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Yang Y, Wang Y, Gao J, Shi Z, Chen W, Huangfu H, Li Z, Liu Y. Characterisation of Fusarium oxysporum f. sp. radicis- lycopersici in Infected Tomatoes in Inner Mongolia, China. J Fungi (Basel) 2024; 10:622. [PMID: 39330382 PMCID: PMC11433067 DOI: 10.3390/jof10090622] [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: 06/26/2024] [Revised: 08/25/2024] [Accepted: 08/29/2024] [Indexed: 09/28/2024] Open
Abstract
Fusarium crown and root rot (FCRR), caused by Fusarium oxysporum f. sp. radicis-lycopersici (FORL), is an economically important disease that affects tomatoes worldwide and has become more prevalent in China in recent years. In 2021 and 2022, tomato plants in greenhouses in Hohhot, Inner Mongolia, were observed showing symptoms of stunting, premature loss of lower leaves, and root rot. Fungal pathogens were isolated from 20 infected tomato plants and identified based on morphological observation and DNA sequencing. Twelve isolates were consistently identified as Fusarium oxysporum f. sp. radicis-lycopersici (FORL) via an analysis of the ITS, TEF-1α, and pgx4 genes. This is the first report of FORL in Inner Mongolia, China. The isolates were examined for their pathogenicity by inoculating them on tomatoes, eggplants, peppers, and chickpeas. The fungicide sensitivity of the isolates was determined. Effective concentrations for 50% growth inhibition (EC50) were measured using seven fungicides. The EC50 values of tebuconazole and prochloraz were <1.0 μg·mL-1, exhibiting the most effective inhibition among the fungicides tested. Additionally, FORL resistance screening of tomato germplasms was performed. One tomato variety was resistant to FORL, and the remaining 43 germplasm lines showed various levels of resistance. The rates of highly susceptible, moderately susceptible, susceptible, and moderately resistant germplasms accounted for 29.55%, 22.73%, 40.91%, and 4.55% of the 44 germplasms tested, respectively.
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Affiliation(s)
- Yongqing Yang
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China
| | - Yong Wang
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China
| | - Jing Gao
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China
| | - Zhidan Shi
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China
| | - Wenjin Chen
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China
| | - Haiyan Huangfu
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China
| | - Zhengnan Li
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Yan Liu
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China
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Martínez-de la Parte E, Pérez-Vicente L, Torres DE, van Westerhoven A, Meijer HJG, Seidl MF, Kema GHJ. Genetic diversity of the banana Fusarium wilt pathogen in Cuba and across Latin America and the Caribbean. Environ Microbiol 2024; 26:e16636. [PMID: 38783572 DOI: 10.1111/1462-2920.16636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 04/29/2024] [Indexed: 05/25/2024]
Abstract
Fusarium wilt of bananas (FWB) is a severe plant disease that leads to substantial losses in banana production worldwide. It remains a major concern for Cuban banana cultivation. The disease is caused by members of the soil-borne Fusarium oxysporum species complex. However, the genetic diversity among Fusarium species infecting bananas in Cuba has remained largely unexplored. In our comprehensive survey, we examined symptomatic banana plants across all production zones in the country, collecting 170 Fusarium isolates. Leveraging genotyping-by-sequencing and whole-genome comparisons, we investigated the genetic diversity within these isolates and compared it with a global Fusarium panel. Notably, typical FWB symptoms were observed in Bluggoe cooking bananas and Pisang Awak subgroups across 14 provinces. Our phylogenetic analysis revealed that F. purpurascens, F. phialophorum, and F. tardichlamydosporum are responsible for FWB in Cuba, with F. tardichlamydosporum dominating the population. Furthermore, we identified between five and seven distinct genetic clusters, with F. tardichlamydosporum isolates forming at least two subgroups. This finding underscores the high genetic diversity of Fusarium spp. contributing to FWB in the Americas. Our study sheds light on the population genetic structure and diversity of the FWB pathogen in Cuba and the broader Latin American and Caribbean regions.
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Affiliation(s)
- Einar Martínez-de la Parte
- Laboratory of Phytopathology, Wageningen University & Research, Wageningen, The Netherlands
- Instituto de Investigaciones de Sanidad Vegetal (INISAV), Ministry of Agriculture, Havana, Cuba
| | - Luis Pérez-Vicente
- Instituto de Investigaciones de Sanidad Vegetal (INISAV), Ministry of Agriculture, Havana, Cuba
| | - David E Torres
- Laboratory of Phytopathology, Wageningen University & Research, Wageningen, The Netherlands
- Theoretical Biology and Bioinformatics Group, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Anouk van Westerhoven
- Laboratory of Phytopathology, Wageningen University & Research, Wageningen, The Netherlands
- Theoretical Biology and Bioinformatics Group, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Harold J G Meijer
- BU Biointeractions and Plant Health, Wageningen Plant Research, Wageningen University & Research, Wageningen, The Netherlands
| | - Michael F Seidl
- Theoretical Biology and Bioinformatics Group, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Gert H J Kema
- Laboratory of Phytopathology, Wageningen University & Research, Wageningen, The Netherlands
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Afordoanyi DM, Diabankana RGC, Akosah YA, Validov SZ. Are formae speciales pathogens really host specific? A broadened host specificity in Fusarium oxysporum f.sp. radicis-cucumerinum. Braz J Microbiol 2022; 53:1745-1759. [PMID: 35841534 PMCID: PMC9679123 DOI: 10.1007/s42770-022-00793-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 07/04/2022] [Indexed: 01/13/2023] Open
Abstract
Phytopathogenic strains of Fusarium oxysporum Schlecht exhibit clear host specificity, which appears to be a persistent characteristic and a dependable base for the forma specialis system of these pathogens. Here, we report an altered host specificity of the F. oxysporum f.sp. radicis-cucumerinum strain V03-2 g (Forc V03-2 g) - a causative agent of cucumber root-rot, the clonal derivates of which acquired the ability to infect tomato plants. Since the clonal derivates of Forc V03-2 g with transformed host specificity preserved their ability to parasitize on cucumber plants, the changes that occurred can be classified as broadening of host specificity. To our knowledge, this is the first observation of pathogenicity changes in formae speciales of F. oxysporum. The clonal derivates acquired could be used to trace genetic determinants of the host specificity of phytopathogenic strains of F. oxysporum.
