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Sakane K, Ueno T, Shigyo M, Sasaki K, Ito SI. Pathogenicity Differentiation of Fusarium spp. Causing Fusarium Basal Rot and Wilt Disease in Allium spp. Pathogens 2024; 13:591. [PMID: 39057818 PMCID: PMC11279435 DOI: 10.3390/pathogens13070591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 07/09/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024] Open
Abstract
Here, 12 Fusarium strains, previously described as F. oxysporum f. sp. cepae (Foc), were examined via multi-locus sequencing of calmodulin (cmdA), RNA polymerase II second largest subunit (rpb2), and translation elongation factor 1-alpha (tef1), to verify the taxonomic position of Foc in the newly established epitype of F. oxysporum. The strains in this study were divided into two clades: F. nirenbergiae and Fusarium sp. To further determine the host specifications of the strains, inoculation tests were performed on onion bulbs and Welsh onion seedlings as potential hosts. Four strains (AC145, AP117, Ru-13, and TA) isolated from diseased onions commonly possessed the secreted in xylem (SIX)-3, 5, 7, 9, 10, 12, and 14 genes and were pathogenic and highly aggressive to onion bulbs, whereas all strains except for one strain (AF97) caused significant inhibition of Welsh onion growth. The inoculation test also revealed that the strains harboring the SIX9 gene were highly aggressive to both onion and Welsh onion and the gene was expressed during infection of both onions and Welsh onions, suggesting the important role of the SIX9 gene in pathogenicity. This study provides insights into the evolutionary pathogenicity differentiation of Fusarium strains causing Fusarium basal rot and wilt diseases in Allium species.
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Affiliation(s)
- Kosei Sakane
- The United Graduate School of Agricultural Sciences, Tottori University, Tottori 680-8553, Japan;
| | - Takashi Ueno
- Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yamaguchi 753-8515, Japan; (T.U.); (M.S.)
| | - Masayoshi Shigyo
- Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yamaguchi 753-8515, Japan; (T.U.); (M.S.)
| | - Kazunori Sasaki
- Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yamaguchi 753-8515, Japan; (T.U.); (M.S.)
- Research Center for Thermotolerant Microbial Resources (RCTMR), Yamaguchi University, Yamaguchi 753-8515, Japan
| | - Shin-ichi Ito
- Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yamaguchi 753-8515, Japan; (T.U.); (M.S.)
- Research Center for Thermotolerant Microbial Resources (RCTMR), Yamaguchi University, Yamaguchi 753-8515, Japan
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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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Armitage AD, Taylor A, Sobczyk MK, Baxter L, Greenfield BPJ, Bates HJ, Wilson F, Jackson AC, Ott S, Harrison RJ, Clarkson JP. Characterisation of pathogen-specific regions and novel effector candidates in Fusarium oxysporum f. sp. cepae. Sci Rep 2018; 8:13530. [PMID: 30202022 PMCID: PMC6131394 DOI: 10.1038/s41598-018-30335-7] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 07/20/2018] [Indexed: 12/21/2022] Open
Abstract
A reference-quality assembly of Fusarium oxysporum f. sp. cepae (Foc), the causative agent of onion basal rot has been generated along with genomes of additional pathogenic and non-pathogenic isolates of onion. Phylogenetic analysis confirmed a single origin of the Foc pathogenic lineage. Genome alignments with other F. oxysporum ff. spp. and non pathogens revealed high levels of syntenic conservation of core chromosomes but little synteny between lineage specific (LS) chromosomes. Four LS contigs in Foc totaling 3.9 Mb were designated as pathogen-specific (PS). A two-fold increase in segmental duplication events was observed between LS regions of the genome compared to within core regions or from LS regions to the core. RNA-seq expression studies identified candidate effectors expressed in planta, consisting of both known effector homologs and novel candidates. FTF1 and a subset of other transcription factors implicated in regulation of effector expression were found to be expressed in planta.
