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Madhushan A, Weerasingha DB, Ilyukhin E, Taylor PWJ, Ratnayake AS, Liu JK, Maharachchikumbura SSN. From Natural Hosts to Agricultural Threats: The Evolutionary Journey of Phytopathogenic Fungi. J Fungi (Basel) 2025; 11:25. [PMID: 39852444 PMCID: PMC11766330 DOI: 10.3390/jof11010025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2024] [Accepted: 12/28/2024] [Indexed: 01/26/2025] Open
Abstract
Since the domestication of plants, pathogenic fungi have consistently threatened crop production, evolving genetically to develop increased virulence under various selection pressures. Understanding their evolutionary trends is crucial for predicting and designing control measures against future disease outbreaks. This paper reviews the evolution of fungal pathogens from natural habitats to agricultural settings, focusing on eight significant phytopathogens: Pyricularia oryzae, Botrytis cinerea, Puccinia spp., Fusarium graminearum, F. oxysporum, Blumeria graminis, Zymoseptoria tritici, and Colletotrichum spp. Also, we explore the mechanism used to understand evolutionary trends in these fungi. The studied pathogens have evolved in agroecosystems through either (1) introduction from elsewhere; or (2) local origins involving co-evolution with host plants, host shifts, or genetic variations within existing strains. Genetic variation, generated via sexual recombination and various asexual mechanisms, often drives pathogen evolution. While sexual recombination is rare and mainly occurs at the center of origin of the pathogen, asexual mechanisms such as mutations, parasexual recombination, horizontal gene or chromosome transfer, and chromosomal structural variations are predominant. Farming practices like mono-cropping resistant cultivars and prolonged use of fungicides with the same mode of action can drive the emergence of new pathotypes. Furthermore, host range does not necessarily impact pathogen adaptation and evolution. Although halting pathogen evolution is impractical, its pace can be slowed by managing selective pressures, optimizing farming practices, and enforcing quarantine regulations. The study of pathogen evolution has been transformed by advancements in molecular biology, genomics, and bioinformatics, utilizing methods like next-generation sequencing, comparative genomics, transcriptomics and population genomics. However, continuous research remains essential to monitor how pathogens evolve over time and to develop proactive strategies that mitigate their impact on agriculture.
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Affiliation(s)
- Asanka Madhushan
- School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 611731, China; (A.M.); (D.B.W.)
| | - Dulan Bhanuka Weerasingha
- School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 611731, China; (A.M.); (D.B.W.)
| | - Evgeny Ilyukhin
- Laboratory of Plant Pathology, Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK S9H 3X2, Canada;
| | - Paul W. J. Taylor
- Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia;
| | - Amila Sandaruwan Ratnayake
- Department of Applied Earth Sciences, Faculty of Applied Sciences, Uva Wellassa University, Passara Road, Badulla 90000, Sri Lanka;
| | - Jian-Kui Liu
- School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 611731, China; (A.M.); (D.B.W.)
| | - Sajeewa S. N. Maharachchikumbura
- School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 611731, China; (A.M.); (D.B.W.)
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Achari SR, Mann RC, Sharma M, Edwards J. Diagnosis of Fusarium oxysporum f. sp. ciceris causing Fusarium wilt of chickpea using loop-mediated isothermal amplification (LAMP) and conventional end-point PCR. Sci Rep 2023; 13:2640. [PMID: 36788315 PMCID: PMC9929042 DOI: 10.1038/s41598-023-29730-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 02/09/2023] [Indexed: 02/16/2023] Open
Abstract
Fusarium oxysporum (Fo) is ubiquitous in soil and forms a species complex of pathogenic and putatively non-pathogenic strains. Pathogenic strains cause disease in over 150 plant species. Fusarium oxysporum f. sp. ciceris (Foc) is a major fungal pathogen causing Fusarium wilt in chickpeas (Cicer arietinum). In some countries such as Australia, Foc is a high-priority pest of biosecurity concern. Specific, sensitive, robust and rapid diagnostic assays are essential for effective disease management on the farm and serve as an effective biosecurity control measure. We developed and validated a novel and highly specific PCR and a LAMP assay for detecting the Indian Foc race 1 based on a putative effector gene uniquely present in its genome. These assays were assessed against 39 Fo formae speciales and found to be specific, only amplifying the target species, in a portable real-time fluorometer (Genie III) and qPCR machine in under 13 min with an anneal derivative temperature ranging from 87.7 to 88.3 °C. The LAMP assay is sensitive to low levels of target DNA (> 0.009 ng/µl). The expected PCR product size is 143 bp. The LAMP assay developed in this study was simple, fast, sensitive and specific and could be explored for other Foc races due to the uniqueness of this marker to the Foc genome.
