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Santhanam P, Labbé C, Tremblay V, Bélanger RR. A rapid molecular diagnostic tool to discriminate alleles of avirulence genes and haplotypes of Phytophthora sojae using high-resolution melting analysis. MOLECULAR PLANT PATHOLOGY 2024; 25:e13406. [PMID: 38009407 PMCID: PMC10799203 DOI: 10.1111/mpp.13406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 10/02/2023] [Accepted: 11/03/2023] [Indexed: 11/28/2023]
Abstract
Effectors encoded by avirulence genes (Avr) interact with the Phytophthora sojae resistance gene (Rps) products to generate incompatible interactions. The virulence profile of P. sojae is rapidly evolving as a result of the large-scale deployment of Rps genes in soybean. For a successful exploitation of Rps genes, it is recommended that soybean growers use cultivars containing the Rps genes corresponding to Avr genes present in P. sojae populations present in their fields. Determination of the virulence profile of P. sojae isolates is critical for the selection of soybean cultivars. High-resolution melting curve (HRM) analysis is a powerful tool, first applied in medicine, for detecting mutations with potential applications in different biological fields. Here, we report the development of an HRM protocol, as an original approach to discriminate effectors, to differentiate P. sojae haplotypes for six Avr genes. An HRM assay was performed on 24 P. sojae isolates with different haplotypes collected from soybean fields across Canada. The results clearly confirmed that the HRM assay discriminated different virulence genotypes. Moreover, the HRM assay was able to differentiate multiple haplotypes representing small allelic variations. HRM-based prediction was validated by phenotyping assays. This HRM assay provides a unique, cost-effective and efficient tool to predict virulence pathotypes associated with six different Avr (1b, 1c, 1d, 1k, 3a and 6) genes from P. sojae, which can be applied in the deployment of appropriate Rps genes in soybean fields.
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Affiliation(s)
- Parthasarathy Santhanam
- Département de PhytologieUniversité LavalQuebecQuebecCanada
- Present address:
Agriculture Agri‐Food Canada, MRDCMordenManitobaCanada
| | - Caroline Labbé
- Département de PhytologieUniversité LavalQuebecQuebecCanada
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Rocafort M, Srivastava V, Bowen JK, Díaz-Moreno SM, Guo Y, Bulone V, Plummer KM, Sutherland PW, Anderson MA, Bradshaw RE, Mesarich CH. Cell Wall Carbohydrate Dynamics during the Differentiation of Infection Structures by the Apple Scab Fungus, Venturia inaequalis. Microbiol Spectr 2023; 11:e0421922. [PMID: 37039647 PMCID: PMC10269774 DOI: 10.1128/spectrum.04219-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 03/15/2023] [Indexed: 04/12/2023] Open
Abstract
Scab, caused by the biotrophic fungal pathogen Venturia inaequalis, is the most economically important disease of apples. During infection, V. inaequalis colonizes the subcuticular host environment, where it develops specialized infection structures called runner hyphae and stromata. These structures are thought to be involved in nutrient acquisition and effector (virulence factor) delivery, but also give rise to conidia that further the infection cycle. Despite their importance, very little is known about how these structures are differentiated. Likewise, nothing is known about how these structures are protected from host defenses or recognition by the host immune system. To better understand these processes, we first performed a glycosidic linkage analysis of sporulating tubular hyphae from V. inaequalis developed in culture. This analysis revealed that the V. inaequalis cell wall is mostly composed of glucans (44%) and mannans (37%), whereas chitin represents a much smaller proportion (4%). Next, we used transcriptomics and confocal laser scanning microscopy to provide insights into the cell wall carbohydrate composition of runner hyphae and stromata. These analyses revealed that, during subcuticular host colonization, genes of V. inaequalis putatively associated with the biosynthesis of immunogenic carbohydrates, such as chitin and β-1,6-glucan, are downregulated relative to growth in culture, while on the surface of runner hyphae and stromata, chitin is deacetylated to the less-immunogenic carbohydrate chitosan. These changes are anticipated to enable the subcuticular differentiation of runner hyphae and stromata by V. inaequalis, as well as to protect these structures from host defenses and recognition by the host immune system. IMPORTANCE Plant-pathogenic fungi are a major threat to food security. Among these are subcuticular pathogens, which often cause latent asymptomatic infections, making them difficult to control. A key feature of these pathogens is their ability to differentiate specialized subcuticular infection structures that, to date, remain largely understudied. This is typified by Venturia inaequalis, which causes scab, the most economically important disease of apples. In this study, we show that, during subcuticular host colonization, V. inaequalis downregulates genes associated with the biosynthesis of two immunogenic cell wall carbohydrates, chitin and β-1,6-glucan, and coats its subcuticular infection structures with a less-immunogenic carbohydrate, chitosan. These changes are anticipated to enable host colonization by V. inaequalis and provide a foundation for understanding subcuticular host colonization by other plant-pathogenic fungi. Such an understanding is important, as it may inform the development of novel control strategies against subcuticular plant-pathogenic fungi.
