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See PT, Iagallo EM, Marathamuthu KA, Wood B, Aboukhaddour R, Moffat CS. A new ToxA haplotype in the wheat fungal pathogen Bipolaris sorokiniana. Phytopathology 2024. [PMID: 38530294 DOI: 10.1094/phyto-10-23-0370-r] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
The necrotrophic effector ToxA is a well-studied virulence factor produced by several fungal necrotrophs. Initially cloned from the wheat tan spot pathogen Pyrenophora tritici-repentis in 1996, ToxA was found almost a decade later in another fungal pathogen Parastagonospora nodorum and its sister species Parastagonospora pseudonodorum. In 2018, ToxA was detected in a third wheat fungal pathogenic species: Bipolaris sorokiniana that causes spot blotch disease. However, unlike the case with P. tritici-repentis and P. nodorum, the ToxA in B. sorokiniana has been investigated in recent years only. In this report, five Australian B. sorokiniana isolates were assessed for the presence of ToxA. Four isolates were found to contain ToxA. While one isolate harboured the previously reported ToxA haplotype sequence (ToxA19), three isolates contain a different haplotype, designated herein as ToxA25 that has a non-synonymous mutation resulting in an amino acid change of glycine to arginine at position 168. Both B. sorokiniana ToxA isoforms, when heterologously expressed in Escherichia coli, exhibited the classic ToxA-necrosis inducing activity on ToxA sensitive Tsn1 cultivars. Preliminary analysis of the B. sorokiniana isolates on Australian wheat cultivars showed that isolates with ToxA19, ToxA25 or ToxA-deficient displayed varying degrees of virulence, with the most aggressive isolates observed for those producing ToxA. Differences in spot blotch disease severity between Tsn1 and tsn1 cultivars were observed, however this was not limited to the ToxA-producing isolates. The overall results suggests that the virulence of the Australian B. sorokiniana isolates is diverse with the significance of ToxA-Tsn1 interactions depending on individual isolates.
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Affiliation(s)
- Pao Theen See
- Curtin University, 1649, Kent Street, Bentley, Perth, Western Australia, Australia, 6102;
| | - Elyce M Iagallo
- Curtin University, 1649, kent st, Bentley, Perth, Western Australia, Australia, 6102;
| | | | - Blake Wood
- Curtin University, 1649, Perth, Western Australia, Australia;
| | - Reem Aboukhaddour
- Agriculture and Agri-Food Canada Lethbridge Research and Development Centre, 98670, 5403 1Ave south, Lethbridge, Alberta, Canada, T1J 4B1;
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Hafez M, Gourlie R, McDonald M, Telfer M, Carmona MA, Sautua FJ, Moffat CS, Moolhuijzen PM, See PT, Aboukhaddour R. Evolution of the Toxb Gene in Pyrenophora tritici-repentis and Related Species. Mol Plant Microbe Interact 2024; 37:327-337. [PMID: 37759383 DOI: 10.1094/mpmi-08-23-0114-fi] [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] [Subscribe] [Scholar Register] [Indexed: 09/29/2023]
Abstract
Pyrenophora tritici-repentis (tan spot) is a destructive foliar pathogen of wheat with global impact. This ascomycete fungus possesses a highly plastic open pangenome shaped by the gain and loss of effector genes. This study investigated the allelic variations in the chlorosis-encoding gene ToxB across 422 isolates representing all identified pathotypes and worldwide origins. To gain better insights into ToxB evolution, we examined its presence and variability in other Pyrenophora spp. A ToxB haplotype network was constructed, revealing the evolutionary relationships of this gene (20 haplotypes) across four Pyrenophora species. Notably, toxb, the homolog of ToxB, was detected for the first time in the barley pathogen Pyrenophora teres. The ToxB/toxb genes display evidence of selection that is characterized by loss of function, duplication, and diverse mutations. Within the ToxB/toxb open reading frame, 72 mutations were identified, including 14 synonymous, 55 nonsynonymous, and 3 indel mutations. Remarkably, a, ∼5.6-kb Copia-like retrotransposon, named Copia-1_Ptr, was found inserted in the toxb gene of a race 3 isolate. This insert disrupted the ToxB gene's function, a first case of effector gene disruption by a transposable element in P. tritici-repentis. Additionally, a microsatellite with 25 nucleotide repeats (0 to 10) in the upstream region of ToxB suggested a potential mechanism influencing ToxB expression and regulation. Exploring ToxB-like protein distribution in other ascomycetes revealed the presence of ToxB-like proteins in 19 additional species, including the Leotiomycetes class for the first time. The presence/absence pattern of ToxB-like proteins defied species relatedness compared with a phylogenetic tree, suggesting a past horizontal gene transfer event during the evolution of the ToxB gene. [Formula: see text] Copyright © 2024 His Majesty the King in Right of Canada, as represented by the Minister of Agriculture and Agri-Food. This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Mohamed Hafez
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB, Canada
- Botany and Microbiology Department, Faculty of Science, Suez University, Suez, Egypt
| | - Ryan Gourlie
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB, Canada
| | - Megan McDonald
- School of Biosciences, University of Birmingham, Institute of Microbiology and Infection, Edgbaston, Birmingham, U.K
| | - Melissa Telfer
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB, Canada
| | - Marcelo A Carmona
- Cátedra de Fitopatología, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Francisco J Sautua
- Cátedra de Fitopatología, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Caroline S Moffat
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Australia
| | - Paula M Moolhuijzen
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Australia
| | - Pao Theen See
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Australia
| | - Reem Aboukhaddour
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB, Canada
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See PT, Marathamuthu KA, Cupitt CF, Iagallo EM, Moffat CS. A Race Profile of Tan Spot in Australia Reveals Race 2 Isolates Harboring ToxC1. Phytopathology 2023; 113:1202-1209. [PMID: 36750556 DOI: 10.1094/phyto-11-22-0422-r] [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] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Tan spot disease is caused by Pyrenophora tritici-repentis (Ptr), one of the major necrotrophic fungal pathogens that affects wheat crops globally. Extensive research has shown that the necrotrophic fungal effectors ToxA, ToxB, and ToxC underlie the genetic interactions of Ptr race classification. ToxA and ToxB are both small proteins secreted during infection; however, the structure of ToxC remains unknown. In line with the recent discovery of the ToxC1 gene that is involved in ToxC production, a subset of 68 isolates collected from the Australian wheat cropping regions were assessed for the presence of all three effectors by pathotyping against four tan spot wheat differential lines and PCR amplification of ToxA, ToxB, and ToxC1. Based on the disease phenotypes, the 68 isolates were grouped into two races with 63 classified as race 1 and five as race 2. A representative selection of each race was tested against eight Australian commercial wheat cultivars and showed no distinction between the virulence levels. Sequencing of ToxA showed that both races had identical gene sequences of haplotype PtrA1. All the race 1 isolates possessed ToxC1 but three race 2 isolates also contained ToxC1 despite being unable to induce a spreading chlorotic symptom on the ToxC differential line. Quantitative trait loci mapping confirmed the absence of the ToxC-Tsc1 association in disease response caused by the ToxC1-containing race 2 isolate; however, ToxC1 expression was detected during plant infection. Altogether, these results suggest that there is a complex regulatory process involved in the production of ToxC within the Australian race 2 isolates.