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Affiliation(s)
- Saidi R. Achari
- grid.452283.a0000 0004 0407 2669AgriBio, Agriculture Victoria Research, DJPR, Bundoora, VIC Australia
| | - Ross C. Mann
- grid.452283.a0000 0004 0407 2669AgriBio, Agriculture Victoria Research, DJPR, Bundoora, VIC Australia
| | - Mamta Sharma
- grid.419337.b0000 0000 9323 1772International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
| | - Jacqueline Edwards
- grid.452283.a0000 0004 0407 2669AgriBio, Agriculture Victoria Research, DJPR, Bundoora, VIC Australia ,grid.1018.80000 0001 2342 0938School of Applied Systems Biology, La Trobe University, Bundoora, VIC Australia
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Adams TM, Armitage AD, Sobczyk MK, Bates HJ, Tabima JF, Kronmiller BA, Tyler BM, Grünwald NJ, Dunwell JM, Nellist CF, Harrison RJ. Genomic Investigation of the Strawberry Pathogen Phytophthora fragariae Indicates Pathogenicity Is Associated With Transcriptional Variation in Three Key Races. Front Microbiol 2020; 11:490. [PMID: 32351458 PMCID: PMC7174552 DOI: 10.3389/fmicb.2020.00490] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Accepted: 03/06/2020] [Indexed: 01/08/2023] Open
Abstract
The oomycete Phytophthora fragariae is a highly destructive pathogen of cultivated strawberry (Fragaria × ananassa), causing the root rotting disease, "red core". The host-pathogen interaction has a well described gene-for-gene resistance relationship, but to date neither candidate avirulence nor resistance genes have been identified. We sequenced a set of American, Canadian, and United Kingdom isolates of known race type, along with three representatives of the closely related pathogen of the raspberry (Rubus idaeus), P. rubi, and found a clear population structure, with a high degree of nucleotide divergence seen between some race types and abundant private variation associated with race types 4 and 5. In contrast, between isolates defined as United Kingdom races 1, 2, and 3 (UK1-2-3) there was no evidence of gene loss or gain; or the presence of insertions/deletions (INDELs) or Single Nucleotide Polymorphisms (SNPs) within or in proximity to putative pathogenicity genes could be found associated with race variation. Transcriptomic analysis of representative UK1-2-3 isolates revealed abundant expression variation in key effector family genes associated with pathogen race; however, further long read sequencing did not reveal any long range polymorphisms to be associated with avirulence to race UK2 or UK3 resistance, suggesting either control in trans or other stable forms of epigenetic modification modulating gene expression. This work reveals the combined power of population resequencing to uncover race structure in pathosystems and in planta transcriptomic analysis to identify candidate avirulence genes. This work has implications for the identification of putative avirulence genes in the absence of associated expression data and points toward the need for detailed molecular characterisation of mechanisms of effector regulation and silencing in oomycete plant pathogens.
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Affiliation(s)
- Thomas M. Adams
- Department of Genetics, Genomics and Breeding, NIAB EMR, Kent, United Kingdom
- School of Agriculture, Policy and Development, University of Reading, Reading, United Kingdom
| | - Andrew D. Armitage
- Department of Genetics, Genomics and Breeding, NIAB EMR, Kent, United Kingdom
| | - Maria K. Sobczyk
- Department of Genetics, Genomics and Breeding, NIAB EMR, Kent, United Kingdom
| | - Helen J. Bates
- Department of Genetics, Genomics and Breeding, NIAB EMR, Kent, United Kingdom
| | - Javier F. Tabima
- Department of Botany and Plant Pathology, Center for Genome Biology and Biocomputing, Oregon State University, Corvallis, OR, United States
| | - Brent A. Kronmiller
- Center for Genome Biology and Biocomputing, Oregon State University, Corvallis, OR, United States
| | - Brett M. Tyler
- Department of Botany and Plant Pathology, Center for Genome Biology and Biocomputing, Oregon State University, Corvallis, OR, United States
- Center for Genome Biology and Biocomputing, Oregon State University, Corvallis, OR, United States
| | - Niklaus J. Grünwald
- Horticultural Crops Research Unit, Agricultural Research Service, United States Department of Agriculture, Corvallis, OR, United States
| | - Jim M. Dunwell
- School of Agriculture, Policy and Development, University of Reading, Reading, United Kingdom
| | | | - Richard J. Harrison
- Department of Genetics, Genomics and Breeding, NIAB EMR, Kent, United Kingdom