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Affiliation(s)
- Daniel Mawuena Afordoanyi
- Laboratory of Molecular Genetics and Microbiological Methods, FRC Kazan Scientific Center, Russian Academy of Sciences, Kazan, Russia ,Department of Animal Husbandry and Veterinary Medicine, Tatar Scientific Research Institute of Agrochemistry and Soil Science, FRC Kazan Scientific Center, Russian Academy of Sciences, Kazan, Russia
| | | | - Yaw Abayie Akosah
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York City, USA
| | - Shamil Zavdatovich Validov
- Laboratory of Molecular Genetics and Microbiological Methods, FRC Kazan Scientific Center, Russian Academy of Sciences, Kazan, Russia
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Development of PCR-Based Race-Specific Markers for Differentiation of Indian Fusarium oxysporum f. sp. cubense, the Causal Agent of Fusarium Wilt in Banana. J Fungi (Basel) 2022; 8:jof8010053. [PMID: 35049993 PMCID: PMC8782045 DOI: 10.3390/jof8010053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/31/2021] [Accepted: 01/03/2022] [Indexed: 12/10/2022] Open
Abstract
Fusarium wilt caused by Fusarium oxysporum f. sp. cubense (Foc), is the most lethal soil-borne fungal pathogen infecting bananas. Foc race 1 (R1) and 4 (R4) are the two most predominant races affecting the economically important Cavendish group of bananas in India. A total of seven vegetative compatibility groups (VCGs) from three pathogenic races were isolated during our field survey and were found to be highly virulent towards cv. Grande Naine. According to comparative genome analyses, these Indian Foc VCGs were diverse in genomic organization and effector gene profiles. As a result, false-positive results were obtained with currently available molecular markers. In this context, the study has been initiated to develop PCR-based molecular markers for the unambiguous identification of Indian Foc R1 and R4 isolates. Whole-genome sequences of Foc R1 (GCA_011316005.3), Foc TR4 (GCA_014282265.3), and Foc STR4 (GCA_016802205.1), as well as the reference genomes of Foc (ASM799451v1) and F. oxysporum f. sp. lycopersici (Fol; ASM14995v2), were aligned to identify unique variable regions among the Foc races. Using putative chromosome and predicted gene comparison, race-specific unique Foc virulence genes were identified. The putative lineage-specific identified genes encoding products secreted in xylem (SIX) that may be necessary for disease development in the banana. An in silico analysis was performed and primers were designed from a region where sequences were dissimilar with other races to develop a specific marker for Foc R1, R4, TR4, and STR4. These race-specific markers allowed target amplification in the characterized highly virulent Foc isolates, and did not show any cross-amplification to any other Foc races, VCGs or banana pathogens, Fusarium species, and non-pathogenic Fusarium oxysporum isolates. The study demonstrated that the molecular markers developed for all the three Foc races of India could detect the pathogen in planta and up to 0.025 pg µL−1 DNA levels. Thus, the markers developed in this study are novel and could potentially be useful for the accurate diagnosis and detection of the Indian Foc races which are important for the effective management of the disease.
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Jangir P, Mehra N, Sharma K, Singh N, Rani M, Kapoor R. Secreted in Xylem Genes: Drivers of Host Adaptation in Fusarium oxysporum. FRONTIERS IN PLANT SCIENCE 2021; 12:628611. [PMID: 33968096 PMCID: PMC8101498 DOI: 10.3389/fpls.2021.628611] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 03/01/2021] [Indexed: 05/17/2023]
Abstract
Fusarium oxysporum (Fo) is a notorious pathogen that significantly contributes to yield losses in crops of high economic status. It is responsible for vascular wilt characterized by the browning of conductive tissue, wilting, and plant death. Individual strains of Fo are host specific (formae speciales), and approximately, 150 forms have been documented so far. The pathogen secretes small effector proteins in the xylem, termed as Secreted in Xylem (Six), that contribute to its virulence. Most of these proteins contain cysteine residues in even numbers. These proteins are encoded by SIX genes that reside on mobile pathogenicity chromosomes. So far, 14 proteins have been reported. However, formae speciales vary in SIX protein profile and their respective gene sequence. Thus, SIX genes have been employed as ideal markers for pathogen identification. Acquisition of SIX-encoding mobile pathogenicity chromosomes by non-pathogenic lines, through horizontal transfer, results in the evolution of new virulent lines. Recently, some SIX genes present on these pathogenicity chromosomes have been shown to be involved in defining variation in host specificity among formae speciales. Along these lines, the review entails the variability (formae speciales, races, and vegetative compatibility groups) and evolutionary relationships among members of F. oxysporum species complex (FOSC). It provides updated information on the diversity, structure, regulation, and (a)virulence functions of SIX genes. The improved understanding of roles of SIX in variability and virulence of Fo has significant implication in establishment of molecular framework and techniques for disease management. Finally, the review identifies the gaps in current knowledge and provides insights into potential research landscapes that can be explored to strengthen the understanding of functions of SIX genes.
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Affiliation(s)
| | | | | | | | | | - Rupam Kapoor
- Department of Botany, University of Delhi, New Delhi, India
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Multilocus Sequence Analysis of Selected Housekeeping- and Pathogenicity-Related Genes in Venturia inaequalis. Pathogens 2021; 10:pathogens10040447. [PMID: 33918069 PMCID: PMC8068995 DOI: 10.3390/pathogens10040447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/06/2021] [Accepted: 04/06/2021] [Indexed: 11/17/2022] Open
Abstract
The relationship between housekeeping and pathogenicity-related genes and virulence or avirulence towards the primary Malus resistance genes (R) has not been previously studied for Venturia inaequalis fungus, the causal agent of apple scab. In this study, the sequences of two housekeeping genes encoding elongation factor alpha (EF-1α) and β-tubulin and two previously unstudied effector genes of V. inaequalis from mannosidase and glucosidase families of 100 strains collected from apple cultivars with Rvi6, Rvi1, and Rvi17 and without known scab resistance genes were submitted to the analyses. Based on the phylogenetic and diversity data, as well as recombination analyses of the sequenced regions, we assessed the phylogenetic relationships and genetic structure of the pathogen within the species and the evolutionary forces that are currently acting upon this microorganism. The topology of the obtained phylograms demonstrates the lack of a relationship between the phylogenetic position of the strain and the host cultivar and the geographical origin or race of the strain. The isolates from different hosts were differentiated but did not form diagnosable, distinct phylogenetic groups. These results suggest that the analyzed genes may be too conserved to reflect the adaptation of pathogens to apple genotypes with different R genes; thus, they do not adequately reflect race discrimination. In contrast, based on variation and gene flow estimation, genetic divergence was observed among strains virulent to apple trees containing Rvi6. The results of this study confirmed a lack of free recombination between strains and demonstrated that the analyzed regions are in linkage disequilibrium and contain non-random polymorphisms associated with the strain.
