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Kaur N, Mehl HL, Langston D, Haak DC. Evaluation of Stagonospora Nodorum Blotch Severity and Parastagonospora nodorum Population Structure and Genetic Diversity Across Multiple Locations and Wheat Varieties in Virginia. PHYTOPATHOLOGY 2024; 114:258-268. [PMID: 37316953 DOI: 10.1094/phyto-10-22-0392-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Parastagonospora nodorum is a necrotrophic pathogen that causes Stagonospora nodorum blotch (SNB) in wheat. Wheat varieties grown in Virginia vary in susceptibility to SNB, and the severity of SNB varies across locations and years. However, the impacts of wheat genetic backgrounds and environments on SNB severity and the structure of P. nodorum populations in the region have not been well studied. Thus, a population genetic study was conducted utilizing P. nodorum isolates collected from different wheat varieties and locations in Virginia. A total of 320 isolates were collected at seven locations over 2 years from five wheat varieties. Isolates were genotyped using multilocus simple sequence repeat markers, and necrotrophic effector (NE) and mating type genes were amplified using gene-specific primers. Wheat varieties varied in susceptibility to SNB, but site-specific environmental conditions were the primary drivers of disease severity. Fungal populations were genetically diverse, but no genetic subdivision was observed among locations or varieties. The ratio of the two mating type idiomorphs was not significantly different from 1:1, consistent with the P. nodorum population undergoing sexual reproduction. Three major NE genes were detected within the P. nodorum population, but not with equal frequency. However, NE gene profiles were similar for groups of isolates originating from different varieties, suggesting that wheat genetic backgrounds do not differentially select for NEs. There was no evidence of population structure among P. nodorum populations in Virginia and, thus, no support for wheat genetic backgrounds shaping these populations. Finally, although varieties only exhibited moderate resistance to SNB, current levels of resistance are likely to be durable over time and remain a useful tool for integrated management of SNB in the region. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Navjot Kaur
- School of Plant and Environmental Sciences, VA Tech, Blacksburg, VA 24061
- Virginia Tech Tidewater Agricultural Research and Extension Center, Suffolk, VA 23437
| | - Hillary L Mehl
- School of Plant and Environmental Sciences, VA Tech, Blacksburg, VA 24061
- Virginia Tech Tidewater Agricultural Research and Extension Center, Suffolk, VA 23437
| | - David Langston
- School of Plant and Environmental Sciences, VA Tech, Blacksburg, VA 24061
- Virginia Tech Tidewater Agricultural Research and Extension Center, Suffolk, VA 23437
| | - David C Haak
- School of Plant and Environmental Sciences, VA Tech, Blacksburg, VA 24061
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Gupta PK, Vasistha NK, Singh S, Joshi AK. Genetics and breeding for resistance against four leaf spot diseases in wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1023824. [PMID: 37063191 PMCID: PMC10096043 DOI: 10.3389/fpls.2023.1023824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 02/28/2023] [Indexed: 06/19/2023]
Abstract
In wheat, major yield losses are caused by a variety of diseases including rusts, spike diseases, leaf spot and root diseases. The genetics of resistance against all these diseases have been studied in great detail and utilized for breeding resistant cultivars. The resistance against leaf spot diseases caused by each individual necrotroph/hemi-biotroph involves a complex system involving resistance (R) genes, sensitivity (S) genes, small secreted protein (SSP) genes and quantitative resistance loci (QRLs). This review deals with resistance for the following four-leaf spot diseases: (i) Septoria nodorum blotch (SNB) caused by Parastagonospora nodorum; (ii) Tan spot (TS) caused by Pyrenophora tritici-repentis; (iii) Spot blotch (SB) caused by Bipolaris sorokiniana and (iv) Septoria tritici blotch (STB) caused by Zymoseptoria tritici.
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Affiliation(s)
- Pushpendra Kumar Gupta
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, India
- Murdoch’s Centre for Crop and Food Innovation, Murdoch University, Murdoch, WA, Australia
- Borlaug Institute for South Asia (BISA), National Agricultural Science Complex (NASC), Dev Prakash Shastri (DPS) Marg, New Delhi, India
| | - Neeraj Kumar Vasistha
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, India
- Department of Genetics-Plant Breeding and Biotechnology, Dr Khem Singh Gill, Akal College of Agriculture, Eternal University, Baru Sahib, Sirmour, India
| | - Sahadev Singh
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, India
| | - Arun Kumar Joshi
- Borlaug Institute for South Asia (BISA), National Agricultural Science Complex (NASC), Dev Prakash Shastri (DPS) Marg, New Delhi, India
- The International Maize and Wheat Improvement Center (CIMMYT), National Agricultural Science Complex (NASC), Dev Prakash Shastri (DPS) Marg, New Delhi, India
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White NH, Neves DL, Nuckles EM, Vaillancourt LJ, Zhang J, Zhang G, Bradley CA. Identification of Quinone Outside Inhibitor Fungicide-Resistant Isolates of Parastagonospora nodorum from Illinois and Kentucky. PLANT DISEASE 2023; 107:38-45. [PMID: 35722914 DOI: 10.1094/pdis-01-22-0180-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Stagonospora leaf and glume blotch, caused by Parastagonospora nodorum, is a major disease of winter wheat (Triticum aestivum) in the United States capable of significantly reducing grain yield and quality. Pathogens such as P. nodorum that overwinter in crop residue are often an increased concern in cropping systems that utilize no-till farming. In addition, the lack of wheat cultivars with complete resistance to P. nodorum has led to the reliance on foliar fungicides for disease management. Quinone outside inhibitor (QoI) fungicides (Fungicide Resistance Action Committee group 11) are one of the major classes used to manage foliar diseases in wheat. Use of the QoI class of fungicides tends to select isolates of fungal pathogens with resistance due to mutations in the fungal cytochrome b gene. Isolates of P. nodorum were collected from Illinois in 2014 and Kentucky in 2018, 2019, and 2020. Amplification and sequencing of a segment of the cytochrome b gene from these isolates revealed a mutation at codon 143 that confers a change from glycine to alanine in the amino acid sequence (known as the G143A mutation). In vitro plate assays and greenhouse trials were used to confirm and characterize the QoI resistance caused by the G143A mutation. The frequency of the tested isolates with the G143A mutation was 46% (57 of 123 isolates) and 5% (3 of 60 isolates) for Kentucky and Illinois, respectively. This research is the first to identify the G143A mutation in P. nodorum isolates with resistance to QoI fungicides in Illinois and Kentucky.