- NIAB Cambridge Crop Research, NIAB, Cambridge, United Kingdom
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Li J, Wang Q, Li C, Bi Y, Fu X, Wang R. Novel haplotypes and networks of AVR-Pik alleles in Magnaporthe oryzae. BMC PLANT BIOLOGY 2019; 19:204. [PMID: 31096914 PMCID: PMC6524238 DOI: 10.1186/s12870-019-1817-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 05/02/2019] [Indexed: 05/22/2023]
Abstract
BACKGROUND Rice blast disease is one of the most destructive fungal disease of rice worldwide. The avirulence (AVR) genes of Magnaporthe oryzae are recognized by the cognate resistance (R) genes of rice and trigger race-specific resistance. The variation in AVR is one of the major drivers of new races. Detecting the variation in the AVR gene in isolates from a population of Magnaporthe oryzae collected from rice production fields will aid in evaluating the effectiveness of R genes in rice production areas. The Pik gene contains 5 R alleles (Pik, Pikh, Pikp, Pikm and Piks) corresponding to the AVR alleles (AVR-Pik/kh/kp/km/ks) of M. oryzae. The Pik gene specifically recognizes and prevents infections by isolates of M. oryzae that contain AVR-Pik. The molecular variation in AVR-Pik alleles of M. oryzae and Pik alleles of rice remains unclear. RESULTS We studied the possible evolutionary pathways of AVR-Pik alleles by analyzing their DNA sequence variation and assaying their avirulence to the cognate Pik alleles of resistance genes under field conditions in China. The results of PCR products from genomic DNA showed that 278 of the 366 isolates of M. oryzae collected from Yunnan Province, China, carried AVR-Pik alleles. Among the isolates from six regions of Yunnan, 66.7-90.3% carried AVR-Pik alleles. Moreover, 10 AVR-Pik haplotypes encoding five novel AVR-Pik variants were identified among 201 isolates. The AVR-Pik alleles evolved to virulent from avirulent forms via stepwise base substitution. These findings demonstrate that AVR-Pik alleles are under positive selection and that mutations are responsible for defeating race-specific resistant Pik alleles in nature. CONCLUSIONS We demonstrated the polymorphism and distribution of AVR-Pik alleles in Yunnan Province, China. By pathogenicity assays used to detect the function of the different haplotypes of AVR-Pik, for the first time, we showed the avoidance and stepwise evolution of AVR-Pik alleles in rice production areas of Yunnan. The functional AVR-Pik possesses diversified sequence structures and is under positive selection in nature.
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Affiliation(s)
- Jinbin Li
- Agricultural Environment and Resources Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Qun Wang
- Agricultural Environment and Resources Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Chengyun Li
- The Ministry of Education Key Laboratory for Agricultural Biodiversity and Pest Management, Yunnan Agricultural University, Kunming, China
| | - Yunqing Bi
- Agricultural Environment and Resources Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Xue Fu
- Agricultural Environment and Resources Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Raoquan Wang
- Agricultural Environment and Resources Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
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Lombard L, Sandoval-Denis M, Lamprecht S, Crous P. Epitypification of Fusarium oxysporum - clearing the taxonomic chaos. PERSOONIA 2018; 43:1-47. [PMID: 32214496 PMCID: PMC7085860 DOI: 10.3767/persoonia.2019.43.01] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 10/19/2018] [Indexed: 01/06/2023]
Abstract
Fusarium oxysporum is the most economically important and commonly encountered species of Fusarium. This soil-borne fungus is known to harbour both pathogenic (plant, animal and human) and non-pathogenic strains. However, in its current concept F. oxysporum is a species complex consisting of numerous cryptic species. Identification and naming these cryptic species is complicated by multiple subspecific classification systems and the lack of living ex-type material to serve as basic reference point for phylogenetic inference. Therefore, to advance and stabilise the taxonomic position of F. oxysporum as a species and allow naming of the multiple cryptic species recognised in this species complex, an epitype is designated for F. oxysporum. Using multi-locus phylogenetic inference and subtle morphological differences with the newly established epitype of F. oxysporum as reference point, 15 cryptic taxa are resolved in this study and described as species.