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Affiliation(s)
- Pao Theen See
- Centre for Crop and Disease Management, Molecular and Life Sciences, School of Science, Curtin University, Bentley, WA 6102, Australia
| | - Kalai A Marathamuthu
- Centre for Crop and Disease Management, Molecular and Life Sciences, School of Science, Curtin University, Bentley, WA 6102, Australia
| | - Catherine F Cupitt
- Centre for Crop and Disease Management, Molecular and Life Sciences, School of Science, Curtin University, Bentley, WA 6102, Australia
| | - Elyce M Iagallo
- Centre for Crop and Disease Management, Molecular and Life Sciences, School of Science, Curtin University, Bentley, WA 6102, Australia
| | - Caroline S Moffat
- Centre for Crop and Disease Management, Molecular and Life Sciences, School of Science, Curtin University, Bentley, WA 6102, Australia
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Aboukhaddour R, Hafez M, McDonald M, Moffat CS, Navathe S, Friesen TL, Strelkov SE, Oliver RP, Tan KC, Liu Z, Moolhuijzen PM, Phan H, See PT, Solomon PS. A Revised Nomenclature for ToxA Haplotypes Across Multiple Fungal Species. Phytopathology 2023; 113:1180-1184. [PMID: 36809076 DOI: 10.1094/phyto-01-23-0017-sc] [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] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
ToxA is one of the most studied proteinaceous necrotrophic effectors produced by plant pathogens. It has been identified in four pathogens (Pyrenophora tritici-repentis, Parastagonospora nodorum, Parastagonospora pseudonodorum [formerly Parastagonospora avenaria f. sp. tritici], and Bipolaris sorokiniana) causing leaf spot diseases on cereals worldwide. To date, 24 different ToxA haplotypes have been identified. Some P. tritici-repentis and related species also express ToxB, another small protein necrotrophic effector. We present here a revised and standardized nomenclature for these effectors, which could be extended to other poly-haplotypic genes found across multiple species.
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Affiliation(s)
- Reem Aboukhaddour
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Center, Lethbridge, Alberta, Canada
| | - Mohamed Hafez
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Center, Lethbridge, Alberta, Canada
| | - Megan McDonald
- School of Biosciences, University of Birmingham, Institute of Microbiology and Infection, Edgbaston, Birmingham, U.K
| | - Caroline S Moffat
- Centre for Crop Disease and Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Sudhir Navathe
- Agharkar Research Institute, Department Science and Technology, Govt. of India, Pune, 411004, India
| | - Timothy L Friesen
- USDA-ARS, Edward T. Schafer Agricultural Research Center, Cereal Crops Research Unit, Fargo, ND 58102-2765, U.S.A
- Department of Plant Pathology, North Dakota State University, Fargo, ND, U.S.A
| | - Stephen E Strelkov
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | | | - Kar-Chun Tan
- Centre for Crop Disease and Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Zhaohui Liu
- Department of Plant Pathology, North Dakota State University, Fargo, ND, U.S.A
| | - Paula M Moolhuijzen
- Centre for Crop Disease and Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Huyen Phan
- Centre for Crop Disease and Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Pao Theen See
- Centre for Crop Disease and Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Peter S Solomon
- Division of Plant Sciences, Research School of Biology, The Australian National University ACT, Australia
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See PT, Moffat CS. Profiling the Pyrenophora tritici-repentis secretome: The Pf2 transcription factor regulates the secretion of the effector proteins ToxA and ToxB. Mol Microbiol 2023; 119:612-629. [PMID: 37059688 DOI: 10.1111/mmi.15058] [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: 02/28/2022] [Revised: 02/13/2023] [Accepted: 03/19/2023] [Indexed: 04/16/2023]
Abstract
The global wheat disease tan spot is caused by the necrotrophic fungal pathogen Pyrenophora tritici-repentis (Ptr) which secretes necrotrophic effectors to facilitate host plant colonization. We previously reported a role of the Zn2 Cys6 binuclear cluster transcription factor Pf2 in the regulation of the Ptr effector ToxA. Here, we show that Pf2 is also a positive regulator of ToxB, via targeted deletion of PtrPf2 which resulted in reduced ToxB expression and defects in conidiation and pathogenicity. To further investigate the function of Ptr Pf2 in regulating protein secretion, the secretome profiles of two Δptrpf2 mutants of two Ptr races (races 1 and 5) were evaluated using a SWATH-mass spectrometry (MS) quantitative approach. Analysis of the secretomes of the Δptrpf2 mutants from in vitro culture filtrate identified more than 500 secreted proteins, with 25% unique to each race. Of the identified proteins, less than 6% were significantly differentially regulated by Ptr Pf2. Among the downregulated proteins were ToxA and ToxB, specific to race 1 and race 5 respectively, demonstrating the role of Ptr Pf2 as a positive regulator of both effectors. Significant motif sequences identified in both ToxA and ToxB putative promoter regions were further explored via GFP reporter assays.
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Affiliation(s)
- Pao Theen See
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australian, 6102, Australia
| | - Caroline S Moffat
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australian, 6102, Australia
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Taylor J, Jorgensen D, Moffat CS, Chalmers KJ, Fox R, Hollaway GJ, Cook MJ, Neate SM, See PT, Shankar M. An international wheat diversity panel reveals novel sources of genetic resistance to tan spot in Australia. Theor Appl Genet 2023; 136:61. [PMID: 36912976 PMCID: PMC10011302 DOI: 10.1007/s00122-023-04332-y] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 02/23/2023] [Indexed: 06/18/2023]
Abstract
Novel sources of genetic resistance to tan spot in Australia have been discovered using one-step GWAS and genomic prediction models that accounts for additive and non-additive genetic variation. Tan spot is a foliar disease in wheat caused by the fungal pathogen Pyrenophora tritici-repentis (Ptr) and has been reported to generate up to 50% yield losses under favourable disease conditions. Although farming management practices are available to reduce disease, the most economically sustainable approach is establishing genetic resistance through plant breeding. To further understand the genetic basis for disease resistance, we conducted a phenotypic and genetic analysis study using an international diversity panel of 192 wheat lines from the Maize and Wheat Improvement Centre (CIMMYT), the International Centre for Agriculture in the Dry Areas (ICARDA) and Australian (AUS) wheat research programmes. The panel was evaluated using Australian Ptr isolates in 12 experiments conducted in three Australian locations over two years, with assessment for tan spot symptoms at various plant development stages. Phenotypic modelling indicated high heritability for nearly all tan spot traits with ICARDA lines displaying the greatest average resistance. We then conducted a one-step whole-genome analysis of each trait using a high-density SNP array, revealing a large number of highly significant QTL exhibiting a distinct lack of repeatability across the traits. To better summarise the genetic resistance of the lines, a one-step genomic prediction of each tan spot trait was conducted by combining the additive and non-additive predicted genetic effects of the lines. This revealed multiple CIMMYT lines with broad genetic resistance across the developmental stages of the plant which can be utilised in Australian wheat breeding programmes to improve tan spot disease resistance.