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Affiliation(s)
- Mercedes Rocafort
- Laboratory of Molecular Plant Pathology, School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Vaibhav Srivastava
- Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology (KTH), AlbaNova University Centre, Stockholm, Sweden
| | - Joanna K. Bowen
- The New Zealand Institute for Plant and Food Research Limited, Mount Albert Research Centre, Auckland, New Zealand
| | - Sara M. Díaz-Moreno
- Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology (KTH), AlbaNova University Centre, Stockholm, Sweden
| | - Yanan Guo
- Laboratory of Molecular Plant Pathology, School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Vincent Bulone
- Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology (KTH), AlbaNova University Centre, Stockholm, Sweden
- School of Food, Agriculture and Wine, The University of Adelaide, Waite Campus, Adelaide, South Australia, Australia
| | - Kim M. Plummer
- Department of Animal, Plant and Soil Sciences, AgriBio, Centre for AgriBiosciences, La Trobe University, Bundoora, Melbourne, Victoria, Australia
| | - Paul W. Sutherland
- The New Zealand Institute for Plant and Food Research Limited, Mount Albert Research Centre, Auckland, New Zealand
| | - Marilyn A. Anderson
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Melbourne, Victoria, Australia
| | - Rosie E. Bradshaw
- Laboratory of Molecular Plant Pathology, School of Natural Sciences, Massey University, Palmerston North, New Zealand
- Bioprotection Aotearoa, Massey University, Palmerston North, New Zealand
| | - Carl H. Mesarich
- Laboratory of Molecular Plant Pathology, School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
- Bioprotection Aotearoa, Massey University, Palmerston North, New Zealand
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Lu Y, Yang H, Bai J, He Q, Deng R. CRISPR-Cas based molecular diagnostics for foodborne pathogens. Crit Rev Food Sci Nutr 2022; 64:5269-5289. [PMID: 36476134 DOI: 10.1080/10408398.2022.2153792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Foodborne pathogenic infection has brought multifaceted issues to human life, leading to an urgent demand for advanced detection technologies. CRISPR/Cas-based biosensors have the potential to address various challenges that exist in conventional assays such as insensitivity, long turnaround time and complex pretreatments. In this perspective, we review the relevant strategies of CRISPR/Cas-assisted diagnostics on foodborne pathogens, focusing on biosensing platforms for foodborne pathogens based on fluorescence, colorimetric, (electro)chemiluminescence, electrochemical, and surface-enhanced Raman scattering detection. It summarizes their detection principles by the clarification of foodborne pathogenic bacteria, fungi, and viruses. Finally, we discuss the current challenges or technical barriers of these methods against broad application, and put forward alternative solutions to improve CRISPR/Cas potential for food safety.