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Affiliation(s)
- L. Lombard
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - M. Sandoval-Denis
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Faculty of Natural and Agricultural Sciences, Department of Plant Sciences, University of the Free State, P.O. Box 339, Bloemfontein 9300, South Africa
| | - S.C. Lamprecht
- ARC-Plant Health and Protection, Private Bag X5017, Stellenbosch, 7599, Western Cape, South Africa
| | - P.W. Crous
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Faculty of Natural and Agricultural Sciences, Department of Plant Sciences, University of the Free State, P.O. Box 339, Bloemfontein 9300, South Africa
- Wageningen University and Research Centre (WUR), Laboratory of Phytopathology, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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Gurjar G, Barve M, Giri A, Gupta V. Identification of Indian pathogenic races ofFusarium oxysporumf. sp.ciceriswith gene specific, ITS and random markers. Mycologia 2017; 101:484-95. [DOI: 10.3852/08-085] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Gayatri Gurjar
- Plant Molecular Biology Unit, Division of Biochemical Sciences, National Chemical Laboratory, Dr Homi Bhabha Road, Pune 411008, India
| | - Maneesha Barve
- Visiting Scientist, Protein Crystallography Section, Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400 085, India
| | | | - Vidya Gupta
- Plant Molecular Biology Unit, Division of Biochemical Sciences, National Chemical Laboratory, Dr Homi Bhabha Road, Pune 411008, India
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Williams AH, Sharma M, Thatcher LF, Azam S, Hane JK, Sperschneider J, Kidd BN, Anderson JP, Ghosh R, Garg G, Lichtenzveig J, Kistler HC, Shea T, Young S, Buck SAG, Kamphuis LG, Saxena R, Pande S, Ma LJ, Varshney RK, Singh KB. Comparative genomics and prediction of conditionally dispensable sequences in legume-infecting Fusarium oxysporum formae speciales facilitates identification of candidate effectors. BMC Genomics 2016; 17:191. [PMID: 26945779 PMCID: PMC4779268 DOI: 10.1186/s12864-016-2486-8] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 02/17/2016] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Soil-borne fungi of the Fusarium oxysporum species complex cause devastating wilt disease on many crops including legumes that supply human dietary protein needs across many parts of the globe. We present and compare draft genome assemblies for three legume-infecting formae speciales (ff. spp.): F. oxysporum f. sp. ciceris (Foc-38-1) and f. sp. pisi (Fop-37622), significant pathogens of chickpea and pea respectively, the world's second and third most important grain legumes, and lastly f. sp. medicaginis (Fom-5190a) for which we developed a model legume pathosystem utilising Medicago truncatula. RESULTS Focusing on the identification of pathogenicity gene content, we leveraged the reference genomes of Fusarium pathogens F. oxysporum f. sp. lycopersici (tomato-infecting) and F. solani (pea-infecting) and their well-characterised core and dispensable chromosomes to predict genomic organisation in the newly sequenced legume-infecting isolates. Dispensable chromosomes are not essential for growth and in Fusarium species are known to be enriched in host-specificity and pathogenicity-associated genes. Comparative genomics of the publicly available Fusarium species revealed differential patterns of sequence conservation across F. oxysporum formae speciales, with legume-pathogenic formae speciales not exhibiting greater sequence conservation between them relative to non-legume-infecting formae speciales, possibly indicating the lack of a common ancestral source for legume pathogenicity. Combining predicted dispensable gene content with in planta expression in the model legume-infecting isolate, we identified small conserved regions and candidate effectors, four of which shared greatest similarity to proteins from another legume-infecting ff. spp. CONCLUSIONS We demonstrate that distinction of core and potential dispensable genomic regions of novel F. oxysporum genomes is an effective tool to facilitate effector discovery and the identification of gene content possibly linked to host specificity. While the legume-infecting isolates didn't share large genomic regions of pathogenicity-related content, smaller regions and candidate effector proteins were highly conserved, suggesting that they may play specific roles in inducing disease on legume hosts.
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Affiliation(s)
- Angela H Williams
- The Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.
- CSIRO Agriculture, Centre for Environment and Life Sciences, Wembley, WA, 6913, Australia.
| | - Mamta Sharma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Greater Hyderabad, 502324, Telangana, India.
| | - Louise F Thatcher
- CSIRO Agriculture, Centre for Environment and Life Sciences, Wembley, WA, 6913, Australia.
| | - Sarwar Azam
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Greater Hyderabad, 502324, Telangana, India.
| | - James K Hane
- CSIRO Agriculture, Centre for Environment and Life Sciences, Wembley, WA, 6913, Australia.
- Department of Environment and Agriculture, Curtin Institute for Computation, and CCDM Bioinformatics, Centre for Crop and Disease Management, Curtin University, Perth, WA, 6102, Australia.
| | - Jana Sperschneider
- CSIRO Agriculture, Centre for Environment and Life Sciences, Wembley, WA, 6913, Australia.
| | - Brendan N Kidd
- CSIRO Agriculture, Centre for Environment and Life Sciences, Wembley, WA, 6913, Australia.
| | - Jonathan P Anderson
- The Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.
- CSIRO Agriculture, Centre for Environment and Life Sciences, Wembley, WA, 6913, Australia.
| | - Raju Ghosh
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Greater Hyderabad, 502324, Telangana, India.
| | - Gagan Garg
- CSIRO Agriculture, Centre for Environment and Life Sciences, Wembley, WA, 6913, Australia.
| | - Judith Lichtenzveig
- Department of Environment and Agriculture, Pulse Pathology and Genetics, Centre for Crop and Disease Management and Curtin Institute for Computation, Curtin University, Perth, WA, 6102, Australia.
| | - H Corby Kistler
- USDA-ARS, Cereal Disease Laboratory, University of Minnesota, St Paul, MN, 55108, USA.
| | | | - Sarah Young
- The Broad Institute, Cambridge, MA, 02141, USA.
| | - Sally-Anne G Buck
- CSIRO Agriculture, Centre for Environment and Life Sciences, Wembley, WA, 6913, Australia.
| | - Lars G Kamphuis
- The Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.
