Yunnan, China
| | - Almuth Hammerbacher
- Department of Zoology Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
| | | | - Yan Li
- Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77054, USA
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Huiying Li
- Kunming University of Science and Technology, Kunming 650500, Yunnan, China
| | - Kuan Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qiang Li
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610065, Sichuan, China
| | - Xingzhong Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiao Ma
- Yunnan Plateau Characteristic Agricultural Industry Research Institute, Kunming 650201, Yunnan, China
| | - Kershney Naidoo
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
| | - Sarah J. Pethybridge
- School of Integrative Plant Science, Plant Pathology & Plant-Microbe Biology Section, Cornell University, Geneva, NY 14456, USA
| | - Jingzu Sun
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Emma T. Steenkamp
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
| | - Magriet A. van der Nest
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
| | - Stephanie van Wyk
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
| | - Michael J. Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
| | - Chuan Xiong
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610065, Sichuan, China
| | - Qun Yue
- Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77054, USA
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaoling Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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Sayari M, Steenkamp ET, van der Nest MA, Wingfield BD. Diversity and evolution of polyketide biosynthesis gene clusters in the Ceratocystidaceae. Fungal Biol 2018; 122:856-66. [PMID: 30115319 DOI: 10.1016/j.funbio.2018.04.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 03/30/2018] [Accepted: 04/25/2018] [Indexed: 01/26/2023]
Abstract
Polyketides are secondary metabolites with diverse biological activities. Polyketide synthases (PKS) are often encoded from genes clustered in the same genomic region. Functional analyses and genomic studies show that most fungi are capable of producing a repertoire of polyketides. We considered the potential of Ceratocystidaceae for producing polyketides using a comparative genomics approach. Our aims were to identify the putative polyketide biosynthesis gene clusters, to characterize them and predict the types of polyketide compounds they might produce. We used sequences from nineteen species in the genera, Ceratocystis, Endoconidiophora, Davidsoniella, Huntiella, Thielaviopsis and Bretziella, to identify and characterize PKS gene clusters, by employing a range of bioinformatics and phylogenetic tools. We showed that the genomes contained putative clusters containing a non-reducing type I PKS and a type III PKS. Phylogenetic analyses suggested that these genes were already present in the ancestor of the Ceratocystidaceae. By contrast, the various reducing type I PKS-containing clusters identified in these genomes appeared to have distinct evolutionary origins. Although one of the identified clusters potentially allows for the production of melanin, their functional characterization will undoubtedly reveal many novel and important compounds implicated in the biology of the Ceratocystidaceae.
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