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Magdama F, Monserrate-Maggi L, Serrano L, García Onofre J, Jiménez-Gasco MDM. Genetic Diversity of Fusarium oxysporum f. sp. cubense, the Fusarium Wilt Pathogen of Banana, in Ecuador. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1133. [PMID: 32882937 PMCID: PMC7570379 DOI: 10.3390/plants9091133] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 08/27/2020] [Accepted: 08/28/2020] [Indexed: 12/23/2022]
Abstract
The continued dispersal of Fusarium oxysporum f. sp. cubense Tropical race 4 (FocTR4), a quarantine soil-borne pathogen that kills banana, has placed this worldwide industry on alert and triggered enormous pressure on National Plant Protection (NPOs) agencies to limit new incursions. Accordingly, biosecurity plays an important role while long-term control strategies are developed. Aiming to strengthen the contingency response plan of Ecuador against FocTR4, a population biology study-including phylogenetics, mating type, vegetative compatibility group (VCG), and pathogenicity testing-was performed on isolates affecting local bananas, presumably associated with race 1 of F. oxysporum f. sp. cubense (Foc). Our results revealed that Foc populations in Ecuador comprise a single clonal lineage, associated with VCG0120. The lack of diversity observed in Foc populations is consistent with a single introduction event from which secondary outbreaks originated. The predominance of VCG0120, together with previous reports of its presence in Latin America countries, suggests this group as the main cause of the devastating Fusarium wilt epidemics that occurred in the 1950s associated to the demise of 'Gros Michel' bananas in the region. The isolates sampled from Ecuador caused disease in cultivars that are susceptible to races 1 and 2 under greenhouse experiments, although Fusarium wilt symptoms in the field were only found in 'Gros Michel'. Isolates belonging to the same VCG0120 have historically caused disease on Cavendish cultivars in the subtropics. Overall, this study shows how Foc can be easily dispersed to other areas if restriction of contaminated materials is not well enforced. We highlight the need of major efforts on awareness and monitoring campaigns to analyze suspected cases and to contain potential first introduction events of FocTR4 in Ecuador.
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Affiliation(s)
- Freddy Magdama
- Facultad de Ciencias de la Vida, Escuela Superior Politécnica del Litoral, Campus Gustavo Galindo Km. 30.5 Vía Perimetral, Guayaquil 09015863, Ecuador;
- Centro de Investigaciones Biotecnológicas del Ecuador, Escuela Superior Politécnica del Litoral, Campus Gustavo Galindo Km. 30.5 Vía Perimetral, Guayaquil E C090112, Ecuador; (L.M.-M.); (L.S.); (J.G.O.)
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Lorena Monserrate-Maggi
- Centro de Investigaciones Biotecnológicas del Ecuador, Escuela Superior Politécnica del Litoral, Campus Gustavo Galindo Km. 30.5 Vía Perimetral, Guayaquil E C090112, Ecuador; (L.M.-M.); (L.S.); (J.G.O.)
| | - Lizette Serrano
- Centro de Investigaciones Biotecnológicas del Ecuador, Escuela Superior Politécnica del Litoral, Campus Gustavo Galindo Km. 30.5 Vía Perimetral, Guayaquil E C090112, Ecuador; (L.M.-M.); (L.S.); (J.G.O.)
| | - José García Onofre
- Centro de Investigaciones Biotecnológicas del Ecuador, Escuela Superior Politécnica del Litoral, Campus Gustavo Galindo Km. 30.5 Vía Perimetral, Guayaquil E C090112, Ecuador; (L.M.-M.); (L.S.); (J.G.O.)
| | - María del Mar Jiménez-Gasco
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA 16802, USA
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Ye Q, Wang R, Ruan M, Yao Z, Cheng Y, Wan H, Li Z, Yang Y, Zhou G. Genetic Diversity and Identification of Wilt and Root Rot Pathogens of Tomato in China. PLANT DISEASE 2020; 104:1715-1724. [PMID: 32293997 DOI: 10.1094/pdis-09-19-1873-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Fungal wilt and root rot diseases affecting tomato have become prevalent in China in recent years and have caused considerable damage. In 2016 to 2018, symptoms of putative wilt and root rot diseases were observed in several locations in tomato cultivars with resistance to Fusarium oxysporum f. sp. lycopersici races 1 and 2. The objective of this study was to identify the causative agents of wilt and root rot of tomato in China and provide a basis for disease prevention and resistance breeding programs. Based on DNA sequence analyses of the internal transcribed spacer (ITS) region, 91 isolates from the roots of tomato plants showing symptoms of wilt and root rot were identified, including F. oxysporum (64 isolates), Fusarium solani (11 isolates), Fusarium proliferatum (2 isolates), Fusarium graminearum (2 isolates), Fusarium equiseti (1 isolate), Pythium aphanidermatum (6 isolates), Ascomycota sp. (2 isolates), and Plectosphaerella cucumerina (3 isolates). F. oxysporum accounted for 70.33% of the isolates obtained. In this case, using PCR-based methods for differentiation of F. oxysporum, we identified several formae speciales and races of F. oxysporum: 7 isolates were identified as F. oxysporum f. sp. lycopersici race 1, 2 isolates as F. oxysporum f. sp. lycopersici race 2, 35 isolates as F. oxysporum f. sp. lycopersici race 3, and 13 isolates as F. oxysporum f. sp. radicis-lycopersici. Pathogenicity tests revealed 55 isolates of tomato wilt and root rot pathogens to be virulent. This study demonstrated that F. oxysporum f. sp. lycopersici race 3 was the most widespread and highly virulent race among these tomato pathogens in China, followed by F. oxysporum f. sp. radicis-lycopersici. Therefore, the development of resistant varieties of tomato against F. oxysporum f. sp. lycopersici race 3 and F. oxysporum f. sp. radicis-lycopersici would aid efforts to develop effective disease management strategies.