- CSIRO Agriculture, Centre for Environment and Life Sciences, Wembley, WA, 6913, Australia.
| | - Rachit Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Greater Hyderabad, 502324, Telangana, India.
| | - Suresh Pande
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Greater Hyderabad, 502324, Telangana, India.
| | - Li-Jun Ma
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, 01003, USA.
| | - Rajeev K Varshney
- The Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Greater Hyderabad, 502324, Telangana, India.
| | - Karam B Singh
- The Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.
- CSIRO Agriculture, Centre for Environment and Life Sciences, Wembley, WA, 6913, Australia.
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Wu W, Wang L, Zhang S, Li Z, Zhang Y, Lin F, Pan Q. Stepwise arms race between AvrPik and Pik alleles in the rice blast pathosystem. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2014; 27:759-69. [PMID: 24742074 DOI: 10.1094/mpmi-02-14-0046-r] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
A stepwise mutation that occurred in both pathogens and their respective hosts has played a seminal role in the co-evolutionary arms race evolution in diverse pathosystems. The process driven by rice blast AvrPik and Pik alleles was investigated through population genetic and evolutionary approaches. The genetic diversity of the non-signal domain of AvrPik was higher than that in its signal peptide domain. Positive selection for particular AvrPik alleles in the northeastern region of China was stronger than in the south. The perfect relationship between the functional lineages and AvrPik allele-specific pathotypes was established by ruling out the nonfunctional lineages derived from additional copies. Only four alleles conditioning stepwise pathotypes were detected in natural populations, which were likely created by only one evolutionary pathway with three recognizable mutation steps. Two non-stepwise pathotypes were determined by two blocks in a network constructed by all 16 possible alleles, indicating that a natural evolution process can be artificially changed by a combination of specific single-nucleotide polymorphisms. Assuming that AvrPik evolution has been largely driven by host selection, the co-evolutionary stepwise relationships between AvrPik and Pik was established. The experimental validation of stepwise mutation is required for the development of sustainable management strategies against plant disease.
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Sharma M, Nagavardhini A, Thudi M, Ghosh R, Pande S, Varshney RK. Development of DArT markers and assessment of diversity in Fusarium oxysporum f. sp. ciceris, wilt pathogen of chickpea (Cicer arietinum L.). BMC Genomics 2014; 15:454. [PMID: 24912854 PMCID: PMC4070567 DOI: 10.1186/1471-2164-15-454] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 05/30/2014] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Fusarium oxysporum f. sp. ciceris (Foc), the causal agent of Fusarium wilt of chickpea is highly variable and frequent recurrence of virulent forms have affected chickpea production and exhausted valuable genetic resources. The severity and yield losses of Fusarium wilt differ from place to place owing to existence of physiological races among isolates. Diversity study of fungal population associated with a disease plays a major role in understanding and devising better disease control strategies. The advantages of using molecular markers to understand the distribution of genetic diversity in Foc populations is well understood. The recent development of Diversity Arrays Technology (DArT) offers new possibilities to study the diversity in pathogen population. In this study, we developed DArT markers for Foc population, analysed the genetic diversity existing within and among Foc isolates, compared the genotypic and phenotypic diversity and infer the race scenario of Foc in India. RESULTS We report the successful development of DArT markers for Foc and their utility in genotyping of Foc collections representing five chickpea growing agro-ecological zones of India. The DArT arrays revealed a total 1,813 polymorphic markers with an average genotyping call rate of 91.16% and a scoring reproducibility of 100%. Cluster analysis, principal coordinate analysis and population structure indicated that the different isolates of Foc were partially classified based on geographical source. Diversity in Foc population was compared with the phenotypic variability and it was found that DArT markers were able to group the isolates consistent with its virulence group. A number of race-specific unique and rare alleles were also detected. CONCLUSION The present study generated significant information in terms of pathogenic and genetic diversity of Foc which could be used further for development and deployment of region-specific resistant cultivars of chickpea. The DArT markers were proved to be a powerful diagnostic tool to study the genotypic diversity in Foc. The high number of DArT markers allowed a greater resolution of genetic differences among isolates and enabled us to examine the extent of diversity in the Foc population present in India, as well as provided support to know the changing race scenario in Foc population.