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Affiliation(s)
- Julian Taylor
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Glen Osmond, SA, 5064, Australia.
| | - Dorthe Jorgensen
- Department of Primary Industries and Regional Development, Agriculture and Food, 3 Baron Hay Ct, South Perth, WA, 6151, Australia
| | - Caroline S Moffat
- Centre for Crop Disease and Management, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA, 6102, Australia
| | - Ken J Chalmers
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Glen Osmond, SA, 5064, Australia
| | - Rebecca Fox
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Glen Osmond, SA, 5064, Australia
| | - Grant J Hollaway
- Agriculture Victoria, Private Bag 260, Horsham, VIC, 3401, Australia
| | - Melissa J Cook
- Agriculture Victoria, Private Bag 260, Horsham, VIC, 3401, Australia
| | - Stephen M Neate
- Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD, 4350, Australia
| | - Pao Theen See
- Centre for Crop Disease and Management, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA, 6102, Australia
| | - Manisha Shankar
- Department of Primary Industries and Regional Development, Agriculture and Food, 3 Baron Hay Ct, South Perth, WA, 6151, Australia.
- School of Agriculture and Environment, University of Western Australia, 35 Stirling Hwy, Crawley, WA, 6009, Australia.
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Moolhuijzen PM, See PT, Shi G, Powell HR, Cockram J, Jørgensen LN, Benslimane H, Strelkov SE, Turner J, Liu Z, Moffat CS. A global pangenome for the wheat fungal pathogen Pyrenophora tritici-repentis and prediction of effector protein structural homology. Microb Genom 2022; 8:mgen000872. [PMID: 36214662 PMCID: PMC9676058 DOI: 10.1099/mgen.0.000872] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The adaptive potential of plant fungal pathogens is largely governed by the gene content of a species, consisting of core and accessory genes across the pathogen isolate repertoire. To approximate the complete gene repertoire of a globally significant crop fungal pathogen, a pan genomic analysis was undertaken for Pyrenophora tritici-repentis (Ptr), the causal agent of tan (or yellow) spot disease in wheat. In this study, 15 new Ptr genomes were sequenced, assembled and annotated, including isolates from three races not previously sequenced. Together with 11 previously published Ptr genomes, a pangenome for 26 Ptr isolates from Australia, Europe, North Africa and America, representing nearly all known races, revealed a conserved core-gene content of 57 % and presents a new Ptr resource for searching natural homologues (orthologues not acquired by horizontal transfer from another species) using remote protein structural homology. Here, we identify for the first time a non-synonymous mutation in the Ptr necrotrophic effector gene ToxB, multiple copies of the inactive toxb within an isolate, a distant natural Pyrenophora homologue of a known Parastagonopora nodorum necrotrophic effector (SnTox3), and clear genomic break points for the ToxA effector horizontal transfer region. This comprehensive genomic analysis of Ptr races includes nine isolates sequenced via long read technologies. Accordingly, these resources provide a more complete representation of the species, and serve as a resource to monitor variations potentially involved in pathogenicity.
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Affiliation(s)
- Paula M. Moolhuijzen
- Centre for Crop Disease and Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
- *Correspondence: Paula M. Moolhuijzen,
| | - Pao Theen See
- Centre for Crop Disease and Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Gongjun Shi
- Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, USA
| | - Harold R. Powell
- Department of Life Sciences, Centre for Integrative Systems Biology and Bioinformatics, Imperial College London, London, England, UK
| | - James Cockram
- NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | | | - Hamida Benslimane
- Département de Botanique, Ecole Nationale Supérieure Agronomique (ENSA), Hassan Badi, El-Harrach, Algiers, Algeria
| | - Stephen E. Strelkov
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | | | - Zhaohui Liu
- Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, USA
- *Correspondence: Zhaohui Liu,
| | - Caroline S. Moffat
- Centre for Crop Disease and Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
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Dinglasan EG, Peressini T, Marathamuthu KA, See PT, Snyman L, Platz G, Godwin I, Voss-Fels KP, Moffat CS, Hickey LT. Genetic characterization of adult-plant resistance to tan spot (syn, yellow spot) in wheat. Theor Appl Genet 2021; 134:2823-2839. [PMID: 34061222 DOI: 10.1007/s00122-021-03861-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 05/11/2021] [Indexed: 06/12/2023]
Abstract
QTL mapping identified key genomic regions associated with adult-plant resistance to tan spot, which are effective even in the presence of the sensitivity gene Tsn1, thus serving as a new genetic solution to develop disease-resistant wheat cultivars. Improving resistance to tan spot (Pyrenophora tritici-repentis; Ptr) in wheat by eliminating race-specific susceptibility genes is a common breeding approach worldwide. The potential to exploit variation in quantitative forms of resistance, such as adult-plant resistance (APR), offers an alternative approach that could lead to broad-spectrum protection. We previously identified wheat landraces in the Vavilov diversity panel that exhibited high levels of APR despite carrying the sensitivity gene Tsn1. In this study, we characterised the genetic control of APR by developing a recombinant inbred line population fixed for Tsn1, but segregating for the APR trait. Linkage mapping using DArTseq markers and disease response phenotypes identified a QTL associated with APR to Ptr race 1 (producing Ptr ToxA- and Ptr ToxC) on chromosome 2B (Qts.313-2B), which was consistently detected in multiple adult-plant experiments. Additional loci were also detected on chromosomes 2A, 3D, 5A, 5D, 6A, 6B and 7A at the seedling stage, and on chromosomes 1A and 5B at the adult stage. We demonstrate that Qts.313-2B can be combined with other adult-plant QTL (i.e. Qts.313-1A and Qts.313-5B) to strengthen resistance levels. The APR QTL reported in this study provide a new genetic solution to tan spot in Australia and could be deployed in wheat cultivars, even in the presence of Tsn1, to decrease production losses and reduce the application of fungicides.