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Affiliation(s)
- Nathaniel H White
- Department of Plant Pathology, University of Kentucky, Princeton, KY 42445
| | - Danilo L Neves
- Department of Plant Pathology, University of Kentucky, Princeton, KY 42445
| | - Etta M Nuckles
- Department of Plant Pathology, University of Kentucky, Lexington, KY 40546
| | | | - Jiawen Zhang
- Department of Crop Sciences, University of Illinois, Urbana, IL 61801
| | - Guirong Zhang
- Department of Crop Sciences, University of Illinois, Urbana, IL 61801
| | - Carl A Bradley
- Department of Plant Pathology, University of Kentucky, Princeton, KY 42445
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Peters Haugrud AR, Zhang Z, Friesen TL, Faris JD. Genetics of resistance to septoria nodorum blotch in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3685-3707. [PMID: 35050394 DOI: 10.1007/s00122-022-04036-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 12/23/2021] [Indexed: 05/12/2023]
Abstract
Septoria nodorum blotch (SNB) is a foliar disease of wheat caused by the necrotrophic fungal pathogen Parastagonospora nodorum. Research over the last two decades has shown that the wheat-P. nodorum pathosystem mostly follows an inverse gene-for-gene model. The fungus produces necrotrophic effectors (NEs) that interact with specific host gene products encoded by dominant sensitivity (S) genes. When a compatible interaction occurs, a 'defense response' in the host leads to programmed cell death thereby provided dead/dying cells from which the pathogen, being a necrotroph, can acquire nutrients allowing it to grow and sporulate. To date, nine S gene-NE interactions have been characterized in this pathosystem. Five NE-encoding genes, SnTox1, SnTox3, SnToxA, SnTox5, and SnTox267, have been cloned along with three host S genes, Tsn1, Snn1, and Snn3-D1. Studies have shown that P. nodorum hijacks multiple and diverse host targets to cause disease. SNB resistance is often quantitative in nature because multiple compatible interactions usually occur concomitantly. NE gene expression plays a key role in disease severity, and the effect of each compatible interaction can vary depending on the other existing compatible interactions. Numerous SNB-resistance QTL have been identified in addition to the known S genes, and more research is needed to understand the nature of these resistance loci. Marker-assisted elimination of S genes through conventional breeding practices and disruption of S genes using gene editing techniques are both effective strategies for the development of SNB-resistant wheat cultivars, which will become necessary as the global demand for sustenance grows.
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Affiliation(s)
| | - Zengcui Zhang
- USDA-ARS Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND, 58102, USA
| | - Timothy L Friesen
- USDA-ARS Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND, 58102, USA
| | - Justin D Faris
- USDA-ARS Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND, 58102, USA.
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Kariyawasam GK, Richards JK, Wyatt NA, Running KLD, Xu SS, Liu Z, Borowicz P, Faris JD, Friesen TL. The Parastagonospora nodorum necrotrophic effector SnTox5 targets the wheat gene Snn5 and facilitates entry into the leaf mesophyll. THE NEW PHYTOLOGIST 2022; 233:409-426. [PMID: 34231227 PMCID: PMC9291777 DOI: 10.1111/nph.17602] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 06/27/2021] [Indexed: 05/11/2023]
Abstract
Parastagonospora nodorum is an economically important necrotrophic fungal pathogen of wheat. Parastagonospora nodorum secretes necrotrophic effectors that target wheat susceptibility genes to induce programmed cell death (PCD). In this study, we cloned and functionally validated SnTox5 and characterized its role in pathogenesis. We used whole genome sequencing, genome-wide association study (GWAS) mapping, CRISPR-Cas9-based gene disruption, gain-of-function transformation, quantitative trait locus (QTL) analysis, haplotype and isoform analysis, protein modeling, quantitative PCR, and laser confocal microscopy to validate SnTox5 and functionally characterize SnTox5. SnTox5 is a mature 16.26 kDa protein with high structural similarity to SnTox3. Wild-type and mutant P. nodorum strains and wheat genotypes of SnTox5 and Snn5, respectively, were used to show that SnTox5 not only targets Snn5 to induce PCD but also facilitates the colonization of the mesophyll layer even in the absence of Snn5. Here we show that SnTox5 facilitates the efficient colonization of the mesophyll tissue and elicits PCD specific to host lines carrying Snn5. The homology to SnTox3 and the ability of SnTox5 to facilitate the colonizing of the mesophyll also suggest a role in the suppression of host defense before PCD induction.