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Affiliation(s)
- Qingjing Ye
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021 Zhejiang, China
| | - Rongqing Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021 Zhejiang, China
| | - Meiying Ruan
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021 Zhejiang, China
| | - Zhuping Yao
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021 Zhejiang, China
| | - Yuan Cheng
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021 Zhejiang, China
| | - Hongjian Wan
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021 Zhejiang, China
| | - Zhimiao Li
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021 Zhejiang, China
| | - Yuejian Yang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021 Zhejiang, China
| | - Guozhi Zhou
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021 Zhejiang, China
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Srinivas C, Nirmala Devi D, Narasimha Murthy K, Mohan CD, Lakshmeesha TR, Singh B, Kalagatur NK, Niranjana SR, Hashem A, Alqarawi AA, Tabassum B, Abd Allah EF, Chandra Nayaka S. Fusarium oxysporum f. sp. lycopersici causal agent of vascular wilt disease of tomato: Biology to diversity- A review. Saudi J Biol Sci 2019; 26:1315-1324. [PMID: 31762590 PMCID: PMC6864208 DOI: 10.1016/j.sjbs.2019.06.002] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 06/01/2019] [Accepted: 06/02/2019] [Indexed: 01/01/2023] Open
Abstract
Tomato (Lycopersicon esculentum) is one of the widely grown vegetables worldwide. Fusarium oxysporum f. sp. lycopersici (FOL) is the significant contributory pathogen of tomato vascular wilt. The initial symptoms of the disease appear in the lower leaves gradually, trail by wilting of the plants. It has been reported that FOL penetrates the tomato plant, colonizing and leaving the vascular tissue dark brown, and this discoloration extends to the apex, leading to the plants wilting, collapsing and dying. Therefore, it has been widely accepted that wilting caused by this fungus is the result of a combination of various physiological activities, including the accumulation of fungal mycelia in and around xylem, mycotoxin production, inactivation of host defense, and the production of tyloses; however, wilting symptoms are variable. Therefore, the selection of molecular markers may be a more effective means of screening tomato races. Several studies on the detection of FOL have been carried out and have suggested the potency of the technique for diagnosing FOL. This review focuses on biology and variability of FOL, understanding and presenting a holistic picture of the vascular wilt disease of tomato in relation to disease model, biology, virulence. We conclude that genomic and proteomic approachesare greater tools for identification of informative candidates involved in pathogenicity, which can be considered as one of the approaches in managing the disease.
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Affiliation(s)
- C Srinivas
- Department of Studies in Microbiology and Biotechnology, Bangalore University, Bengaluru, Karnataka, India
| | - D Nirmala Devi
- Department of Microbiology, Ramaiah College of Arts, Science and Commerce, Bengaluru, Karnataka, India
| | - K Narasimha Murthy
- Department of Studies in Biotechnology, University of Mysore, Manasagangotri, Mysore,India
| | | | - T R Lakshmeesha
- Department of Studies in Biotechnology, University of Mysore, Manasagangotri, Mysore,India
| | | | - Naveen Kumar Kalagatur
- Department of Immunology and Toxicology, DRDO-BU-Centre for Life Sciences, Coimbatore, India
| | - S R Niranjana
- Department of Studies in Biotechnology, University of Mysore, Manasagangotri, Mysore,India
| | - Abeer Hashem
- Plant Production Department, College of Food and Agriculture Science, King SaudUniversity, P.O. Box 2460, Riyadh 11451, Saudi Arabia
| | - Abdulaziz A Alqarawi
- Plant Production Department, College of Food and Agriculture Science, King SaudUniversity, P.O. Box 2460, Riyadh 11451, Saudi Arabia
| | - Baby Tabassum
- Toxicology Laboratory, Department of Zoology, Govt. Raza P.G. College Rampur, 244901 U.P., India
| | - Elsayed Fathi Abd Allah
- Plant Production Department, College of Food and Agriculture Science, King SaudUniversity, P.O. Box 2460, Riyadh 11451, Saudi Arabia
| | - S Chandra Nayaka
- Department of Studies in Biotechnology, University of Mysore, Manasagangotri, Mysore,India
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Edel-Hermann V, Lecomte C. Current Status of Fusarium oxysporum Formae Speciales and Races. PHYTOPATHOLOGY 2019; 109:512-530. [PMID: 30461350 DOI: 10.1094/phyto-08-18-0320-rvw] [Citation(s) in RCA: 139] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The Fusarium oxysporum species complex includes both plant pathogenic and nonpathogenic strains, which are commonly found in soils. F. oxysporum has received considerable attention from plant pathologists for more than a century owing to its broad host range and the economic losses it causes. The narrow host specificity of pathogenic strains has led to the concept of formae speciales, each forma specialis grouping strains with the same host range. Initially restricted to one plant species, this host range was later found to be broader for many formae speciales. In addition, races were identified in some formae speciales, generally with cultivar-level specialization. In 1981, Armstrong and Armstrong listed 79 F. oxysporum formae speciales and mentioned races in 16 of them. Since then, the known host range of F. oxysporum has considerably increased, and many new formae speciales and races have been identified. We carried out a comprehensive search of the literature to propose this review of F. oxysporum formae speciales and races. We recorded 106 well-characterized formae speciales, together with 37 insufficiently documented ones, and updated knowledge on races and host ranges. We also recorded 58 plant species/genera susceptible to F. oxysporum but for which a forma specialis has not been characterized yet. This review raises issues regarding the nomenclature and the description of F. oxysporum formae speciales and races.
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Affiliation(s)
- V Edel-Hermann
- Agroécologie, AgroSup Dijon, INRA, University of Bourgogne Franche-Comté, F-21000 Dijon, France
| | - C Lecomte
- Agroécologie, AgroSup Dijon, INRA, University of Bourgogne Franche-Comté, F-21000 Dijon, France
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11
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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: 83] [Impact Index Per Article: 13.8] [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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Tremblay ÉD, Duceppe MO, Bérubé JA, Kimoto T, Lemieux C, Bilodeau GJ. Screening for Exotic Forest Pathogens to Increase Survey Capacity Using Metagenomics. PHYTOPATHOLOGY 2018; 108:1509-1521. [PMID: 29923801 DOI: 10.1094/phyto-02-18-0028-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Anthropogenic activities have a major impact on the global environment. Canada's natural resources are threatened by the spread of fungal pathogens, which is facilitated by agricultural practices and international trade. Fungi are introduced to new environments and sometimes become established, in which case they can cause disease outbreaks resulting in extensive forest decline. Here, we describe how a nationwide sample collection strategy coupled to next-generation sequencing (NGS) (i.e., metagenomics) can achieve fast and comprehensive screening for exotic invasive species. This methodology can help provide guidance to phytopathology stakeholders such as regulatory agencies. Several regulated invasive species were monitored by processing field samples collected over 3 years (2013 to 2015) near high-risk areas across Canada. Fifteen sequencing runs were required on the Ion Torrent platform to process 398 samples that yielded 45 million reads. High-throughput screening of fungal and oomycete operational taxonomic units using customized fungi-specific ribosomal internal transcribed spacer 1 barcoded primers was performed. Likewise, Phytophthora-specific barcoded primers were used to amplify the adenosine triphosphate synthase subunit 9-nicotinamide adenine dinucleotide dehydrogenase subunit 9 spacer. Several Phytophthora spp. were detected by NGS and confirmed by species-specific quantitative polymerase chain reaction (qPCR) assays. The target species Heterobasidion annosum sensu stricto could be detected only through metagenomics. We demonstrated that screening target species using a variety of sampling techniques and NGS-the results of which were validated by qPCR-has the potential to increase survey capacity and detection sensitivity, reduce hands-on time and costs, and assist regulatory agencies to identify ports of entry. Considering that early detection and prevention are the keys in mitigating invasive species damage, our method represents a substantial asset in plant pathology management.