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Affiliation(s)
- Eric G Dinglasan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| | - Tamaya Peressini
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| | | | - Pao Theen See
- Centre for Crop and Disease Management, Curtin University, Perth, WA, Australia
| | - Lisle Snyman
- Department of Agriculture and Fisheries, Hermitage Research Facility, Warwick, QLD, Australia
| | - Greg Platz
- Department of Agriculture and Fisheries, Hermitage Research Facility, Warwick, QLD, Australia
| | - Ian Godwin
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| | - Kai P Voss-Fels
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| | - Caroline S Moffat
- Centre for Crop and Disease Management, Curtin University, Perth, WA, Australia
| | - Lee T Hickey
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia.
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Moolhuijzen P, See PT, Moffat CS. The first genome assembly of fungal pathogen Pyrenophora tritici-repentis race 1 isolate using Oxford Nanopore MinION sequencing. BMC Res Notes 2021; 14:334. [PMID: 34454585 PMCID: PMC8403381 DOI: 10.1186/s13104-021-05751-0] [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] [Received: 05/09/2021] [Accepted: 08/19/2021] [Indexed: 11/16/2022] Open
Abstract
Objectives The assembly of fungal genomes using short-reads is challenged by long repetitive and low GC regions. However, long-read sequencing technologies, such as PacBio and Oxford Nanopore, are able to overcome many problematic regions, thereby providing an opportunity to improve fragmented genome assemblies derived from short reads only. Here, a necrotrophic fungal pathogen Pyrenophora tritici-repentis (Ptr) isolate 134 (Ptr134), which causes tan spot disease on wheat, was sequenced on a MinION using Oxford Nanopore Technologies (ONT), to improve on a previous Illumina short-read genome assembly and provide a more complete genome resource for pan-genomic analyses of Ptr. Results The genome of Ptr134 sequenced on a MinION using ONT was assembled into 28 contiguous sequences with a total length of 40.79 Mb and GC content of 50.81%. The long-read assembly provided 6.79 Mb of new sequence and 2846 extra annotated protein coding genes as compared to the previous short-read assembly. This improved genome sequence represents near complete chromosomes, an important resource for large scale and pan genomic comparative analyses.
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Affiliation(s)
- Paula Moolhuijzen
- Centre for Crop Disease and Management, School of Molecular Life Sciences, Curtin University, Bentley, WA, 6102, Australia.
| | - Pao Theen See
- Centre for Crop Disease and Management, School of Molecular Life Sciences, Curtin University, Bentley, WA, 6102, Australia
| | - Caroline S Moffat
- Centre for Crop Disease and Management, School of Molecular Life Sciences, Curtin University, Bentley, WA, 6102, Australia
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Moolhuijzen P, See PT, Moffat CS. Correction to: PacBio genome sequencing reveals new insights into the genomic organisation of the multi-copy ToxB gene of the wheat fungal pathogen Pyrenophora tritici-repentis. BMC Genomics 2021; 22:608. [PMID: 34372759 PMCID: PMC8353772 DOI: 10.1186/s12864-021-07836-3] [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: 11/10/2022] Open
Affiliation(s)
- Paula Moolhuijzen
- Centre for Crop Disease and Management, School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia.
| | - Pao Theen See
- Centre for Crop Disease and Management, School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
| | - Caroline S Moffat
- Centre for Crop Disease and Management, School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
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11
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Moolhuijzen P, See PT, Moffat CS. PacBio genome sequencing reveals new insights into the genomic organisation of the multi-copy ToxB gene of the wheat fungal pathogen Pyrenophora tritici-repentis. BMC Genomics 2020; 21:645. [PMID: 32957933 PMCID: PMC7507622 DOI: 10.1186/s12864-020-07029-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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: 05/06/2020] [Accepted: 08/27/2020] [Indexed: 11/13/2022] Open
Abstract
Background Necrotrophic effector proteins secreted by fungal pathogens are important virulence factors that mediate the development of disease in wheat. Pyrenophora tritici-repentis (Ptr), the causal agent of wheat tan spot, has a race structure dependent on the combination of effectors. In Ptr, ToxA and ToxB are known proteinaceous effectors responsible for necrosis and chlorosis respectively. While Ptr ToxA is encoded by the single gene ToxA, ToxB has multiple loci in the Ptr genome, which is postulated to be directly related to the level of ToxB production and leaf chlorosis. Although previous analysis has indicated that the majority of the ToxB loci lie on a single chromosome, the exact number and chromosomal locations for all the ToxB loci have not been fully identified. Results In this study, we have sequenced the genome of a race 5 ToxB-producing isolate (DW5), using PacBio long read technology, and found that ToxB duplications are nested in the complex subtelomeric chromosomal regions. A total of ten identical ToxB gene copies were identified and based on flanking sequence identity, nine loci appeared associated with chromosome 11 and a single copy with chromosome 5. Chromosome 11 multiple ToxB gene loci were separated by large sequence regions between 31 and 66 kb within larger segmental duplications in an alternating pattern related to loci strand, and flanked by transposable elements. Conclusion This work provides for the first time the full accompaniment of ToxB loci and surrounding regions, and identifies the organization and distribution of ten ToxB loci to subtelomeric regions. To our knowledge, this is the first report of an interwoven strand-related duplication pattern event. This study further highlights the importance of resolving the highly complex distal chromosomal regions, that remain difficult to assemble, and can harbour important effectors and virulence factors. Supplementary information Supplementary information accompanies this paper at 10.1186/s12864-020-07029-4.
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Affiliation(s)
- Paula Moolhuijzen
- Centre for Crop Disease and Management, School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia.
| | - Pao Theen See
- Centre for Crop Disease and Management, School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
| | - Caroline S Moffat
- Centre for Crop Disease and Management, School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
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Moolhuijzen PM, Muria-Gonzalez MJ, Syme R, Rawlinson C, See PT, Moffat CS, Ellwood SR. Expansion and Conservation of Biosynthetic Gene Clusters in Pathogenic Pyrenophora spp. Toxins (Basel) 2020; 12:toxins12040242. [PMID: 32283749 PMCID: PMC7232245 DOI: 10.3390/toxins12040242] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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: 03/13/2020] [Revised: 04/02/2020] [Accepted: 04/04/2020] [Indexed: 12/28/2022] Open
Abstract
Pyrenophora is a fungal genus responsible for a number of major cereal diseases. Although fungi produce many specialised or secondary metabolites for defence and interacting with the surrounding environment, the repertoire of specialised metabolites (SM) within Pyrenophora pathogenic species remains mostly uncharted. In this study, an in-depth comparative analysis of the P. teres f. teres, P teres f. maculata and P. tritici-repentis potential to produce SMs, based on in silico predicted biosynthetic gene clusters (BGCs), was conducted using genome assemblies from PacBio DNA reads. Conservation of BGCs between the Pyrenophora species included type I polyketide synthases, terpene synthases and the first reporting of a type III polyketide synthase in P teres f. maculata. P. teres isolates exhibited substantial expansion of non-ribosomal peptide synthases relative to P. tritici-repentis, hallmarked by the presence of tailoring cis-acting nitrogen methyltransferase domains. P. teres isolates also possessed unique non-ribosomal peptide synthase (NRPS)-indole and indole BGCs, while a P. tritici-repentis phytotoxin BGC for triticone production was absent in P. teres. These differences highlight diversification between the pathogens that reflects their different evolutionary histories, host adaption and lifestyles.