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Affiliation(s)
- Mamta Sharma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, PO 502324 Andhra Pradesh India
| | - Avuthu Nagavardhini
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, PO 502324 Andhra Pradesh India
| | - Mahendar Thudi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, PO 502324 Andhra Pradesh India
| | - Raju Ghosh
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, PO 502324 Andhra Pradesh India
| | - Suresh Pande
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, PO 502324 Andhra Pradesh India
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, PO 502324 Andhra Pradesh India
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Okubara PA, Harrison LA, Gatch EW, Vandemark G, Schroeder KL, du Toit LJ. Development and Evaluation of a TaqMan Real-Time PCR Assay for Fusarium oxysporum f. sp. spinaciae. PLANT DISEASE 2013; 97:927-937. [PMID: 30722577 DOI: 10.1094/pdis-03-12-0317-re] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Fusarium oxysporum f. sp. spinaciae, causal agent of spinach Fusarium wilt, is an important soilborne pathogen in many areas of the world where spinach is grown. The pathogen is persistent in acid soils of maritime western Oregon and Washington, the only region of the United States suitable for commercial spinach seed production. A TaqMan real-time polymerase chain reaction (PCR) assay was developed for rapid identification and quantification of the pathogen, based on sequencing the intergenic spacer (IGS) region of rDNA of isolates of the pathogen. A guanine single-nucleotide polymorphism (G SNP) was detected in the IGS sequences of 36 geographically diverse isolates of F. oxysporum f. sp. spinaciae but not in the sequences of 64 isolates representing other formae speciales and 33 isolates representing other fungal species or genera. The SNP was used to develop a probe for a real-time PCR assay. The real-time PCR assay detected F. oxysporum f. sp. spinaciae at 3-14,056 CFU/g of soil in 82 soil samples collected over 3 years from naturally infested spinach seed production sites in western Washington, although a reliable detection limit of the assay was determined to be 11 CFU/g of soil. A significant (P < 0.05), positive correlation between enumeration of F. oxysporum on Komada's agar and quantification of the pathogen using the TaqMan assay was observed in a comparison of 82 soil samples. Correlations between pathogen DNA levels, Fusarium wilt severity ratings, and spinach biomass were significantly positive for one set of naturally infested soils but not between pathogen DNA levels, wilt incidence ratings, and spinach biomass for other soil samples, suggesting that soilborne pathogen population is not the sole determinant of spinach Fusarium wilt incidence or severity. The presence of the G SNP detected in one isolate of each of F. oxysporum ff. spp. lageneriae, lilii, melongenae, and raphani and reaction of the real-time PCR assay with 16 of 22 nonpathogenic isolates of F. oxysporum associated with spinach plants or soil in which spinach had been grown potentially limits the application of this assay. Nonetheless, because all isolates of F. oxysporum f. sp. spinaciae tested positive with the real-time PCR assay, the assay may provide a valuable means of screening for resistance to Fusarium wilt by quantifying development of the pathogen in spinach plants inoculated with the pathogen.
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Affiliation(s)
- P A Okubara
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Root Disease and Biological Control Research Unit, Pullman, WA 99164
| | | | - E W Gatch
- graduate student, Washington State University Mount Vernon NWREC, Mount Vernon 98273
| | - G Vandemark
- USDA-ARS, Grain Legume Genetics and Physiology Research Unit, Pullman, WA 99164
| | - K L Schroeder
- Department of Plant Pathology, Washington State University, Pullman 99164
| | - L J du Toit
- Washington State University Mount Vernon NWREC
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Southwood MJ, Viljoen A, Mostert G, McLeod A. Molecular identification of two vegetative compatibility groups of Fusarium oxysporum f. sp. cepae. PHYTOPATHOLOGY 2012; 102:204-213. [PMID: 21970568 DOI: 10.1094/phyto-04-11-0107] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Fusarium oxysporum f. sp. cepae, which causes basal rot of onion, consists of seven vegetative compatibility groups (VCGs 0420 to 0426) and several single-member VCGs (SMVs). F. oxysporum f. sp. cepae populations in South Africa and Colorado each consist of one main VCG (namely, VCG 0425 and 0421, respectively). The aim of this study was to develop sequence-characterized amplified region (SCAR) markers for the identification of VCGs 0425 and 0421, using 79 previously characterized F. oxysporum isolates. A second aim was to investigate the prevalence of VCG 0425 among 88 uncharacterized South African onion F. oxysporum isolates using (i) the developed SCAR markers and (ii) inter-retrotransposon (IR)- and random amplified polymorphic DNA (RAPD) fingerprinting. Only two RAPD primers provided informative fingerprints for VCG 0425 isolates but these could not be developed into SCAR markers, although they provided diagnostic fragments for differentiation of VCG 0425 from VCG 0421. IR fingerprinting data were used to develop a multiplex IR-SCAR polymerase chain reaction method for the identification of VCG 0421, VCG 0425, and SMV 4 isolates as a group. Molecular identification of the uncharacterized collection of 88 F. oxysporum isolates (65 F. oxysporum f. sp. cepae and 23 F. oxysporum isolates nonpathogenic to onion) confirmed that VCG 0425 is the main VCG in South Africa, with all but 3 of the 65 F. oxysporum f. sp. cepae isolates having the molecular characteristics of this VCG. Genotyping and VCG testing showed that two of the three aforementioned isolates were new SMVs (SMV 6 and SMV 7), whereas the third (previously known as SMV 3) now belongs to VGC 0247.