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Affiliation(s)
| | - Jonathan K. Richards
- Department of Plant Pathology and Crop PhysiologyLouisiana State University – Agricultural CenterBaton RougeLA70803USA
| | - Nathan A. Wyatt
- Cereal Crops Research UnitUnited States Department of Agriculture‐Agricultural Research ServiceEdward T. Schafer Agricultural Research CenterFargoND58102USA
| | | | - Steven S. Xu
- Cereal Crops Research UnitUnited States Department of Agriculture‐Agricultural Research ServiceEdward T. Schafer Agricultural Research CenterFargoND58102USA
| | - Zhaohui Liu
- Department of Plant PathologyNorth Dakota State UniversityFargoND58102USA
| | - Pawel Borowicz
- Department of Animal SciencesNorth Dakota State UniversityFargoND58102USA
| | - Justin D. Faris
- Cereal Crops Research UnitUnited States Department of Agriculture‐Agricultural Research ServiceEdward T. Schafer Agricultural Research CenterFargoND58102USA
- Department of Plant ScienceNorth Dakota State UniversityFargoND58102USA
| | - Timothy L. Friesen
- Department of Plant PathologyNorth Dakota State UniversityFargoND58102USA
- Cereal Crops Research UnitUnited States Department of Agriculture‐Agricultural Research ServiceEdward T. Schafer Agricultural Research CenterFargoND58102USA
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Katoch S, Sharma V, Sharma D, Salwan R, Rana SK. Biology and molecular interactions of Parastagonospora nodorum blotch of wheat. PLANTA 2021; 255:21. [PMID: 34914013 DOI: 10.1007/s00425-021-03796-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 11/14/2021] [Indexed: 06/14/2023]
Abstract
Parastagonospora nodorum is one of the important necrotrophic pathogens of wheat which causes severe economical loss to crop yield. So far, a number of effectors of Parastagonospora nodorum origin and their target interacting genes on the host plant have been characterized. Since targeting effector-sensitive gene carefully can be helpful in breeding for resistance. Therefore, constant efforts are required to further characterize the effectors, their interacting genes, and underlying biochemical pathways. Furthermore, to develop effective counter-strategies against emerging diseases, continuous efforts are required to determine the qualitative resistance that demands to screen of diverse genotypes for host resistance. Stagonospora nodorum blotch also refers to as Stagonospora glume blotch and leaf is caused by Parastagonospora nodorum. The pathogen deploys necrotrophic effectors for the establishment and development on wheat plants. The necrotrophic effectors and their interaction with host receptors lead to the establishment of infection on leaves and extensive lesions formation which either results in host cell death or suppression/activation of host defence mechanisms. The wheat Stagonospora nodorum interaction involves a set of nine host gene-necrotrophic effector interactions. Out of these, Snn1-SnTox1, Tsn1-SnToxA and Snn-SnTox3 are one of the most studied interaction, due to its role in the suppression of reactive oxygen species production, regulating the cytokinin content through ethylene-dependent wayduring initial infection stage. Further, although the molecular basis is not fully unveiled, these effectors regulate the redox state and influence the ethylene biosynthesis in infected wheat plants. Here, we have discussed the biology of the wheat pathogen Parastagonospora nodorum, role of its necrotrophic effectors and their interacting sensitivity genes on the redox state, how they hijack the resistance mechanisms, hormonal regulated immunity and other signalling pathways in susceptible wheat plants. The information generated from effectors and their corresponding sensitivity genes and other biological processes could be utilized effectively for disease management strategies.
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Affiliation(s)
- Shabnam Katoch
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Vivek Sharma
- University Centre for Research and Development, Chandigarh University, Gharuan, 140413, Punjab, India.
| | - Devender Sharma
- Crop Improvement Division, ICAR-Vivekananda Parvatiya Krishi Anusandhan Sansthan, Almora, Uttarakhand, India
| | - Richa Salwan
- College of Horticulture and Forestry, Neri, Dr YS Parmar University of Horticulture and Forestry, Solan, Hamirpur, 177 001, India
| | - S K Rana
- Department of Plant Pathology, CSK HPKV Palampur, Palampur, 176062, Himachal Pradesh, India
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Outram MA, Sung YC, Yu D, Dagvadorj B, Rima SA, Jones DA, Ericsson DJ, Sperschneider J, Solomon PS, Kobe B, Williams SJ. The crystal structure of SnTox3 from the necrotrophic fungus Parastagonospora nodorum reveals a unique effector fold and provides insight into Snn3 recognition and pro-domain protease processing of fungal effectors. THE NEW PHYTOLOGIST 2021; 231:2282-2296. [PMID: 34053091 DOI: 10.1111/nph.17516] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 05/20/2021] [Indexed: 05/22/2023]
Abstract
Plant pathogens cause disease through secreted effector proteins, which act to promote infection. Typically, the sequences of effectors provide little functional information and further targeted experimentation is required. Here, we utilized a structure/function approach to study SnTox3, an effector from the necrotrophic fungal pathogen Parastagonospora nodorum, which causes cell death in wheat-lines carrying the sensitivity gene Snn3. We developed a workflow for the production of SnTox3 in a heterologous host that enabled crystal structure determination and functional studies. We show this approach can be successfully applied to study effectors from other pathogenic fungi. The β-barrel fold of SnTox3 is a novel fold among fungal effectors. Structure-guided mutagenesis enabled the identification of residues required for Snn3 recognition. SnTox3 is a pre-pro-protein, and the pro-domain of SnTox3 can be cleaved in vitro by the protease Kex2. Complementing this, an in silico study uncovered the prevalence of a conserved motif (LxxR) in an expanded set of putative pro-domain-containing fungal effectors, some of which can be cleaved by Kex2 in vitro. Our in vitro and in silico study suggests that Kex2-processed pro-domain (designated here as K2PP) effectors are common in fungi and this may have broad implications for the approaches used to study their functions.
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Affiliation(s)
- Megan A Outram
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Yi-Chang Sung
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Daniel Yu
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Bayantes Dagvadorj
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Sharmin A Rima
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - David A Jones
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Daniel J Ericsson
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
- Australian Synchrotron, Macromolecular Crystallography, Clayton, VIC, 3168, Australia
| | - Jana Sperschneider
- Biological Data Science Institute, The Australian National University, Canberra, ACT, 2601, Australia
| | - Peter S Solomon
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Simon J Williams
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
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Outram MA, Sung YC, Yu D, Dagvadorj B, Rima SA, Jones DA, Ericsson DJ, Sperschneider J, Solomon PS, Kobe B, Williams SJ. The crystal structure of SnTox3 from the necrotrophic fungus Parastagonospora nodorum reveals a unique effector fold and provides insight into Snn3 recognition and pro-domain protease processing of fungal effectors. THE NEW PHYTOLOGIST 2021; 231:2282-2296. [PMID: 34053091 DOI: 10.1101/2020.05.27.120113] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 05/20/2021] [Indexed: 05/25/2023]
Abstract
Plant pathogens cause disease through secreted effector proteins, which act to promote infection. Typically, the sequences of effectors provide little functional information and further targeted experimentation is required. Here, we utilized a structure/function approach to study SnTox3, an effector from the necrotrophic fungal pathogen Parastagonospora nodorum, which causes cell death in wheat-lines carrying the sensitivity gene Snn3. We developed a workflow for the production of SnTox3 in a heterologous host that enabled crystal structure determination and functional studies. We show this approach can be successfully applied to study effectors from other pathogenic fungi. The β-barrel fold of SnTox3 is a novel fold among fungal effectors. Structure-guided mutagenesis enabled the identification of residues required for Snn3 recognition. SnTox3 is a pre-pro-protein, and the pro-domain of SnTox3 can be cleaved in vitro by the protease Kex2. Complementing this, an in silico study uncovered the prevalence of a conserved motif (LxxR) in an expanded set of putative pro-domain-containing fungal effectors, some of which can be cleaved by Kex2 in vitro. Our in vitro and in silico study suggests that Kex2-processed pro-domain (designated here as K2PP) effectors are common in fungi and this may have broad implications for the approaches used to study their functions.