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Affiliation(s)
- Paula M. Moolhuijzen
- Centre for Crop Disease and Management, Department of Environment and Agriculture, Curtin University, Bentley, WA 6102, Australia
- Correspondence:
| | - Mariano Jordi Muria-Gonzalez
- Centre for Crop Disease and Management, Department of Environment and Agriculture, Curtin University, Bentley, WA 6102, Australia
| | - Robert Syme
- Canadian Centre for Computational Genomics, McGill University and Genome Quebec Innovation Center, Montréal, QC H3A 0G1, Canada
| | - Catherine Rawlinson
- Centre for Crop Disease and Management, Department of Environment and Agriculture, Curtin University, Bentley, WA 6102, Australia
| | - Pao Theen See
- Centre for Crop Disease and Management, Department of Environment and Agriculture, Curtin University, Bentley, WA 6102, Australia
| | - Caroline S. Moffat
- Centre for Crop Disease and Management, Department of Environment and Agriculture, Curtin University, Bentley, WA 6102, Australia
| | - Simon R. Ellwood
- Centre for Crop Disease and Management, Department of Environment and Agriculture, Curtin University, Bentley, WA 6102, Australia
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13
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Corsi B, Percival-Alwyn L, Downie RC, Venturini L, Iagallo EM, Campos Mantello C, McCormick-Barnes C, See PT, Oliver RP, Moffat CS, Cockram J. Genetic analysis of wheat sensitivity to the ToxB fungal effector from Pyrenophora tritici-repentis, the causal agent of tan spot. Theor Appl Genet 2020; 133:935-950. [PMID: 31915874 PMCID: PMC7021774 DOI: 10.1007/s00122-019-03517-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 12/17/2019] [Indexed: 05/05/2023]
Abstract
Genetic mapping of sensitivity to the Pyrenophora tritici-repentis effector ToxB allowed development of a diagnostic genetic marker, and investigation of wheat pedigrees allowed transmission of sensitive alleles to be tracked. Tan spot, caused by the necrotrophic fungal pathogen Pyrenophora tritici-repentis, is a major disease of wheat (Triticum aestivum). Secretion of the P. tritici-repentis effector ToxB is thought to play a part in mediating infection, causing chlorosis of plant tissue. Here, genetic analysis using an association mapping panel (n = 480) and a multiparent advanced generation intercross (MAGIC) population (n founders = 8, n progeny = 643) genotyped with a 90,000 feature single nucleotide polymorphism (SNP) array found ToxB sensitivity to be highly heritable (h2 ≥ 0.9), controlled predominantly by the Tsc2 locus on chromosome 2B. Genetic mapping of Tsc2 delineated a 1921-kb interval containing 104 genes in the reference genome of ToxB-insensitive variety 'Chinese Spring'. This allowed development of a co-dominant genetic marker for Tsc2 allelic state, diagnostic for ToxB sensitivity in the association mapping panel. Phenotypic and genotypic analysis in a panel of wheat varieties post-dated the association mapping panel further supported the diagnostic nature of the marker. Combining ToxB phenotype and genotypic data with wheat pedigree datasets allowed historic sources of ToxB sensitivity to be tracked, finding the variety 'Maris Dove' to likely be the historic source of sensitive Tsc2 alleles in the wheat germplasm surveyed. Exploration of the Tsc2 region gene space in the ToxB-sensitive line 'Synthetic W7984' identified candidate genes for future investigation. Additionally, a minor ToxB sensitivity QTL was identified on chromosome 2A. The resources presented here will be of immediate use for marker-assisted selection for ToxB insensitivity and the development of germplasm with additional genetic recombination within the Tsc2 region.
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Affiliation(s)
- Beatrice Corsi
- John Bingham Laboratory, NIAB, Huntingdon Road, Cambridge, CB3 0LE, UK
| | | | - Rowena C Downie
- John Bingham Laboratory, NIAB, Huntingdon Road, Cambridge, CB3 0LE, UK
- Plant Sciences Department, University of Cambridge, Cambridge, UK
| | - Luca Venturini
- Life Sciences Department, Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Elyce M Iagallo
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, Australia
| | - Camila Campos Mantello
- John Bingham Laboratory, NIAB, Huntingdon Road, Cambridge, CB3 0LE, UK
- Genetracer Biotech, Calle Albert Einstein 22, 39011, Santander, Spain
| | - Charlie McCormick-Barnes
- John Bingham Laboratory, NIAB, Huntingdon Road, Cambridge, CB3 0LE, UK
- Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Pao Theen See
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, Australia
| | - Richard P Oliver
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, Australia
| | - Caroline S Moffat
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, Australia.
| | - James Cockram
- John Bingham Laboratory, NIAB, Huntingdon Road, Cambridge, CB3 0LE, UK.
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Rawlinson C, See PT, Moolhuijzen P, Li H, Moffat CS, Chooi YH, Oliver RP. The identification and deletion of the polyketide synthase-nonribosomal peptide synthase gene responsible for the production of the phytotoxic triticone A/B in the wheat fungal pathogen Pyrenophora tritici-repentis. Environ Microbiol 2019; 21:4875-4886. [PMID: 31698543 PMCID: PMC6915911 DOI: 10.1111/1462-2920.14854] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 11/04/2019] [Accepted: 11/05/2019] [Indexed: 12/21/2022]
Abstract
The economically important necrotrophic fungal pathogen, Pyrenophora tritici-repentis (Ptr), causes tan spot of wheat, a disease typified by foliar necrosis and chlorosis. The culture filtrate of an Australian Ptr isolate, M4, possesses phytotoxic activity and plant bioassay guided discovery led to the purification of necrosis inducing toxins called triticone A and B. High-resolution LC-MS/MS analysis of the culture filtrate identified an additional 37 triticone-like compounds. The biosynthetic gene cluster responsible for triticone production (the Ttc cluster) was identified and deletion of TtcA, a hybrid polyketide synthase (PKS)-nonribosomal peptide synthase (NRPS), abolished production of all triticones. The pathogenicity of mutant (ttcA) strains was not visibly affected in our assays. We hypothesize that triticones possess general antimicrobial activity important for competition in multi-microbial environments.