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Affiliation(s)
- Émilie D Tremblay
- First, second, and sixth authors: Canadian Food Inspection Agency (CFIA), 3851 Fallowfield Road, Ottawa, Ontario, K2H 8P9, Canada; third author: Natural Resources Canada, Laurentian Forestry Centre, 1055 Du P.E.P.S. Street, P.O. Box 10380 Québec, Québec, G1V 4C7, Canada; fourth author: CFIA, 4321 Still Creek Dr, Burnaby, British Columbia, V5C 6S7, Canada; and fifth author: Institut de biologie intégrative et des systèmes, 1030 avenue de la Médecine, Québec, Québec, G1V 0A6, Canada
| | - Marc-Olivier Duceppe
- First, second, and sixth authors: Canadian Food Inspection Agency (CFIA), 3851 Fallowfield Road, Ottawa, Ontario, K2H 8P9, Canada; third author: Natural Resources Canada, Laurentian Forestry Centre, 1055 Du P.E.P.S. Street, P.O. Box 10380 Québec, Québec, G1V 4C7, Canada; fourth author: CFIA, 4321 Still Creek Dr, Burnaby, British Columbia, V5C 6S7, Canada; and fifth author: Institut de biologie intégrative et des systèmes, 1030 avenue de la Médecine, Québec, Québec, G1V 0A6, Canada
| | - Jean A Bérubé
- First, second, and sixth authors: Canadian Food Inspection Agency (CFIA), 3851 Fallowfield Road, Ottawa, Ontario, K2H 8P9, Canada; third author: Natural Resources Canada, Laurentian Forestry Centre, 1055 Du P.E.P.S. Street, P.O. Box 10380 Québec, Québec, G1V 4C7, Canada; fourth author: CFIA, 4321 Still Creek Dr, Burnaby, British Columbia, V5C 6S7, Canada; and fifth author: Institut de biologie intégrative et des systèmes, 1030 avenue de la Médecine, Québec, Québec, G1V 0A6, Canada
| | - Troy Kimoto
- First, second, and sixth authors: Canadian Food Inspection Agency (CFIA), 3851 Fallowfield Road, Ottawa, Ontario, K2H 8P9, Canada; third author: Natural Resources Canada, Laurentian Forestry Centre, 1055 Du P.E.P.S. Street, P.O. Box 10380 Québec, Québec, G1V 4C7, Canada; fourth author: CFIA, 4321 Still Creek Dr, Burnaby, British Columbia, V5C 6S7, Canada; and fifth author: Institut de biologie intégrative et des systèmes, 1030 avenue de la Médecine, Québec, Québec, G1V 0A6, Canada
| | - Claude Lemieux
- First, second, and sixth authors: Canadian Food Inspection Agency (CFIA), 3851 Fallowfield Road, Ottawa, Ontario, K2H 8P9, Canada; third author: Natural Resources Canada, Laurentian Forestry Centre, 1055 Du P.E.P.S. Street, P.O. Box 10380 Québec, Québec, G1V 4C7, Canada; fourth author: CFIA, 4321 Still Creek Dr, Burnaby, British Columbia, V5C 6S7, Canada; and fifth author: Institut de biologie intégrative et des systèmes, 1030 avenue de la Médecine, Québec, Québec, G1V 0A6, Canada
| | - Guillaume J Bilodeau
- First, second, and sixth authors: Canadian Food Inspection Agency (CFIA), 3851 Fallowfield Road, Ottawa, Ontario, K2H 8P9, Canada; third author: Natural Resources Canada, Laurentian Forestry Centre, 1055 Du P.E.P.S. Street, P.O. Box 10380 Québec, Québec, G1V 4C7, Canada; fourth author: CFIA, 4321 Still Creek Dr, Burnaby, British Columbia, V5C 6S7, Canada; and fifth author: Institut de biologie intégrative et des systèmes, 1030 avenue de la Médecine, Québec, Québec, G1V 0A6, Canada
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Devran Z, Kahveci E, Hong Y, Studholme DJ, Tör M. Identifying molecular markers suitable for Frl selection in tomato breeding. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:2099-2105. [PMID: 29982848 PMCID: PMC6154021 DOI: 10.1007/s00122-018-3136-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 06/21/2018] [Indexed: 05/31/2023]
Abstract
Modern plant breeding heavily relies on the use of molecular markers. In recent years, next generation sequencing (NGS) emerged as a powerful technology to discover DNA sequence polymorphisms and generate molecular markers very rapidly and cost effectively, accelerating the plant breeding programmes. A single dominant locus, Frl, in tomato provides resistance to the fungal pathogen Fusarium oxysporum f. sp. radicis-lycopersici (FORL), causative agent of Fusarium crown and root rot. In this study, we describe the generation of molecular markers associated with the Frl locus. An F2 mapping population between an FORL resistant and a susceptible cultivar was generated. NGS technology was then used to sequence the genomes of a susceptible and a resistant parent as well the genomes of bulked resistant and susceptible F2 lines. We zoomed into the Frl locus and mapped the locus to a 900 kb interval on chromosome 9. Polymorphic single-nucleotide polymorphisms (SNPs) within the interval were identified and markers co-segregating with the resistant phenotype were generated. Some of these markers were tested successfully with commercial tomato varieties indicating that they can be used for marker-assisted selection in large-scale breeding programmes.
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Affiliation(s)
- Zübeyir Devran
- Faculty of Agriculture, Department of Plant Protection, University of Akdeniz, Antalya, Turkey
| | - Erdem Kahveci
- Department of Plant Pathology, M.Y. Genetik Agriculture Technology Laboratory, Antalya, Turkey
| | - Yiguo Hong
- College of Life and Environmental Sciences, Research Centre for Plant RNA Signaling, Hangzhou Normal University, Hangzhou, China
- Institute of Science and the Environment, University of Worcester, Worcester, WR2 6AJ, UK
| | - David J Studholme
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Mahmut Tör
- Institute of Science and the Environment, University of Worcester, Worcester, WR2 6AJ, UK.