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Affiliation(s)
- Megan A Outram
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Yi-Chang Sung
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Daniel Yu
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Bayantes Dagvadorj
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Sharmin A Rima
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - David A Jones
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Daniel J Ericsson
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
- Australian Synchrotron, Macromolecular Crystallography, Clayton, VIC, 3168, Australia
| | - Jana Sperschneider
- Biological Data Science Institute, The Australian National University, Canberra, ACT, 2601, Australia
| | - Peter S Solomon
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Simon J Williams
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
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Cowger C, Ward B, Brown-Guedira G, Brown JKM. Role of Effector-Sensitivity Gene Interactions and Durability of Quantitative Resistance to Septoria Nodorum Blotch in Eastern U.S. Wheat. FRONTIERS IN PLANT SCIENCE 2020; 11:155. [PMID: 32210986 PMCID: PMC7067980 DOI: 10.3389/fpls.2020.00155] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 01/31/2020] [Indexed: 05/02/2023]
Abstract
Important advances have been made in understanding the relationship of necrotrophic effectors (NE) and host sensitivity (Snn) genes in the Parastagonospora nodorum-wheat pathosystem. Yet much remains to be learned about the role of these interactions in determining wheat resistance levels in the field, and there is mixed evidence on whether breeding programs have selected against Snn genes due to their role in conferring susceptibility. SNB occurs ubiquitously in the U.S. Atlantic seaboard, and the environment is especially well suited to field studies of resistance to natural P. nodorum populations, as there are no other important wheat leaf blights. Insights into the nature of SNB resistance have been gleaned from multi-year data on phenotypes and markers in cultivars representative of the region's germplasm. In this perspective article, we review the evidence that in this eastern region of the U.S., wheat cultivars have durable quantitative SNB resistance and Snn-NE interactions are of limited importance. This conclusion is discussed in light of the relevant available information from other parts of the world.
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Affiliation(s)
- Christina Cowger
- U.S. Department of Agriculture – Agricultural Research Service, North Carolina State University, Raleigh, NC, United States
- *Correspondence: Christina Cowger,
| | - Brian Ward
- U.S. Department of Agriculture – Agricultural Research Service, North Carolina State University, Raleigh, NC, United States
| | - Gina Brown-Guedira
- U.S. Department of Agriculture – Agricultural Research Service, North Carolina State University, Raleigh, NC, United States
| | - James K. M. Brown
- Department of Crop Genetics, John Innes Centre, Norwich, United Kingdom
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Richards JK, Stukenbrock EH, Carpenter J, Liu Z, Cowger C, Faris JD, Friesen TL. Local adaptation drives the diversification of effectors in the fungal wheat pathogen Parastagonospora nodorum in the United States. PLoS Genet 2019; 15:e1008223. [PMID: 31626626 PMCID: PMC6821140 DOI: 10.1371/journal.pgen.1008223] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 10/30/2019] [Accepted: 08/25/2019] [Indexed: 12/22/2022] Open
Abstract
Filamentous fungi rapidly evolve in response to environmental selection pressures in part due to their genomic plasticity. Parastagonospora nodorum, a fungal pathogen of wheat and causal agent of septoria nodorum blotch, responds to selection pressure exerted by its host, influencing the gain, loss, or functional diversification of virulence determinants, known as effector genes. Whole genome resequencing of 197 P. nodorum isolates collected from spring, durum, and winter wheat production regions of the United States enabled the examination of effector diversity and genomic regions under selection specific to geographically discrete populations. 1,026,859 SNPs/InDels were used to identify novel loci, as well as SnToxA and SnTox3 as factors in disease. Genes displaying presence/absence variation, predicted effector genes, and genes localized on an accessory chromosome had significantly higher pN/pS ratios, indicating a higher rate of sequence evolution. Population structure analyses indicated two P. nodorum populations corresponding to the Upper Midwest (Population 1) and Southern/Eastern United States (Population 2). Prevalence of SnToxA varied greatly between the two populations which correlated with presence of the host sensitivity gene Tsn1 in the most prevalent cultivars in the corresponding regions. Additionally, 12 and 5 candidate effector genes were observed to be under diversifying selection among isolates from Population 1 and 2, respectively, but under purifying selection or neutrally evolving in the opposite population. Selective sweep analysis revealed 10 and 19 regions that had recently undergone positive selection in Population 1 and 2, respectively, involving 92 genes in total. When comparing genes with and without presence/absence variation, those genes exhibiting this variation were significantly closer to transposable elements. Taken together, these results indicate that P. nodorum is rapidly adapting to distinct selection pressures unique to spring and winter wheat production regions by rapid adaptive evolution and various routes of genomic diversification, potentially facilitated through transposable element activity.