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Affiliation(s)
- Yunhao Lu
- College of Food and Biological Engineering, Chengdu University, Chengdu, P.R. China
| | - Hao Yang
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, P.R. China
| | - Jinrong Bai
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, P.R. China
| | - Qiang He
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, P.R. China
| | - Ruijie Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, P.R. China
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Rocafort M, Bowen JK, Hassing B, Cox MP, McGreal B, de la Rosa S, Plummer KM, Bradshaw RE, Mesarich CH. The Venturia inaequalis effector repertoire is dominated by expanded families with predicted structural similarity, but unrelated sequence, to avirulence proteins from other plant-pathogenic fungi. BMC Biol 2022; 20:246. [PMID: 36329441 PMCID: PMC9632046 DOI: 10.1186/s12915-022-01442-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Scab, caused by the biotrophic fungus Venturia inaequalis, is the most economically important disease of apples worldwide. During infection, V. inaequalis occupies the subcuticular environment, where it secretes virulence factors, termed effectors, to promote host colonization. Consistent with other plant-pathogenic fungi, many of these effectors are expected to be non-enzymatic proteins, some of which can be recognized by corresponding host resistance proteins to activate plant defences, thus acting as avirulence determinants. To develop durable control strategies against scab, a better understanding of the roles that these effector proteins play in promoting subcuticular growth by V. inaequalis, as well as in activating, suppressing, or circumventing resistance protein-mediated defences in apple, is required. RESULTS We generated the first comprehensive RNA-seq transcriptome of V. inaequalis during colonization of apple. Analysis of this transcriptome revealed five temporal waves of gene expression that peaked during early, mid, or mid-late infection. While the number of genes encoding secreted, non-enzymatic proteinaceous effector candidates (ECs) varied in each wave, most belonged to waves that peaked in expression during mid-late infection. Spectral clustering based on sequence similarity determined that the majority of ECs belonged to expanded protein families. To gain insights into function, the tertiary structures of ECs were predicted using AlphaFold2. Strikingly, despite an absence of sequence similarity, many ECs were predicted to have structural similarity to avirulence proteins from other plant-pathogenic fungi, including members of the MAX, LARS, ToxA and FOLD effector families. In addition, several other ECs, including an EC family with sequence similarity to the AvrLm6 avirulence effector from Leptosphaeria maculans, were predicted to adopt a KP6-like fold. Thus, proteins with a KP6-like fold represent another structural family of effectors shared among plant-pathogenic fungi. CONCLUSIONS Our study reveals the transcriptomic profile underpinning subcuticular growth by V. inaequalis and provides an enriched list of ECs that can be investigated for roles in virulence and avirulence. Furthermore, our study supports the idea that numerous sequence-unrelated effectors across plant-pathogenic fungi share common structural folds. In doing so, our study gives weight to the hypothesis that many fungal effectors evolved from ancestral genes through duplication, followed by sequence diversification, to produce sequence-unrelated but structurally similar proteins.
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Affiliation(s)
- Mercedes Rocafort
- Laboratory of Molecular Plant Pathology/Bioprotection Aotearoa, School of Agriculture and Environment, Massey University, Private Bag 11222, Palmerston North, 4442, New Zealand
| | - Joanna K Bowen
- The New Zealand Institute for Plant and Food Research Limited, Mount Albert Research Centre, Auckland, 1025, New Zealand
| | - Berit Hassing
- Laboratory of Molecular Plant Pathology/Bioprotection Aotearoa, School of Agriculture and Environment, Massey University, Private Bag 11222, Palmerston North, 4442, New Zealand
| | - Murray P Cox
- Bioprotection Aotearoa, School of Natural Sciences, Massey University, Private Bag 11222, Palmerston North, 4442, New Zealand
| | - Brogan McGreal
- The New Zealand Institute for Plant and Food Research Limited, Mount Albert Research Centre, Auckland, 1025, New Zealand
| | - Silvia de la Rosa
- Laboratory of Molecular Plant Pathology/Bioprotection Aotearoa, School of Agriculture and Environment, Massey University, Private Bag 11222, Palmerston North, 4442, New Zealand
| | - Kim M Plummer
- Department of Animal, Plant and Soil Sciences, La Trobe University, AgriBio, Centre for AgriBiosciences, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - Rosie E Bradshaw
- Bioprotection Aotearoa, School of Natural Sciences, Massey University, Private Bag 11222, Palmerston North, 4442, New Zealand
| | - Carl H Mesarich
- Laboratory of Molecular Plant Pathology/Bioprotection Aotearoa, School of Agriculture and Environment, Massey University, Private Bag 11222, Palmerston North, 4442, New Zealand.