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Pastrana AM, Kirkpatrick SC, Kong M, Broome JC, Gordon TR. Fusarium oxysporum f. sp. mori, a New Forma Specialis Causing Fusarium Wilt of Blackberry. PLANT DISEASE 2017; 101:2066-2072. [PMID: 30677374 DOI: 10.1094/pdis-03-17-0428-re] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Fusarium oxysporum has recently been identified as the cause of a wilt disease affecting blackberry in California and Mexico. Thirty-six isolates of F. oxysporum obtained from symptomatic blackberry plants in California and Mexico were comprised of nine distinct somatic compatibility groups (SCGs). Phylogenetic analysis of a concatenated data set, consisting of sequences of the translation elongation factor 1-α and β-tubulin genes and the intergenic spacer of the ribosomal DNA, identified nine three-locus sequence types, each of which corresponded to an SCG. Six SCGs were present only in California, two only in Mexico, and one in both California and Mexico. An isolate associated with the most common SCG in California was tested for pathogenicity on blueberry, raspberry, strawberry, and lettuce. All blueberry, raspberry, and lettuce plants that were inoculated remained healthy, but two of the five strawberry cultivars tested developed symptoms. The three strawberry cultivars that were resistant to the blackberry pathogen were also resistant to F. oxysporum f. sp. fragariae, the cause of Fusarium wilt of strawberry. We propose to designate strains of F. oxysporum that are pathogenic to blackberry as Fusarium oxysporum f. sp. mori forma specialis nov.
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Affiliation(s)
- A M Pastrana
- Department of Plant Pathology, University of California, Davis 95616
| | - S C Kirkpatrick
- Department of Plant Pathology, University of California, Davis 95616
| | - M Kong
- Driscoll's Inc., Watsonville, CA 95076
| | | | - T R Gordon
- Department of Plant Pathology, University of California, Davis 95616
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Zhang Y, Ma LJ. Deciphering Pathogenicity of Fusarium oxysporum From a Phylogenomics Perspective. ADVANCES IN GENETICS 2017; 100:179-209. [PMID: 29153400 DOI: 10.1016/bs.adgen.2017.09.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Fusarium oxysporum is a large species complex of both plant and human pathogens that attack a diverse array of species in a host-specific manner. Comparative genomic studies have revealed that the host-specific pathogenicity of the F. oxysporum species complex (FOSC) was determined by distinct sets of supernumerary (SP) chromosomes. In contrast to common vertical transfer, where genetic materials are transmitted via cell division, SP chromosomes can be transmitted horizontally between phylogenetic lineages, explaining the polyphyletic nature of the host-specific pathogenicity of the FOSC. The existence of a diverse array of SP chromosomes determines the broad host range of this species complex, while the conserved core genome maintains essential house-keeping functions. Recognition of these SP chromosomes enables the functional and structural compartmentalization of F. oxysporum genomes. In this review, we examine the impact of this group of cross-kingdom pathogens on agricultural productivity and human health. Focusing on the pathogenicity of F. oxysporum in the phylogenomic framework of the genus Fusarium, we elucidate the evolution of pathogenicity within the FOSC. We conclude that a population genomics approach within a clearly defined phylogenomic framework is essential not only for understanding the evolution of the pathogenicity mechanism but also for identifying informative candidates associated with pathogenicity that can be developed as targets in disease management programs.
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Affiliation(s)
- Yong Zhang
- University of Massachusetts Amherst, Amherst, MA, United States
| | - Li-Jun Ma
- University of Massachusetts Amherst, Amherst, MA, United States.
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16
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Jelinski NA, Broz K, Jonkers W, Ma LJ, Kistler HC. Effector Gene Suites in Some Soil Isolates of Fusarium oxysporum Are Not Sufficient Predictors of Vascular Wilt in Tomato. PHYTOPATHOLOGY 2017; 107:842-851. [PMID: 28323535 DOI: 10.1094/phyto-12-16-0437-r] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Seventy-four Fusarium oxysporum soil isolates were assayed for known effector genes present in an F. oxysporum f. sp. lycopersici race 3 tomato wilt strain (FOL MN-25) obtained from the same fields in Manatee County, Florida. Based on the presence or absence of these genes, four haplotypes were defined, two of which represented 96% of the surveyed isolates. These two most common effector haplotypes contained either all or none of the assayed race 3 effector genes. We hypothesized that soil isolates with all surveyed effector genes, similar to FOL MN-25, would be pathogenic toward tomato, whereas isolates lacking all effectors would be nonpathogenic. However, inoculation experiments revealed that presence of the effector genes alone was not sufficient to ensure pathogenicity on tomato. Interestingly, a nonpathogenic isolate containing the full suite of unmutated effector genes (FOS 4-4) appears to have undergone a chromosomal rearrangement yet remains vegetatively compatible with FOL MN-25. These observations confirm the highly dynamic nature of the F. oxysporum genome and support the conclusion that pathogenesis among free-living populations of F. oxysporum is a complex process. Therefore, the presence of effector genes alone may not be an accurate predictor of pathogenicity among soil isolates of F. oxysporum.
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Affiliation(s)
- Nicolas A Jelinski
- First author: Department of Soil, Water and Climate, University of Minnesota-Twin Cities, 1991 Upper Buford Circle, Saint Paul 55108; second and fifth authors: U.S. Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory, 1551 Lindig Street, University of Minnesota-Twin Cities, Saint Paul 55108; third author: Bejo Zaden BV, Trambaan 1, 1749CZ Warmenhuizen, The Netherlands; and fourth author: Department of Biochemistry and Molecular Biology, University of Massachusetts-Amherst, Amherst 01003
| | - Karen Broz
- First author: Department of Soil, Water and Climate, University of Minnesota-Twin Cities, 1991 Upper Buford Circle, Saint Paul 55108; second and fifth authors: U.S. Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory, 1551 Lindig Street, University of Minnesota-Twin Cities, Saint Paul 55108; third author: Bejo Zaden BV, Trambaan 1, 1749CZ Warmenhuizen, The Netherlands; and fourth author: Department of Biochemistry and Molecular Biology, University of Massachusetts-Amherst, Amherst 01003
| | - Wilfried Jonkers
- First author: Department of Soil, Water and Climate, University of Minnesota-Twin Cities, 1991 Upper Buford Circle, Saint Paul 55108; second and fifth authors: U.S. Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory, 1551 Lindig Street, University of Minnesota-Twin Cities, Saint Paul 55108; third author: Bejo Zaden BV, Trambaan 1, 1749CZ Warmenhuizen, The Netherlands; and fourth author: Department of Biochemistry and Molecular Biology, University of Massachusetts-Amherst, Amherst 01003
| | - Li-Jun Ma
- First author: Department of Soil, Water and Climate, University of Minnesota-Twin Cities, 1991 Upper Buford Circle, Saint Paul 55108; second and fifth authors: U.S. Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory, 1551 Lindig Street, University of Minnesota-Twin Cities, Saint Paul 55108; third author: Bejo Zaden BV, Trambaan 1, 1749CZ Warmenhuizen, The Netherlands; and fourth author: Department of Biochemistry and Molecular Biology, University of Massachusetts-Amherst, Amherst 01003
| | - H Corby Kistler
- First author: Department of Soil, Water and Climate, University of Minnesota-Twin Cities, 1991 Upper Buford Circle, Saint Paul 55108; second and fifth authors: U.S. Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory, 1551 Lindig Street, University of Minnesota-Twin Cities, Saint Paul 55108; third author: Bejo Zaden BV, Trambaan 1, 1749CZ Warmenhuizen, The Netherlands; and fourth author: Department of Biochemistry and Molecular Biology, University of Massachusetts-Amherst, Amherst 01003