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Affiliation(s)
- Jonathan K. Richards
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, United States of America
| | - Eva H. Stukenbrock
- Department of Environmental Genomics, Christian-Albrechts University of Kiel, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Jessica Carpenter
- Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, United States of America
| | - Zhaohui Liu
- Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, United States of America
| | - Christina Cowger
- Plant Science Research Unit, USDA-ARS, Raleigh, North Carolina, United States of America
| | - Justin D. Faris
- Cereal Crops Research Unit, Edward T. Schaefer Agricultural Research Center, USDA-ARS, Fargo, North Dakota, United States of America
| | - Timothy L. Friesen
- Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, United States of America
- Cereal Crops Research Unit, Edward T. Schaefer Agricultural Research Center, USDA-ARS, Fargo, North Dakota, United States of America
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Bertazzoni S, Williams AH, Jones DA, Syme RA, Tan KC, Hane JK. Accessories Make the Outfit: Accessory Chromosomes and Other Dispensable DNA Regions in Plant-Pathogenic Fungi. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:779-788. [PMID: 29664319 DOI: 10.1094/mpmi-06-17-0135-fi] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Fungal pathogen genomes can often be divided into core and accessory regions. Accessory regions ARs) may be comprised of either ARs (within core chromosomes (CCs) or wholly dispensable (accessory) chromosomes (ACs). Fungal ACs and ARs typically accumulate mutations and structural rearrangements more rapidly over time than CCs and many harbor genes relevant to host-pathogen interactions. These regions are of particular interest in plant pathology and include host-specific virulence factors and secondary metabolite synthesis gene clusters. This review outlines known ACs and ARs in fungal genomes, methods used for their detection, their common properties that differentiate them from the core genome, and what is currently known of their various roles in pathogenicity. Reports on the evolutionary processes generating and shaping AC and AR compartments are discussed, including repeat induced point mutation and breakage fusion bridge cycles. Previously ACs have been studied extensively within key genera, including Fusarium, Zymoseptoria, and Alternaria, but are growing in frequency of observation and perceived importance across a wider range of fungal species. Recent advances in sequencing technologies permit affordable genome assembly and resequencing of populations that will facilitate further discovery and routine screening of ACs.
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Affiliation(s)
- Stefania Bertazzoni
- 1 Centre for Crop & Disease Management, Curtin University, Perth, Western Australia, Australia; and
| | - Angela H Williams
- 1 Centre for Crop & Disease Management, Curtin University, Perth, Western Australia, Australia; and
| | - Darcy A Jones
- 1 Centre for Crop & Disease Management, Curtin University, Perth, Western Australia, Australia; and
| | - Robert A Syme
- 1 Centre for Crop & Disease Management, Curtin University, Perth, Western Australia, Australia; and
| | - Kar-Chun Tan
- 1 Centre for Crop & Disease Management, Curtin University, Perth, Western Australia, Australia; and
| | - James K Hane
- 1 Centre for Crop & Disease Management, Curtin University, Perth, Western Australia, Australia; and
- 2 Curtin Institute for Computation, Curtin University, Perth, Western Australia, Australia
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12
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Sumabat LG, Kemerait RC, Brewer MT. Phylogenetic Diversity and Host Specialization of Corynespora cassiicola Responsible for Emerging Target Spot Disease of Cotton and Other Crops in the Southeastern United States. PHYTOPATHOLOGY 2018; 108:892-901. [PMID: 29436985 DOI: 10.1094/phyto-12-17-0407-r] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Corynespora cassiicola is a ubiquitous fungus causing emerging plant diseases worldwide, including target spot of cotton, soybean, and tomato, which have rapidly increased in incidence and severity throughout the southeastern United States. The objectives of this study were to understand the causes for the emerging target spot epidemics in the United States by comparing phylogenetic relationships of isolates from cotton, tomato, soybean, and other crop plants and ornamental hosts, and through the determination of the host range of isolates from emerging populations. Fifty-three isolates were sampled from plants in the southeastern United States and 1,380 nucleotides from four nuclear loci were sequenced. Additionally, sequences of the same loci from 23 isolates representing each of the distinct lineages of C. cassiicola described from previous studies were included. Isolates clustered based on host of origin, regardless of the geographic location of sampling. There was no genetic diversity detected among isolates from cotton, which were genetically distinct from isolates from other host species. Furthermore, pathogenicity and virulence assays of 40 isolates from various hosts onto cotton, soybean, tomato, and cucumber showed that isolates from cotton were more aggressive to cotton than those from other hosts. Soybean and tomato were most susceptible to isolates that originated from the same host, providing evidence of host specialization. These results suggest that emerging target spot epidemics in the United States are caused by either the introduction of host-specific isolates or the evolution of more aggressive strains on each host.
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Affiliation(s)
- Leilani G Sumabat
- First and third authors: Department of Plant Pathology, University of Georgia, Athens 30602; and second author: Department of Plant Pathology, University of Georgia, Tifton 31793
| | - Robert C Kemerait
- First and third authors: Department of Plant Pathology, University of Georgia, Athens 30602; and second author: Department of Plant Pathology, University of Georgia, Tifton 31793
| | - Marin Talbot Brewer
- First and third authors: Department of Plant Pathology, University of Georgia, Athens 30602; and second author: Department of Plant Pathology, University of Georgia, Tifton 31793
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13
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Ruud AK, Windju S, Belova T, Friesen TL, Lillemo M. Mapping of SnTox3-Snn3 as a major determinant of field susceptibility to Septoria nodorum leaf blotch in the SHA3/CBRD × Naxos population. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:1361-1374. [PMID: 28365817 DOI: 10.1007/s00122-017-2893-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 03/18/2017] [Indexed: 05/03/2023]
Abstract
The effect of the SnTox3-Snn3 interaction was documented for the first time under natural infection at the adult plant stage in the field. Co-segregating SNP markers were identified. Parastagonospora nodorum is a necrotrophic pathogen of wheat, causing Septoria nodorum blotch (SNB) affecting both the leaf and glume. P. nodorum is the major leaf blotch pathogen on spring wheat in Norway. Resistance to the disease is quantitative, but several host-specific interactions between necrotrophic effectors (NEs) and host sensitivity (Snn) genes have been identified, playing a major role at the seedling stage. However, the effect of these interactions in the field under natural infection has not been investigated. In the present study, we saturated the genetic map of the recombinant inbred (RI) population SHA3/CBRD × Naxos using the Illumina 90 K SNP chip. The population had previously been evaluated for segregation of SNB susceptibility in field trials. Here, we infiltrated the population with the purified NEs SnToxA, SnTox1 and SnTox3, and mapped the Snn3 locus on 5BS based on sensitivity segregation and SNP marker data. We also conducted inoculation and culture filtrate (CF) infiltration experiments on the population with four selected P. nodorum isolates from Norway and North America. Remapping of quantitative trait loci (QTL) for field resistance showed that the SnTox3-Snn3 interaction could explain 24% of the phenotypic variation in the field, and more than 51% of the variation in seedling inoculations. To our knowledge, this is the first time the effect of this interaction has been documented at the adult plant stage under natural infection in the field.