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Affiliation(s)
- Catherine Rawlinson
- Centre for Crop and Disease Management, Curtin University, Perth, 6150, Western Australia, Australia
| | - Pao Theen See
- Centre for Crop and Disease Management, Curtin University, Perth, 6150, Western Australia, Australia
| | - Paula Moolhuijzen
- Centre for Crop and Disease Management, Curtin University, Perth, 6150, Western Australia, Australia
| | - Hang Li
- School of Molecular Sciences, The University of Western Australia, Perth, 6009, Western Australia, Australia
| | - Caroline S Moffat
- Centre for Crop and Disease Management, Curtin University, Perth, 6150, Western Australia, Australia
| | - Yit-Heng Chooi
- School of Molecular Sciences, The University of Western Australia, Perth, 6009, Western Australia, Australia
| | - Richard P Oliver
- Centre for Crop and Disease Management, Curtin University, Perth, 6150, Western Australia, Australia
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15
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Moolhuijzen P, See PT, Moffat CS. A new PacBio genome sequence of an Australian Pyrenophora tritici-repentis race 1 isolate. BMC Res Notes 2019; 12:642. [PMID: 31585535 PMCID: PMC6778365 DOI: 10.1186/s13104-019-4681-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [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: 04/10/2019] [Accepted: 09/28/2019] [Indexed: 01/08/2023] Open
Abstract
OBJECTIVES The necrotrophic fungal pathogen Pyrenophora tritici-repentis (Ptr) is the causal agent of tan spot a major disease of wheat. We have generated a new genome resource for an Australian Ptr race 1 isolate V1 to support comparative 'omics analyses. In particular, the V1 PacBio Biosciences long-read sequence assembly was generated to confirm the stability of large-scale genome rearrangements of the Australian race 1 isolate M4 when compared to the North American race 1 isolate Pt-1C-BFP. RESULTS Over 1.3 million reads were sequenced by PacBio Sequel small-molecule real-time sequencing (SRMT) cell to yield 11.4 Gb for the genome assembly of V1 (285X coverage), with median and maximum read lengths of 8959 bp and 72,292 bp respectively. The V1 genome was assembled into 33 contiguous sequences with a of total length 40.4 Mb and GC content of 50.44%. A total of 14,050 protein coding genes were predicted and annotated for V1. Of these 11,519 genes were orthologous to both Pt-1C-BFP and M4. Whole genome alignment of the Australian long-read assemblies (V1 to M4) confirmed previously identified large-scale genome rearrangements between M4 and Pt-1C-BFP and presented small scale variations, which included a sequence break within a race-specific region for ToxA, a well-known necrotrophic effector gene.
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Affiliation(s)
- Paula Moolhuijzen
- Centre for Crop Disease and Management, School of Molecular Life Sciences, Curtin University, Perth, Australia.
| | - Pao Theen See
- Centre for Crop Disease and Management, School of Molecular Life Sciences, Curtin University, Perth, Australia
| | - Caroline S Moffat
- Centre for Crop Disease and Management, School of Molecular Life Sciences, Curtin University, Perth, Australia
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16
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See PT, Iagallo EM, Oliver RP, Moffat CS. Heterologous Expression of the Pyrenophora tritici-repentis Effector Proteins ToxA and ToxB, and the Prevalence of Effector Sensitivity in Australian Cereal Crops. Front Microbiol 2019; 10:182. [PMID: 30809209 PMCID: PMC6379657 DOI: 10.3389/fmicb.2019.00182] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [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: 10/18/2018] [Accepted: 01/23/2019] [Indexed: 12/05/2022] Open
Abstract
Here, we evaluate the expression of the proteinaceous effectors ToxA and ToxB, produced by the necrotrophic fungal pathogen Pyrenophora tritici-repentis, which confer tan spot disease susceptibility on wheat. These necrotrophic effectors were expressed in two heterologous systems: Escherichia coli and Pichia pastoris. The E. coli SHuffle system was demonstrated to be superior to P. pastoris in generating high-levels of recombinant proteins that were soluble and stable. In addition, protein extracts from P. pastoris induced non-specific chlorosis on wheat, postulated to be caused by co-purified glucanases secreted by the host. Up to 79.6 μg/ml of ToxB was obtained using the SHuffle system in the absence of the native signal peptide, whilst the ToxA yield was considerably lower at 3.2 μg/ml. Results indicated that a histidine tag at the ToxA C-terminus interfered with effector functionality. Heterologously expressed ToxA and ToxB were tested on a panel of Australian cereals, including 122 varieties of bread wheat, 16 durum, 20 triticale and 5 barley varieties, as well as common plant model species including tobacco and Arabidopsis thaliana. A varying degree of effector sensitivities was observed, with a higher ToxB sensitivity and prevalence in the durum and triticale varieties. ToxB-induced chlorosis was also detected on barley. The heterologous expression of effectors that are easily scalable, will facilitate effector-assisted selection of varieties in wheat breeding programs as well as the investigation of P. tritici-repentis effectors in host and non-host interactions.
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Affiliation(s)
| | | | | | - Caroline S. Moffat
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
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17
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Moolhuijzen P, See PT, Moffat CS. Exploration of wheat and pathogen transcriptomes during tan spot infection. BMC Res Notes 2018; 11:907. [PMID: 30567596 PMCID: PMC6299956 DOI: 10.1186/s13104-018-3993-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 12/06/2018] [Indexed: 11/25/2022] Open
Abstract
Objectives The fungus Pyrenophora tritici-repentis is the causal agent of tan spot, a major disease of wheat (Triticum aestivum). Here, we used RNA sequencing to generate transcriptional datasets for both the host and pathogen during infection and during in vitro pathogen growth stages. Data description To capture gene expression during wheat infection with the P. tritici-repentis isolate M4, RNA datasets were generated for wheat inoculated with P. tritici-repentis (infection) and a mock (control) at 3 and 4 days post-infection, when scorable leaf disease symptoms manifest. The P. tritici-repentis isolate M4 was also RNA sequenced to capture gene expression in vitro at two different growth stages: 7-day old vegetative mycelia and 9-day old sporulating mycelia, to coincide with a latent growth stage and early sporulation respectively. In total, 6 RNA datasets are available to aid in the validation of predicted genes of P. tritici-repentis and wheat. The datasets generated offer an insight into the transcriptomic profile of the host–pathogen interaction and can be used to investigate the expression of a subset of transcripts or targeted genes prior to designing cost-intensive RNA sequencing experiments, that would be best further explored with replication and a time series analysis.