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17
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18
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Nirmaladevi D, Venkataramana M, Srivastava RK, Uppalapati SR, Gupta VK, Yli-Mattila T, Clement Tsui KM, Srinivas C, Niranjana SR, Chandra NS. Molecular phylogeny, pathogenicity and toxigenicity of Fusarium oxysporum f. sp. lycopersici. Sci Rep 2016; 6:21367. [PMID: 26883288 PMCID: PMC4756691 DOI: 10.1038/srep21367] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 01/19/2016] [Indexed: 11/09/2022] Open
Abstract
The present study aimed at the molecular characterization of pathogenic and non pathogenic F. oxysporum f. sp. lycopersici strains isolated from tomato. The causal agent isolated from symptomatic plants and soil samples was identified based on morphological and molecular analyses. Pathogenicity testing of 69 strains on five susceptible tomato varieties showed 45% of the strains were highly virulent and 30% were moderately virulent. Molecular analysis based on the fingerprints obtained through ISSR indicated the presence of wide genetic diversity among the strains. Phylogenetic analysis based on ITS sequences showed the presence of at least four evolutionary lineages of the pathogen. The clustering of F. oxysporum with non pathogenic isolates and with the members of other formae speciales indicated polyphyletic origin of F. oxysporum f. sp. lycopersici. Further analysis revealed intraspecies variability and nucleotide insertions or deletions in the ITS region among the strains in the study and the observed variations were found to be clade specific. The high genetic diversity in the pathogen population demands for development of effective resistance breeding programs in tomato. Among the pathogenic strains tested, toxigenic strains harbored the Fum1 gene clearly indicating that the strains infecting tomato crops have the potential to produce Fumonisin.
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Affiliation(s)
- D. Nirmaladevi
- Department of Microbiology and Biotechnology, Jnanabarathi Campus, Bangalore University, Bangalore, Karnataka, India
| | - M. Venkataramana
- DRDO-BU-CLS, Barathiar University Campus, Coimbatore, Tamil Nadu, India
| | - Rakesh K. Srivastava
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - S. R. Uppalapati
- Defence Food Research Laboratory, Siddarthanagar, Mysore, Karnataka, India
| | - Vijai Kumar Gupta
- Molecular Glycobiotechnology Group, Discipline of Biochemistry, School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - T. Yli-Mattila
- Molecular Plant Biology, Department of Biochemistry, University of Turku, FI-20014 Turku, Finland
| | - K. M. Clement Tsui
- Department of Pathology and Laboratory Medicine, The University of British Columbia, Canada
| | - C. Srinivas
- Department of Microbiology and Biotechnology, Jnanabarathi Campus, Bangalore University, Bangalore, Karnataka, India
| | - S. R. Niranjana
- DOS in Biotechnology, University of Mysore, Manasagangothri, Mysore, Karnataka, India
| | - Nayaka S. Chandra
- DOS in Biotechnology, University of Mysore, Manasagangothri, Mysore, Karnataka, India
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Nagrale DT, Sharma L, Kumar S, Gawande SP. Recent Diagnostics and Detection Tools: Implications for Plant Pathogenic Alternaria and Their Disease Management. Fungal Biol 2016. [DOI: 10.1007/978-3-319-27312-9_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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20
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Schmidt SM, Lukasiewicz J, Farrer R, van Dam P, Bertoldo C, Rep M. Comparative genomics of Fusarium oxysporum f. sp. melonis reveals the secreted protein recognized by the Fom-2 resistance gene in melon. THE NEW PHYTOLOGIST 2016; 209:307-18. [PMID: 26305378 PMCID: PMC5769816 DOI: 10.1111/nph.13584] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 06/29/2015] [Indexed: 05/06/2023]
Abstract
Development of resistant crops is the most effective way to control plant diseases to safeguard food and feed production. Disease resistance is commonly based on resistance genes, which generally mediate the recognition of small proteins secreted by invading pathogens. These proteins secreted by pathogens are called 'avirulence' proteins. Their identification is important for being able to assess the usefulness and durability of resistance genes in agricultural settings. We have used genome sequencing of a set of strains of the melon wilt fungus Fusarium oxysporum f. sp. melonis (Fom), bioinformatics-based genome comparison and genetic transformation of the fungus to identify AVRFOM2, the gene that encodes the avirulence protein recognized by the melon Fom-2 gene. Both an unbiased and a candidate gene approach identified a single candidate for the AVRFOM2 gene. Genetic complementation of AVRFOM2 in three different race 2 isolates resulted in resistance of Fom-2-harbouring melon cultivars. AvrFom2 is a small, secreted protein with two cysteine residues and weak similarity to secreted proteins of other fungi. The identification of AVRFOM2 will not only be helpful to select melon cultivars to avoid melon Fusarium wilt, but also to monitor how quickly a Fom population can adapt to deployment of Fom-2-containing cultivars in the field.
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Affiliation(s)
- Sarah Maria Schmidt
- Molecular Plant Pathology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, 1090 GE, Amsterdam, the Netherlands
| | - Joanna Lukasiewicz
- Molecular Plant Pathology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, 1090 GE, Amsterdam, the Netherlands
| | - Rhys Farrer
- Genome Sequencing and Analysis Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Peter van Dam
- Molecular Plant Pathology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, 1090 GE, Amsterdam, the Netherlands
| | - Chiara Bertoldo
- Molecular Plant Pathology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, 1090 GE, Amsterdam, the Netherlands
| | - Martijn Rep
- Molecular Plant Pathology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, 1090 GE, Amsterdam, the Netherlands
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21
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Inami K, Kashiwa T, Kawabe M, Onokubo-Okabe A, Ishikawa N, Pérez ER, Hozumi T, Caballero LA, de Baldarrago FC, Roco MJ, Madadi KA, Peever TL, Teraoka T, Kodama M, Arie T. The tomato wilt fungus Fusarium oxysporum f. sp. lycopersici shares common ancestors with nonpathogenic F. oxysporum isolated from wild tomatoes in the Peruvian Andes. Microbes Environ 2014; 29:200-10. [PMID: 24909710 PMCID: PMC4103527 DOI: 10.1264/jsme2.me13184] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Fusarium oxysporum is an ascomycetous fungus that is well-known as a soilborne plant pathogen. In addition, a large population of nonpathogenic F. oxysporum (NPF) inhabits various environmental niches, including the phytosphere. To obtain an insight into the origin of plant pathogenic F. oxysporum, we focused on the tomato (Solanum lycopersicum) and its pathogenic F. oxysporum f. sp. lycopersici (FOL). We collected F. oxysporum from wild and transition Solanum spp. and modern cultivars of tomato in Chile, Ecuador, Peru, Mexico, Afghanistan, Italy, and Japan, evaluated the fungal isolates for pathogenicity, VCG, mating type, and distribution of SIX genes related to the pathogenicity of FOL, and constructed phylogenies based on ribosomal DNA intergenic spacer sequences. All F. oxysporum isolates sampled were genetically more diverse than FOL. They were not pathogenic to the tomato and did not carry SIX genes. Certain NPF isolates including those from wild Solanum spp. in Peru were grouped in FOL clades, whereas most of the NPF isolates were not. Our results suggested that the population of NPF isolates in FOL clades gave rise to FOL by gaining pathogenicity.