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Affiliation(s)
- Anja Karine Ruud
- Department of Plant Sciences, Norwegian University of Life Sciences, Post Box 5003, 1432, Ås, Norway
| | - Susanne Windju
- Department of Plant Sciences, Norwegian University of Life Sciences, Post Box 5003, 1432, Ås, Norway
- Graminor AS, Bjørke Gård, Hommelstadvegen 60, 2322, Ridabu, Norway
| | - Tatiana Belova
- Department of Plant Sciences, Norwegian University of Life Sciences, Post Box 5003, 1432, Ås, Norway
| | - Timothy L Friesen
- Northern Crop Science Laboratory, USDA-ARS, 1307 North 18th Street, Fargo, ND, 58102, USA
- Department of Plant Pathology, North Dakota State University, Walster Hall, Fargo, ND, 58102, USA
| | - Morten Lillemo
- Department of Plant Sciences, Norwegian University of Life Sciences, Post Box 5003, 1432, Ås, Norway.
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14
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Syme RA, Tan KC, Hane JK, Dodhia K, Stoll T, Hastie M, Furuki E, Ellwood SR, Williams AH, Tan YF, Testa AC, Gorman JJ, Oliver RP. Comprehensive Annotation of the Parastagonospora nodorum Reference Genome Using Next-Generation Genomics, Transcriptomics and Proteogenomics. PLoS One 2016; 11:e0147221. [PMID: 26840125 PMCID: PMC4739733 DOI: 10.1371/journal.pone.0147221] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Accepted: 12/30/2015] [Indexed: 11/29/2022] Open
Abstract
Parastagonospora nodorum, the causal agent of Septoria nodorum blotch (SNB), is an economically important pathogen of wheat (Triticum spp.), and a model for the study of necrotrophic pathology and genome evolution. The reference P. nodorum strain SN15 was the first Dothideomycete with a published genome sequence, and has been used as the basis for comparison within and between species. Here we present an updated reference genome assembly with corrections of SNP and indel errors in the underlying genome assembly from deep resequencing data as well as extensive manual annotation of gene models using transcriptomic and proteomic sources of evidence (https://github.com/robsyme/Parastagonospora_nodorum_SN15). The updated assembly and annotation includes 8,366 genes with modified protein sequence and 866 new genes. This study shows the benefits of using a wide variety of experimental methods allied to expert curation to generate a reliable set of gene models.
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Affiliation(s)
- Robert A. Syme
- Centre for Crop & Disease Management, Department of Environment and Agriculture, Curtin University, Bentley, WA, Australia
| | - Kar-Chun Tan
- Centre for Crop & Disease Management, Department of Environment and Agriculture, Curtin University, Bentley, WA, Australia
| | - James K. Hane
- Centre for Crop & Disease Management, Department of Environment and Agriculture, Curtin University, Bentley, WA, Australia
- Curtin Institute for Computation, Curtin University, Bentley, WA, Australia
| | - Kejal Dodhia
- Centre for Crop & Disease Management, Department of Environment and Agriculture, Curtin University, Bentley, WA, Australia
| | - Thomas Stoll
- Protein Discovery Centre, QIMR Berghofer Medical Research Institute, Herston, Qld, Australia
| | - Marcus Hastie
- Protein Discovery Centre, QIMR Berghofer Medical Research Institute, Herston, Qld, Australia
| | - Eiko Furuki
- Centre for Crop & Disease Management, Department of Environment and Agriculture, Curtin University, Bentley, WA, Australia
| | - Simon R. Ellwood
- Centre for Crop & Disease Management, Department of Environment and Agriculture, Curtin University, Bentley, WA, Australia
| | - Angela H. Williams
- Centre for Crop & Disease Management, Department of Environment and Agriculture, Curtin University, Bentley, WA, Australia
| | | | - Alison C. Testa
- Centre for Crop & Disease Management, Department of Environment and Agriculture, Curtin University, Bentley, WA, Australia
| | - Jeffrey J. Gorman
- Protein Discovery Centre, QIMR Berghofer Medical Research Institute, Herston, Qld, Australia
| | - Richard P. Oliver
- Centre for Crop & Disease Management, Department of Environment and Agriculture, Curtin University, Bentley, WA, Australia
- * E-mail:
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15
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Tan KC, Phan HTT, Rybak K, John E, Chooi YH, Solomon PS, Oliver RP. Functional redundancy of necrotrophic effectors - consequences for exploitation for breeding. FRONTIERS IN PLANT SCIENCE 2015; 6:501. [PMID: 26217355 PMCID: PMC4495316 DOI: 10.3389/fpls.2015.00501] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Necrotrophic diseases of wheat cause major losses in most wheat growing areas of world. Tan spot (caused by Pyrenophora tritici-repentis) and septoria nodorum blotch (SNB; Parastagonospora nodorum) have been shown to reduce yields by 10-20% across entire agri-ecological zones despite the application of fungicides and a heavy focus over the last 30 years on resistance breeding. Efforts by breeders to improve the resistance of cultivars has been compromised by the universal finding that resistance was quantitative and governed by multiple quantitative trait loci (QTL). Most QTL had a limited effect that was hard to measure precisely and varied significantly from site to site and season to season. The discovery of necrotrophic effectors has given breeding for disease resistance new methods and tools. In the case of tan spot in West Australia, a single effector, PtrToxA and its recogniser gene Tsn1, has a dominating impact in disease resistance. The delivery of ToxA to breeders has had a major impact on cultivar choice and breeding strategies. For P. nodorum, three effectors - SnToxA, SnTox1, and SnTox3 - have been well characterized. Unlike tan spot, no one effector has a dominating role. Genetic analysis of various mapping populations and pathogen isolates has shown that different effectors have varying impact and that epistatic interactions also occur. As a result of these factors the deployment of these effectors for SNB resistance breeding is more complex. We have deleted the three effectors in a strain of P. nodorum and measured effector activity and disease potential of the triple knockout mutant. The culture filtrate causes necrosis in several cultivars and the strain causes disease, albeit the overall levels are less than in the wild type. Modeling of the field disease resistance scores of cultivars from their reactions to the microbially expressed effectors SnToxA, SnTox1, and SnTox3 is significantly improved by including the response to the triple knockout mutant culture filtrate. This indicates that one or more further effectors are secreted into the culture filtrate. We conclude that the in vitro-secreted necrotrophic effectors explain a very large part of the disease response of wheat germplasm and that this method of resistance breeding promises to further reduce the impact of these globally significant diseases.