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Affiliation(s)
- Michael J Southwood
- Department of Plant Pathology, Stellenbosch University, Matieland, 7600, South Africa
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12
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Lievens B, Rep M, Thomma BPHJ. Recent developments in the molecular discrimination of formae speciales of Fusarium oxysporum. PEST MANAGEMENT SCIENCE 2008; 64:781-788. [PMID: 18335459 DOI: 10.1002/ps.1564] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Rapid and reliable detection and identification of potential plant pathogens is required for taking appropriate and timely disease management measures. For many microbial species of which all strains generally are plant pathogens on a known host range, this has become quite straightforward. However, for some fungal species this is quite a challenge. One of these is Fusarium oxysporum Schlechtend:Fr., which, as a species, has a very broad host range, while individual strains are usually highly host-specific. Moreover, many strains of this fungus are non-pathogenic soil inhabitants. Thus, with regard to effective disease management, identification below the species level is highly desirable. So far, the genetic basis of host specificity in F. oxysporum is poorly understood. Furthermore, strains that infect a particular plant species are not necessarily more closely related to each other than to strains that infect other hosts. Despite these difficulties, recently an increasing number of studies have reported the successful development of molecular markers to discriminate F. oxysporum strains below the species level.
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Affiliation(s)
- Bart Lievens
- Scientia Terrae Research Institute, Fortsesteenweg 30A, 2860 Sint-Katelijne-Waver, Belgium.
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Barrett LG, Thrall PH, Burdon JJ, Nicotra AB, Linde CC. Population structure and diversity in sexual and asexual populations of the pathogenic fungus Melampsora lini. Mol Ecol 2008; 17:3401-15. [PMID: 18573166 PMCID: PMC2653454 DOI: 10.1111/j.1365-294x.2008.03843.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Many pathogens undergo both sexual and asexual reproduction to varying degrees, yet the ecological, genetic and evolutionary consequences of different reproductive strategies remain poorly understood. Here we investigate the population genetic structure of wild populations of the plant pathogen Melampsora lini on its host Linum marginale, using amplified fragment length polymorphism (AFLP) markers, two genes underlying pathogen virulence, and phenotypic variation in virulence. In Australia, M. lini occurs as two genetically and geographically divergent lineages (AA and AB), one of which is completely asexual (AB), and the other able to reproduce both clonally and sexually (AA). To quantify the genetic and evolutionary consequences of these different life histories, we sampled five populations in each of two biogeographical regions. Analysis of AFLP data obtained for 275 isolates revealed largely disjunct geographical distributions for the two different lineages, low genetic diversity within lineages, and strong genetic structure among populations within each region. We also detected significant divergence among populations for both Avr genes and virulence phenotypes, although generally these values were lower than those obtained with AFLP markers. Furthermore, isolates belonging to lineage AA collectively harboured significantly higher genotypic and phenotypic diversity than lineage AB isolates. Together these results illustrate the important roles of reproductive modes and geographical structure in the generation and maintenance of virulence diversity in populations of M. lini.
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Affiliation(s)
- Luke G Barrett
- CSIRO Plant Industry, GPO Box 1600, Canberra, ACT 2601, Australia.
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14
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Wang B, Brubaker CL, Tate W, Woods MJ, Burdon JJ. Evolution of virulence in Fusarium oxysporum f. sp. vasinfectum using serial passage assays through susceptible cotton. PHYTOPATHOLOGY 2008; 98:296-303. [PMID: 18944080 DOI: 10.1094/phyto-98-3-0296] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Fifty strains of Fusarium oxysporum, recovered from rhizosphere soil around native Gossypium species and found to be mildly virulent on cotton (Gossypium hirsutum), were used to assay the propensity for evolution of virulence using serial passage assays through cotton. Only one lineage A strain, 2613, successfully completed 10 successive passages, while all others lost the ability to cause foliar disease symptoms at various stages during this process. Based on 46 amplified fragment length polymorphism (AFLP) markers generated with four EcoRI x MseI primer combinations, mutants were identified in offspring isolates from strain 2613 regardless of whether serial passages occurred in cotton or on water agar, suggesting the occurrence of spontaneous mutations. Significantly increased virulence was observed in the offspring isolates generated on cotton, while no increasing virulence was found in those obtained on water agar, suggesting that the evolution of virulence in F. oxysporum f. sp. vasinfectum is associated with the presence of cotton. No clear correlation was observed between the AFLP mutations and increased virulence in this study.
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Affiliation(s)
- B Wang
- CSIRO Plant Industry, G.P.O. Box 1600, Canberra ACT 2601, Australia.
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15
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Barrett LG, Thrall PH, Burdon JJ. EVOLUTIONARY DIVERSIFICATION THROUGH HYBRIDIZATION IN A WILD HOST?PATHOGEN INTERACTION. Evolution 2007; 61:1613-21. [PMID: 17598744 DOI: 10.1111/j.1558-5646.2007.00141.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Coevolutionary outcomes between interacting species are predicted to vary across landscapes, as environmental conditions, gene flow, and the strength of selection vary among populations. Using a combination of molecular, experimental, and field approaches, we describe how broad-scale patterns of environmental heterogeneity, genetic divergence, and regional adaptation have the potential to influence coevolutionary processes in the Linum marginale-Melampsora lini plant-pathogen interaction. We show that two genetically and geographically divergent pathogen lineages dominate interactions with the host across Australia, and demonstrate a hybrid origin for one of the lineages. We further demonstrate that the geographic divergence of the two lineages of M. lini in Australia is related to variation among lineages in virulence, life-history characteristics, and response to environmental conditions. When correlated with data describing regional patterns of variation in host resistance diversity and mating system these observations highlight the potential for gene flow and geographic selection mosaics to generate and maintain coevolutionary diversification in long-standing host-pathogen interactions.