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Affiliation(s)
- Paula Moolhuijzen
- Centre for Crop Disease and Management, Curtin University, Perth, WA, Australia.
| | - Pao Theen See
- Centre for Crop Disease and Management, Curtin University, Perth, WA, Australia
| | - Caroline S Moffat
- Centre for Crop Disease and Management, Curtin University, Perth, WA, Australia
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18
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Moolhuijzen PM, See PT, Oliver RP, Moffat CS. Genomic distribution of a novel Pyrenophora tritici-repentis ToxA insertion element. PLoS One 2018; 13:e0206586. [PMID: 30379913 PMCID: PMC6209302 DOI: 10.1371/journal.pone.0206586] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 10/16/2018] [Indexed: 12/12/2022] Open
Abstract
The ToxA effector is a major virulence gene of Pyrenophora tritici-repentis (Ptr), a necrotrophic fungus and the causal agent of tan spot disease of wheat. ToxA and co-located genes are believed to be the result of a recent horizontally transferred highly conserved 14kb region a major pathogenic event for Ptr. Since this event, monitoring isolates for pathogenic changes has become important to help understand the underlying mechanisms in play. Here we examined ToxA in 100 Ptr isolates from Australia, Europe, North and South America and the Middle East, and uncovered in isolates from Denmark, Germany and New Zealand a new variation, a novel 166 bp insertion element (PtrHp1) which can form a perfectly matched 59 bp inverted repeat hairpin structure located downstream of the ToxA coding sequence in the 3’ UTR exon. A wider examination revealed PtrHp1 elements to be distributed throughout the genome. Analysis of genomes from Australia and North America had 50–112 perfect copies that often overlap other genes. The hairpin element appears to be unique to Ptr and the lack of ancient origins in other species suggests that PtrHp1 emerged after Ptr speciation. Furthermore, the ToxA UTR insertion site is identical for different isolates, which suggests a single insertion event occurred after the ToxA horizontal transfer. In vitro and in planta-detached leaf assays found that the PtrHp1 element insertion had no effect on ToxA expression. However, variation in the expression of ToxA was detected between the Ptr isolates from different demographic locations, which appears to be unrelated to the presence of the element. We envision that this discovery may contribute towards future understanding of the possible role of hairpin elements in Ptr.
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Affiliation(s)
- Paula M Moolhuijzen
- Centre for Crop Disease and Management, Department of Environment and Agriculture, Curtin University, Bentley, Western Australia, Australia
| | - Pao Theen See
- Centre for Crop Disease and Management, Department of Environment and Agriculture, Curtin University, Bentley, Western Australia, Australia
| | - Richard P Oliver
- Centre for Crop Disease and Management, Department of Environment and Agriculture, Curtin University, Bentley, Western Australia, Australia
| | - Caroline S Moffat
- Centre for Crop Disease and Management, Department of Environment and Agriculture, Curtin University, Bentley, Western Australia, Australia
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Moolhuijzen P, See PT, Hane JK, Shi G, Liu Z, Oliver RP, Moffat CS. Correction to: Comparative genomics of the wheat fungal pathogen Pyrenophora tritici-repentis reveals chromosomal variations and genome plasticity. BMC Genomics 2018; 19:673. [PMID: 30213259 PMCID: PMC6136185 DOI: 10.1186/s12864-018-5059-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 09/07/2018] [Indexed: 11/10/2022] Open
Affiliation(s)
- Paula Moolhuijzen
- Centre for Crop Disease and Management, Department of Environment and Agriculture, Curtin University, Bentley, Western Australia, Australia.
| | - Pao Theen See
- Centre for Crop Disease and Management, Department of Environment and Agriculture, Curtin University, Bentley, Western Australia, Australia
| | - James K Hane
- Centre for Crop Disease and Management, Department of Environment and Agriculture, Curtin University, Bentley, Western Australia, Australia
| | - Gongjun Shi
- Department of Plant Pathology, North Dakota State University, Fargo, ND, USA
| | - Zhaohui Liu
- Department of Plant Pathology, North Dakota State University, Fargo, ND, USA
| | - Richard P Oliver
- Centre for Crop Disease and Management, Department of Environment and Agriculture, Curtin University, Bentley, Western Australia, Australia
| | - Caroline S Moffat
- Centre for Crop Disease and Management, Department of Environment and Agriculture, Curtin University, Bentley, Western Australia, Australia
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20
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Moolhuijzen P, See PT, Hane JK, Shi G, Liu Z, Oliver RP, Moffat CS. Comparative genomics of the wheat fungal pathogen Pyrenophora tritici-repentis reveals chromosomal variations and genome plasticity. BMC Genomics 2018; 19:279. [PMID: 29685100 PMCID: PMC5913888 DOI: 10.1186/s12864-018-4680-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [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: 10/23/2017] [Accepted: 04/16/2018] [Indexed: 02/08/2023] Open
Abstract
Background Pyrenophora tritici-repentis (Ptr) is a necrotrophic fungal pathogen that causes the major wheat disease, tan spot. We set out to provide essential genomics-based resources in order to better understand the pathogenicity mechanisms of this important pathogen. Results Here, we present eight new Ptr isolate genomes, assembled and annotated; representing races 1, 2 and 5, and a new race. We report a high quality Ptr reference genome, sequenced by PacBio technology with Illumina paired-end data support and optical mapping. An estimated 98% of the genome coverage was mapped to 10 chromosomal groups, using a two-enzyme hybrid approach. The final reference genome was 40.9 Mb and contained a total of 13,797 annotated genes, supported by transcriptomic and proteogenomics data sets. Conclusions Whole genome comparative analysis revealed major chromosomal segmental rearrangements and fusions, highlighting intraspecific genome plasticity in this species. Furthermore, the Ptr race classification was not supported at the whole genome level, as phylogenetic analysis did not cluster the ToxA producing isolates. This expansion of available Ptr genomics resources will directly facilitate research aimed at controlling tan spot disease. Electronic supplementary material The online version of this article (10.1186/s12864-018-4680-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Paula Moolhuijzen
- Centre for Crop Disease and Management, Department of Environment and Agriculture, Curtin University, Bentley, Western Australia, Australia.