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Affiliation(s)
- Kar-Chun Tan
- Centre for Crop Disease Management, Department of Environment and Agriculture, Curtin University, BentleyWA, Australia
- *Correspondence: Richard P. Oliver and Kar-Chun Tan, Centre for Crop Disease Management, Department of Environment and Agriculture, Curtin University, Bentley, WA 6102, Australia, ;
| | - Huyen T. T. Phan
- Centre for Crop Disease Management, Department of Environment and Agriculture, Curtin University, BentleyWA, Australia
| | - Kasia Rybak
- Centre for Crop Disease Management, Department of Environment and Agriculture, Curtin University, BentleyWA, Australia
| | - Evan John
- Centre for Crop Disease Management, Department of Environment and Agriculture, Curtin University, BentleyWA, Australia
| | - Yit H. Chooi
- Plant Sciences Division, Research School of Biology, Australian National University, CanberraACT, Australia
- School of Chemistry and Biochemistry, University of Western Australia, PerthWA, Australia
| | - Peter S. Solomon
- Plant Sciences Division, Research School of Biology, Australian National University, CanberraACT, Australia
| | - Richard P. Oliver
- Centre for Crop Disease Management, Department of Environment and Agriculture, Curtin University, BentleyWA, Australia
- *Correspondence: Richard P. Oliver and Kar-Chun Tan, Centre for Crop Disease Management, Department of Environment and Agriculture, Curtin University, Bentley, WA 6102, Australia, ;
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16
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Chooi YH, Muria-Gonzalez MJ, Solomon PS. A genome-wide survey of the secondary metabolite biosynthesis genes in the wheat pathogen Parastagonospora nodorum.. Mycology 2014; 5:192-206. [PMID: 25379341 PMCID: PMC4205913 DOI: 10.1080/21501203.2014.928386] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 05/22/2014] [Indexed: 12/02/2022] Open
Abstract
The model pathogen Parastagonospora nodorum is a necrotroph and the causal agent of the wheat disease Septoria nodorum blotch (SNB). The sequenced P. nodorum genome has revealed that the fungus harbours a large number of secondary metabolite genes. Secondary metabolites are known to play important roles in the virulence of plant pathogens, but limited knowledge is available about the SM repertoire of this wheat pathogen. Here, we review the secondary metabolites that have been isolated from P. nodorum and related species of the same genus and provide an in-depth genome-wide overview of the secondary metabolite gene clusters encoded in the P. nodorum genome. The secondary metabolite gene survey reveals that P. nodorum is capable of producing a diverse range of small molecules and exciting prospects exist for discovery of novel virulence factors and bioactive molecules.
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Affiliation(s)
- Yit-Heng Chooi
- Plant Sciences Division, Research School of Biology, The Australian National University , Canberra , 0200 , Australia
| | - Mariano Jordi Muria-Gonzalez
- Plant Sciences Division, Research School of Biology, The Australian National University , Canberra , 0200 , Australia
| | - Peter S Solomon
- Plant Sciences Division, Research School of Biology, The Australian National University , Canberra , 0200 , Australia
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17
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Bertucci M, Brown-Guedira G, Murphy JP, Cowger C. Genes Conferring Sensitivity to Stagonospora nodorum Necrotrophic Effectors in Stagonospora Nodorum Blotch-Susceptible U.S. Wheat Cultivars. PLANT DISEASE 2014; 98:746-753. [PMID: 30708627 DOI: 10.1094/pdis-08-13-0820-re] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Stagonospora nodorum is a necrotrophic fungal pathogen that causes Stagonospora nodorum blotch (SNB), a yield- and quality-reducing disease of wheat. S. nodorum produces a set of necrotrophic effectors (NEs) that interact with the products of host sensitivity genes to cause cell death and increased susceptibility to disease. The focus of this study was determination of NE sensitivity among 25 winter wheat cultivars, many of them from the southeastern United States, that are susceptible to SNB, as well as the moderately resistant 'NC-Neuse'. Thirty-three isolates of S. nodorum previously collected from seven southeastern U.S. states were cultured for NE production, and the culture filtrates were used in an infiltration bioassay. Control strains of Pichia pastoris that expressed SnToxA, SnTox1, or SnTox3 were also used. All SNB-susceptible cultivars were sensitive to at least one NE, while NC-Neuse was insensitive to all NEs tested. Among the sensitive lines, 32% contained sensitivity gene Tsn1 and 64% contained sensitivity gene Snn3. None were sensitive to SnTox1. Additionally, 10 molecular markers for sensitivity genes Tsn1, Snn1, Snn2, and Snn3 were evaluated for diagnostic potential. Only the marker Xfcp623 for Tsn1 was diagnostic, and it was in perfect agreement with the results of the infiltration bioassays. The results illuminate which NE sensitivity genes may be of concern in breeding for resistance to SNB in the southeastern United States.