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Affiliation(s)
- Keigo Inami
- Graduate school of Agriculture, Tokyo University of Agriculture and Technology
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22
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Laurence MH, Summerell BA, Burgess LW, Liew ECY. Genealogical concordance phylogenetic species recognition in the Fusarium oxysporum species complex. Fungal Biol 2014; 118:374-84. [PMID: 24742832 DOI: 10.1016/j.funbio.2014.02.002] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Revised: 02/05/2014] [Accepted: 02/07/2014] [Indexed: 12/30/2022]
Abstract
Fusarium oxysporum is an important plant and human pathogenic ascomycetous group, with near ubiquity in agricultural and non-cultivated ecosystems. Phylogenetic evidence suggests that F. oxysporum is a complex of multiple morphologically cryptic species. Species boundaries and limits of genetic exchange within this complex are poorly defined, largely due to the absence of a sexual state and the paucity of morphological characters. This study determined species boundaries within the F. oxysporum species complex using Genealogical Concordance Phylogenetic Species Recognition (GCPSR) with eight protein coding loci. GCPSR criteria were used firstly to identify independent evolutionary lineages (IEL), which were subsequently collapsed into phylogenetic species. Seventeen IELs were initially identified resulting in the recognition of two phylogenetic species. Further evidence supporting this delineation is discussed.
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Affiliation(s)
- Matthew H Laurence
- Faculty of Agriculture and Environment, The University of Sydney, NSW 2006, Australia; The Royal Botanic Gardens and Domain Trust, Mrs Macquaries Rd, Sydney, NSW 2000, Australia.
| | - Brett A Summerell
- The Royal Botanic Gardens and Domain Trust, Mrs Macquaries Rd, Sydney, NSW 2000, Australia
| | - Lester W Burgess
- Faculty of Agriculture and Environment, The University of Sydney, NSW 2006, Australia
| | - Edward C Y Liew
- The Royal Botanic Gardens and Domain Trust, Mrs Macquaries Rd, Sydney, NSW 2000, Australia
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23
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Haegi A, Catalano V, Luongo L, Vitale S, Scotton M, Ficcadenti N, Belisario A. A newly developed real-time PCR assay for detection and quantification of Fusarium oxysporum and its use in compatible and incompatible interactions with grafted melon genotypes. PHYTOPATHOLOGY 2013; 103:802-10. [PMID: 23464901 DOI: 10.1094/phyto-11-12-0293-r] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
A reliable and species-specific real-time quantitative polymerase chain reaction (qPCR) assay was developed for detection of the complex soilborne anamorphic fungus Fusarium oxysporum. The new primer pair, designed on the translation elongation factor 1-α gene with an amplicon of 142 bp, was highly specific to F. oxysporum without cross reactions with other Fusarium spp. The protocol was applied to grafted melon plants for the detection and quantification of F. oxysporum f. sp. melonis, a devastating pathogen of this cucurbit. Grafting technologies are widely used in melon to confer resistance against new virulent races of F. oxysporum f. sp. melonis, while maintaining the properties of valuable commercial varieties. However, the effects on the vascular pathogen colonization have not been fully investigated. Analyses were performed on 'Charentais-T' (susceptible) and 'Nad-1' (resistant) melon cultivars, both used either as rootstock and scion, and inoculated with F. oxysporum f. sp. melonis race 1 and race 1,2. Pathogen development was compared using qPCR and isolations from stem tissues. Early asymptomatic melon infections were detected with a quantification limit of 1 pg of fungal DNA. The qPCR protocol clearly showed that fungal development was highly affected by host-pathogen interaction (compatible or incompatible) and time (days postinoculation). The principal significant effect (P ≤ 0.01) on fungal development was due to the melon genotype used as rootstock, and this effect had a significant interaction with time and F. oxysporum f. sp. melonis race. In particular, the amount of race 1,2 DNA was significantly higher compared with that estimated for race 1 in the incompatible interaction at 18 days postinoculation. The two fungal races were always present in both the rootstock and scion of grafted plants in either the compatible or incompatible interaction.
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Affiliation(s)
- Anita Haegi
- Centro di Ricerca per la Patologia Vegetale, Rome, Italy
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Laurence MH, Burgess LW, Summerell BA, Liew ECY. High levels of diversity in Fusarium oxysporum from non-cultivated ecosystems in Australia. Fungal Biol 2011; 116:289-97. [PMID: 22289774 DOI: 10.1016/j.funbio.2011.11.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Revised: 11/22/2011] [Accepted: 11/23/2011] [Indexed: 12/22/2022]
Abstract
The Fusarium oxysporum species complex (FOSC) is a ubiquitous ascomycetous group that includes both pathogenic and non-pathogenic strains, the former being responsible for disease in over 100 cultivated plant species. Previous phylogenetic studies have uncovered at least four major clades within the FOSC, with Clade 1 hypothesised as being ancestral. However, the origin of these clades and pathogenic strains is poorly understood. Due to an emphasis on agricultural isolates in previous studies, the underlying diversity of this species complex in non-cultivated soils is largely unknown. To address this imbalance an extensive survey of isolates associated with native vegetation geographically isolated from cultivation throughout the Australian continent was conducted. A multi-gene phylogenetic analysis of the translation elongation factor (EF-1α) and the mitochondrial small subunit (mtSSU) rDNA loci did not recover any novel clades. However, the Australian isolates had high levels of intra-Clade diversity based on EF-1α sequence type (ST) comparison with a global dataset. The ST diversity was not equally distributed across the four clades, with the majority of novel STs recovered from Clade 1. Implications on the origin of the FOSC are discussed.
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Affiliation(s)
- Matthew H Laurence
- Food and Natural Resources, The University of Sydney, NSW 2006, Australia.
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