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Patel R, Mitra B, Vinchurkar M, Adami A, Patkar R, Giacomozzi F, Lorenzelli L, Baghini MS. A review of recent advances in plant-pathogen detection systems. Heliyon 2022; 8:e11855. [DOI: 10.1016/j.heliyon.2022.e11855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/19/2022] [Accepted: 11/16/2022] [Indexed: 11/30/2022] Open
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Miller TA, Hudson DA, Johnson RD, Singh JS, Mace WJ, Forester NT, Maclean PH, Voisey CR, Johnson LJ. Dissection of the epoxyjanthitrem pathway in Epichloë sp. LpTG-3 strain AR37 by CRISPR gene editing. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:944234. [PMID: 37746172 PMCID: PMC10512260 DOI: 10.3389/ffunb.2022.944234] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 07/18/2022] [Indexed: 09/26/2023]
Abstract
Epichloë festucae var. lolii and Epichloë sp. LpTG-3 are filamentous fungal endophytes of perennial ryegrass (Lolium perenne) that have a substantial impact on New Zealand's agricultural economy by conferring biotic advantages to the host grass. Overall, Epichloë endophytes contribute NZ$200 million to the economy annually, with strain AR37 estimated to contribute NZ$3.6 billion to the New Zealand economy over a 20-year period. This strain produces secondary metabolites, including epoxyjanthitrems, which are a class of indole diterpenes, associated with the observed effects of AR37 on livestock and insect pests. Until very recently, AR37 was intractable to genetic modification but this has changed with the application of CRISPR-Cas9 based gene editing techniques. In this paper, gene inactivation by CRISPR-Cas9 was used to deconvolute the genetic basis for epoxyjanthitrem biosynthesis, including creating an AR37 strain that has been edited to remove the biosynthesis of all indole diterpenes. We show that gene editing of Epichloë can be achieved without off-target events or introduction of foreign DNA (footprint-less) through an AMA1-based plasmid that simultaneously expresses the CRISPR-Cas9 system and selectable marker. Genetic modification events in these transformants were investigated through genome sequencing and in planta chemistry.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Linda J. Johnson
- Grasslands Research Centre, AgResearch, Palmerston North, New Zealand
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McCarthy HM, Tarallo M, Mesarich CH, McDougal RL, Bradshaw RE. Targeted Gene Mutations in the Forest Pathogen Dothistroma septosporum Using CRISPR/Cas9. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11081016. [PMID: 35448744 PMCID: PMC9025729 DOI: 10.3390/plants11081016] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/04/2022] [Accepted: 04/04/2022] [Indexed: 05/19/2023]
Abstract
Dothistroma needle blight, caused by Dothistroma septosporum, has increased in incidence and severity over the last few decades and is now one of the most important global diseases of pines. Disease resistance breeding could be accelerated by knowledge of pathogen virulence factors and their host targets. However, this is hindered due to inefficient targeted gene disruption in D. septosporum, which is required for virulence gene characterisation. Here we report the first successful application of CRISPR/Cas9 gene editing to a Dothideomycete forest pathogen, D. septosporum. Disruption of the dothistromin pathway regulator gene AflR, with a known phenotype, was performed using nonhomologous end-joining repair with an efficiency of > 90%. Transformants with a range of disruption mutations in AflR were produced. Disruption of Ds74283, a D. septosporum gene encoding a secreted cell death elicitor, was also achieved using CRISPR/Cas9, by using a specific donor DNA repair template to aid selection where the phenotype was unknown. In this case, 100% of screened transformants were identified as disruptants. In establishing CRISPR/Cas9 as a tool for gene editing in D. septosporum, our research could fast track the functional characterisation of candidate virulence factors in D. septosporum and helps set the foundation for development of this technology in other forest pathogens.
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Affiliation(s)
- Hannah M. McCarthy
- BioProtection Aotearoa, School of Natural Sciences, Massey University, Palmerston North 4472, New Zealand; (M.T.); (R.E.B.)
- Correspondence:
| | - Mariana Tarallo
- BioProtection Aotearoa, School of Natural Sciences, Massey University, Palmerston North 4472, New Zealand; (M.T.); (R.E.B.)
| | - Carl H. Mesarich
- BioProtection Aotearoa, School of Agriculture and Environment, Massey University, Palmerston North 4472, New Zealand;
| | - Rebecca L. McDougal
- Scion, New Zealand Forest Research Institute Ltd., Rotorua 3010, New Zealand;
| | - Rosie E. Bradshaw
- BioProtection Aotearoa, School of Natural Sciences, Massey University, Palmerston North 4472, New Zealand; (M.T.); (R.E.B.)
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