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Affiliation(s)
- Matthew Bertucci
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Department of Plant Pathology, North Carolina State University, Raleigh 27695
| | - Gina Brown-Guedira
- Department of Crop Science, North Carolina State University, Raleigh 27695
| | - J Paul Murphy
- USDA-ARS, Department of Crop Science, North Carolina State University, Raleigh 27606
| | - Christina Cowger
- USDA-ARS, Department of Plant Pathology, North Carolina State University, Raleigh 27695
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18
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Resequencing and comparative genomics of Stagonospora nodorum: sectional gene absence and effector discovery. G3-GENES GENOMES GENETICS 2013; 3:959-69. [PMID: 23589517 PMCID: PMC3689807 DOI: 10.1534/g3.112.004994] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Stagonospora nodorum is an important wheat (Triticum aestivum) pathogen in many parts of the world, causing major yield losses. It was the first species in the large fungal Dothideomycete class to be genome sequenced. The reference genome sequence (SN15) has been instrumental in the discovery of genes encoding necrotrophic effectors that induce disease symptoms in specific host genotypes. Here we present the genome sequence of two further S. nodorum strains (Sn4 and Sn79) that differ in their effector repertoire from the reference. Sn79 is avirulent on wheat and produces no apparent effectors when infiltrated onto many cultivars and mapping population parents. Sn4 is pathogenic on wheat and has virulences not found in SN15. The new strains, sequenced with short-read Illumina chemistry, are compared with SN15 by a combination of mapping and de novo assembly approaches. Each of the genomes contains a large number of strain-specific genes, many of which have no meaningful similarity to any known gene. Large contiguous sections of the reference genome are absent in the two newly sequenced strains. We refer to these differences as “sectional gene absences.” The presence of genes in pathogenic strains and absence in Sn79 is added to computationally predicted properties of known proteins to produce a list of likely effector candidates. Transposon insertion was observed in the mitochondrial genomes of virulent strains where the avirulent strain retained the likely ancestral sequence. The study suggests that short-read enabled comparative genomics is an effective way to both identify new S. nodorum effector candidates and to illuminate evolutionary processes in this species.
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19
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Kabbage M, Williams B, Dickman MB. Cell death control: the interplay of apoptosis and autophagy in the pathogenicity of Sclerotinia sclerotiorum. PLoS Pathog 2013; 9:e1003287. [PMID: 23592997 PMCID: PMC3623803 DOI: 10.1371/journal.ppat.1003287] [Citation(s) in RCA: 175] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Accepted: 02/19/2013] [Indexed: 01/07/2023] Open
Abstract
Programmed cell death is characterized by a cascade of tightly controlled events that culminate in the orchestrated death of the cell. In multicellular organisms autophagy and apoptosis are recognized as two principal means by which these genetically determined cell deaths occur. During plant-microbe interactions cell death programs can mediate both resistant and susceptible events. Via oxalic acid (OA), the necrotrophic phytopathogen Sclerotinia sclerotiorum hijacks host pathways and induces cell death in host plant tissue resulting in hallmark apoptotic features in a time and dose dependent manner. OA-deficient mutants are non-pathogenic and trigger a restricted cell death phenotype in the host that unexpectedly exhibits markers associated with the plant hypersensitive response including callose deposition and a pronounced oxidative burst, suggesting the plant can recognize and in this case respond, defensively. The details of this plant directed restrictive cell death associated with OA deficient mutants is the focus of this work. Using a combination of electron and fluorescence microscopy, chemical effectors and reverse genetics, we show that this restricted cell death is autophagic. Inhibition of autophagy rescued the non-pathogenic mutant phenotype. These findings indicate that autophagy is a defense response in this necrotrophic fungus/plant interaction and suggest a novel function associated with OA; namely, the suppression of autophagy. These data suggest that not all cell deaths are equivalent, and though programmed cell death occurs in both situations, the outcome is predicated on who is in control of the cell death machinery. Based on our data, we suggest that it is not cell death per se that dictates the outcome of certain plant-microbe interactions, but the manner by which cell death occurs that is crucial. During plant-microbe interactions, regulated cell death known as programmed cell death (PCD) can mediate both resistant and susceptible interactions. Sclerotinia sclerotiorum induces an apoptotic spreading cell death during infection, via the secreted virulence determinant oxalic acid. Oxalic acid deficient fungal mutants are non-pathogenic, and trigger a restricted cell death phenotype in the host that unexpectedly exhibits markers associated with the plant hypersensitive response. Using electron and fluorescence microscopy, chemical effectors and reverse genetics, we show that this restricted cell death is autophagic. Inhibition of autophagy rescued the non-pathogenic mutant phenotype. These findings indicate that autophagy is a defense response in this interaction and suggest a novel function associated with oxalic acid: the suppression of autophagy. Thus, the control of cell death, dictated by the plant (autophagy) or the fungus (apoptosis), can lead to opposing outcomes. We propose that the type of cell death is decisive to the outcome of certain plant-microbe interactions.
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Affiliation(s)
- Mehdi Kabbage
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Brett Williams
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Martin B. Dickman
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, Texas, United States of America
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, United States of America
- Center for Cell Death and Differentiation, Texas A&M University, College Station, Texas, United States of America
- * E-mail:
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20
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Oliver RP, Friesen TL, Faris JD, Solomon PS. Stagonospora nodorum: from pathology to genomics and host resistance. ANNUAL REVIEW OF PHYTOPATHOLOGY 2012; 50:23-43. [PMID: 22559071 DOI: 10.1146/annurev-phyto-081211-173019] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Stagonospora nodorum is a major necrotrophic pathogen of wheat that causes the diseases S. nodorum leaf and glume blotch. A series of tools and resources, including functional genomics, a genome sequence, proteomics and metabolomics, host-mapping populations, and a worldwide collection of isolates, have enabled the dissection of pathogenicity mechanisms. Metabolic and signaling genes required for pathogenicity have been defined. Interaction with the host is dominated by interplay of fungal effectors that induce necrosis on wheat lines carrying specific sensitivity loci. As such, the pathogen has emerged as a model for the Pleosporales group of pathogens.
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Affiliation(s)
- Richard P Oliver
- Australian Center for Necrotrophic Fungal Pathogens, Curtin University, Perth WA 6845, Australia.
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