| | - Pao Theen See
- Centre for Crop Disease and Management, Department of Environment and Agriculture, Curtin University, Bentley, Western Australia, Australia
| | - James K Hane
- Centre for Crop Disease and Management, Department of Environment and Agriculture, Curtin University, Bentley, Western Australia, Australia
| | - Gongjun Shi
- Department of Plant Pathology, North Dakota State University, Fargo, ND, USA
| | - Zhaohui Liu
- Department of Plant Pathology, North Dakota State University, Fargo, ND, USA
| | - Richard P Oliver
- Centre for Crop Disease and Management, Department of Environment and Agriculture, Curtin University, Bentley, Western Australia, Australia
| | - Caroline S Moffat
- Centre for Crop Disease and Management, Department of Environment and Agriculture, Curtin University, Bentley, Western Australia, Australia
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Rybak K, See PT, Phan HTT, Syme RA, Moffat CS, Oliver RP, Tan K. A functionally conserved Zn 2 Cys 6 binuclear cluster transcription factor class regulates necrotrophic effector gene expression and host-specific virulence of two major Pleosporales fungal pathogens of wheat. Mol Plant Pathol 2017; 18:420-434. [PMID: 27860150 PMCID: PMC6638278 DOI: 10.1111/mpp.12511] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The fungus Parastagonospora nodorum is the causal agent of Septoria nodorum blotch of wheat (Triticum aestivum). The interaction is mediated by multiple fungal necrotrophic effector-dominant host sensitivity gene interactions. The three best-characterized effector-sensitivity gene systems are SnToxA-Tsn1, SnTox1-Snn1 and SnTox3-Snn3. These effector genes are highly expressed during early infection, but expression decreases as the infection progresses to tissue necrosis and sporulation. However, the mechanism of regulation is unknown. We have identified and functionally characterized a gene, referred to as PnPf2, which encodes a putative zinc finger transcription factor. PnPf2 deletion resulted in the down-regulation of SnToxA and SnTox3 expression. Virulence on Tsn1 and Snn3 wheat cultivars was strongly reduced. The SnTox1-Snn1 interaction remained unaffected. Furthermore, we have also identified and deleted an orthologous PtrPf2 from the tan spot fungus Pyrenophora tritici-repentis which possesses a near-identical ToxA that was acquired from P. nodorum via horizontal gene transfer. PtrPf2 deletion also resulted in the down-regulation of PtrToxA expression and a near-complete loss of virulence on Tsn1 wheat. We have demonstrated, for the first time, evidence for a functionally conserved signalling component that plays a role in the regulation of a common/horizontally transferred effector found in two major fungal pathogens of wheat.
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Affiliation(s)
- Kasia Rybak
- Department of Environment & Agriculture, Centre for Crop and Disease ManagementCurtin University, Bentley, 6102PerthAustralia
| | - Pao Theen See
- Department of Environment & Agriculture, Centre for Crop and Disease ManagementCurtin University, Bentley, 6102PerthAustralia
| | - Huyen T. T. Phan
- Department of Environment & Agriculture, Centre for Crop and Disease ManagementCurtin University, Bentley, 6102PerthAustralia
| | - Robert A. Syme
- Department of Environment & Agriculture, Centre for Crop and Disease ManagementCurtin University, Bentley, 6102PerthAustralia
| | - Caroline S. Moffat
- Department of Environment & Agriculture, Centre for Crop and Disease ManagementCurtin University, Bentley, 6102PerthAustralia
| | - Richard P. Oliver
- Department of Environment & Agriculture, Centre for Crop and Disease ManagementCurtin University, Bentley, 6102PerthAustralia
| | - Kar‐Chun Tan
- Department of Environment & Agriculture, Centre for Crop and Disease ManagementCurtin University, Bentley, 6102PerthAustralia
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See PT, Moffat CS, Morina J, Oliver RP. Evaluation of a Multilocus Indel DNA Region for the Detection of the Wheat Tan Spot Pathogen Pyrenophora tritici-repentis. Plant Dis 2016; 100:2215-2225. [PMID: 30682909 DOI: 10.1094/pdis-03-16-0262-re] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Tan spot or yellow (leaf) spot disease of wheat (Triticum spp.) is caused by Pyrenophora tritici-repentis, a necrotrophic fungal pathogen that is widespread throughout the main wheat-growing regions in the world. This disease is currently the single most economically important crop disease in Australia. In this study, a real-time quantitative polymerase chain reaction (qPCR) assay was developed as a diagnostic tool to detect the pathogen on wheat foliar tissue. A multicopy locus (PtrMulti) present in the P. tritici-repentis genome was assessed for its suitability as a qPCR probe. The primer pair PtrMulti_F/R that targets the region was evaluated with respect to species specificity and sensitivity. A PtrMulti SYBR qPCR assay was developed and proved to be suitable for the identification and relative quantification of P. tritici-repentis with a detection limit of DNA levels at <0.1 pg. Variation of the PtrMulti copy number between the geographical representatives of P. tritici-repentis strains examined was minimal, with the range of 63 to 85 copies per genome. For naturally infected wheat field samples, the incidence of P. tritici-repentis DNA on leaves quantified by qPCR varied up to 1,000-fold difference in the concentration, with a higher incidence of DNA occurring on the lower canopy for most of the growth stages examined. At the early growth stages, qPCR assay was able to detect P. tritici-repentis DNA on the younger leaves in the absence of visible tan spot lesions. These results demonstrate the potential of PtrMulti probe to be used for early detection and rapid screening of tan spot disease on wheat plants.
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Affiliation(s)
- Pao Theen See
- Centre for Crop and Disease Management, Department of Environment and Agriculture, School of Science, Curtin University, Bentley, WA 6102, Australia
| | - Caroline S Moffat
- Centre for Crop and Disease Management, Department of Environment and Agriculture, School of Science, Curtin University, Bentley, WA 6102, Australia
| | - Joseph Morina
- Centre for Crop and Disease Management, Department of Environment and Agriculture, School of Science, Curtin University, Bentley, WA 6102, Australia
| | - Richard P Oliver
- Centre for Crop and Disease Management, Department of Environment and Agriculture, School of Science, Curtin University, Bentley, WA 6102, Australia
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Abstract
The necrotrophic fungal pathogen Pyrenophora tritici-repentis causes tan spot, a major disease of wheat, throughout the world. The proteinaceous effector ToxA is responsible for foliar necrosis on ToxA-sensitive wheat genotypes. The single copy ToxA gene was deleted from a wild-type race 1 P. tritici-repentis isolate via homologous recombination of a knockout construct. Expression of the ToxA transcript was found to be absent in transformants (toxa), as was ToxA protein production in fungal culture filtrates. Plant bioassays were conducted to test transformant pathogenicity. The toxa strains were unable to induce necrosis on ToxA-sensitive wheat genotypes. To our knowledge, this is the first demonstration of a targeted gene knockout in P. tritici-repentis. The ability to undertake gene deletions will facilitate the characterization of other pathogenicity effectors of this economically significant necrotroph.
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Affiliation(s)
- Caroline S Moffat
- Centre for Crop and Disease Management, Department of Environment and Agriculture, School of Science, Curtin University, Perth, WA, 6102, Australia
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