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Affiliation(s)
- Luke G Barrett
- CSIRO Plant Industry, GPO Box 1600, Canberra, Australian Capital Territory, 2601, Australia.
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Navas-Cortés JA, Landa BB, Méndez-Rodríguez MA, Jiménez-Díaz RM. Quantitative Modeling of the Effects of Temperature and Inoculum Density of Fusarium oxysporum f. sp. ciceris Races 0 and 5 on Development of Fusarium Wilt in Chickpea Cultivars. PHYTOPATHOLOGY 2007; 97:564-573. [PMID: 18943575 DOI: 10.1094/phyto-97-5-0564] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
ABSTRACT Races 0 (Foc-0) and 5 (Foc-5) of Fusarium oxysporum f. sp. ciceris differ in virulence and induce yellowing or wilting syndrome, respectively, in chickpea. We modeled the combined effects of soil temperature and inoculum density of Foc-0 and Foc-5 on disease developed in chickpea cvs. P-2245 and PV-61 differing in susceptibility to those races, using quantitative nonlinear models. Disease development over time in the temperature range of 10 to 30 degrees C and inoculum densities between 6 and 8,000 chlamydospores g(1) of soil was described by the Weibull function. Four response variables (the reciprocal incubation period, the final disease intensity, the standardized area under the disease progress curve, and the intrinsic rate of disease development) characterized the disease development. Response surface models that expressed the combined effect of inoculum density and temperature were developed by substituting the intrinsic rate of disease development in the Weibull or exponential functions with a beta function describing the relationship of response variables to temperature. The models estimated 22 to 26 degrees C as the most favorable soil temperature for infection of cvs. P-2245 and PV-61 by Foc-5, and 24 to 28 degrees C for infection of cv. P-2245 by Foc-0. At 10 degrees C, no disease developed except in cv. P-2245 inoculated with Foc-5. At optimum soil temperature, maximum disease intensity developed with Foc-5 and Foc-0 at 6 and 50 chlamydospores g(1) of soil respectively, in cv. P-2245, and with Foc-5 at 1,000 chlamydospores g(1) of soil in cv. PV-61. The models were used to construct risk threshold charts that can be used to estimate the potential risk of Fusarium wilt epidemics in a geographical area based on soil temperature, the race and inoculum density in soil, and the level of susceptibility of the chickpea cultivar.
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Qu X, Christ BJ. Single Cystosorus Isolate Production and Restriction Fragment Length Polymorphism Characterization of the Obligate Biotroph Spongospora subterranea f. sp. subterranea. PHYTOPATHOLOGY 2006; 96:1157-1163. [PMID: 18943505 DOI: 10.1094/phyto-96-1157] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
ABSTRACT Spongospora subterranea f. sp. subterranea causes powdery scab in potatoes and is distributed worldwide. Genetic studies of this pathogen have been hampered due, in part, to its obligate parasitism and the lack of molecular markers for this pathogen. In this investigation, a single cystosorus inoculation technique was developed to produce large amounts of S. subterranea f. sp. subterranea plasmodia or zoosporangia in eastern black nightshade (Solanum ptycanthum) roots from which DNA was extracted. Cryopreservation of zoosporangia was used for long-term storage of the isolates. S. subterranea f. sp. subterranea-specific restriction fragment length polymorphism (RFLP) markers were developed from randomly amplified polymorphic DNA (RAPD) fragments. Cystosori of S. subterranea f. sp. subterranea were used for RAPD assays and putative pathogen-specific RAPD fragments were cloned and sequenced. The fragments were screened for specificity by Southern hybridization and subsequent DNA sequence BLAST search. Four polymorphic S. subterranea f. sp. subterranea-specific probes containing repetitive elements, and one containing single copy DNA were identified. These RFLP probes were then used to analyze 24 single cystosorus isolates derived from eight geographic locations in the United States and Canada. Genetic variation was recorded among, but not within, geographic locations. Cluster analysis separated the isolates into two major groups: group I included isolates originating from western North America, with the exception of those from Colorado, and group II included isolates originating from eastern North America and from Colorado. The techniques developed in this study, i.e., production of single cystosorus isolates of S. subterranea f. sp. subterranea and development of RFLP markers for this pathogen, provide methods to further study the genetic structure of S. subterranea f. sp. subterranea.
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