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Affiliation(s)
| | - Andrew Taylor
- Warwick Crop Centre, School of Life Sciences, University of Warwick, Wellesbourne, Warwick, CV35 9EF, UK
| | | | - Laura Baxter
- Warwick Crop Centre, School of Life Sciences, University of Warwick, Wellesbourne, Warwick, CV35 9EF, UK
| | | | - Helen J Bates
- NIAB-EMR, New Road, East Malling, Kent, ME19 6BJ, UK
| | - Fiona Wilson
- NIAB-EMR, New Road, East Malling, Kent, ME19 6BJ, UK
| | - Alison C Jackson
- Warwick Crop Centre, School of Life Sciences, University of Warwick, Wellesbourne, Warwick, CV35 9EF, UK
| | - Sascha Ott
- Department of Computer Science, University of Warwick, CV4 7AL, Warwick, UK
| | | | - John P Clarkson
- Warwick Crop Centre, School of Life Sciences, University of Warwick, Wellesbourne, Warwick, CV35 9EF, UK
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Taylor A, Vágány V, Jackson AC, Harrison RJ, Rainoni A, Clarkson JP. Identification of pathogenicity-related genes in Fusarium oxysporum f. sp. cepae. MOLECULAR PLANT PATHOLOGY 2016; 17:1032-47. [PMID: 26609905 PMCID: PMC4982077 DOI: 10.1111/mpp.12346] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 11/13/2015] [Accepted: 11/15/2015] [Indexed: 05/06/2023]
Abstract
Pathogenic isolates of Fusarium oxysporum, distinguished as formae speciales (f. spp.) on the basis of their host specificity, cause crown rots, root rots and vascular wilts on many important crops worldwide. Fusarium oxysporum f. sp. cepae (FOC) is particularly problematic to onion growers worldwide and is increasing in prevalence in the UK. We characterized 31 F. oxysporum isolates collected from UK onions using pathogenicity tests, sequencing of housekeeping genes and identification of effectors. In onion seedling and bulb tests, 21 isolates were pathogenic and 10 were non-pathogenic. The molecular characterization of these isolates, and 21 additional isolates comprising other f. spp. and different Fusarium species, was carried out by sequencing three housekeeping genes. A concatenated tree separated the F. oxysporum isolates into six clades, but did not distinguish between pathogenic and non-pathogenic isolates. Ten putative effectors were identified within FOC, including seven Secreted In Xylem (SIX) genes first reported in F. oxysporum f. sp. lycopersici. Two highly homologous proteins with signal peptides and RxLR motifs (CRX1/CRX2) and a gene with no previously characterized domains (C5) were also identified. The presence/absence of nine of these genes was strongly related to pathogenicity against onion and all were shown to be expressed in planta. Different SIX gene complements were identified in other f. spp., but none were identified in three other Fusarium species from onion. Although the FOC SIX genes had a high level of homology with other f. spp., there were clear differences in sequences which were unique to FOC, whereas CRX1 and C5 genes appear to be largely FOC specific.
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Affiliation(s)
- Andrew Taylor
- Warwick Crop Centre, School of Life Sciences, University of Warwick, Wellesbourne, Warwick, CV35 9EF, UK
| | - Viktória Vágány
- Warwick Crop Centre, School of Life Sciences, University of Warwick, Wellesbourne, Warwick, CV35 9EF, UK
| | - Alison C Jackson
- Warwick Crop Centre, School of Life Sciences, University of Warwick, Wellesbourne, Warwick, CV35 9EF, UK
| | | | - Alessandro Rainoni
- Warwick Crop Centre, School of Life Sciences, University of Warwick, Wellesbourne, Warwick, CV35 9EF, UK
| | - John P Clarkson
- Warwick Crop Centre, School of Life Sciences, University of Warwick, Wellesbourne, Warwick, CV35 9EF, UK
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Sasaki K, Nakahara K, Tanaka S, Shigyo M, Ito SI. Genetic and Pathogenic Variability of Fusarium oxysporum f. sp. cepae Isolated from Onion and Welsh Onion in Japan. PHYTOPATHOLOGY 2015; 105:525-32. [PMID: 25412011 DOI: 10.1094/phyto-06-14-0164-r] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Fusarium oxysporum f. sp. cepae causes Fusarium basal rot in onion (common onion) and Fusarium wilt in Welsh onion. Although these diseases have been detected in various areas in Japan, knowledge about the genetic and pathogenic variability of F. oxysporum f. sp. cepae is very limited. In this study, F. oxysporum f. sp. cepae was isolated from onion and Welsh onion grown in 12 locations in Japan, and a total of 55 F. oxysporum f. sp. cepae isolates (27 from onion and 28 from Welsh onion) were characterized based on their rDNA intergenic spacer (IGS) and translation elongation factor-1α (EF-1α) nucleotide sequences, vegetative compatibility groups (VCGs), and the presence of the SIX (secreted in xylem) homologs. Phylogenetic analysis of IGS sequences showed that these isolates were grouped into eight clades (A to H), and 20 onion isolates belonging to clade H were monophyletic and assigned to the same VCG. All the IGS-clade H isolates possessed homologs of SIX3, SIX5, and SIX7. The SIX3 homolog was located on a 4 Mb-sized chromosome in the IGS-clade H isolates. Pathogenicity tests using onion seedlings showed that all the isolates with high virulence were in the IGS-clade H. These results suggest that F. oxysporum f. sp. cepae isolates belonging to the IGS-clade H are genetically and pathogenically different from those belonging to the other IGS clades.
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Affiliation(s)
- Kazunori Sasaki
- First author: The United Graduate School of Agricultural Sciences, Tottori University, 4-101 Koyama-Minami, Tottori, 680-8553, Japan; and second, third, fourth, and fifth authors: Department of Biological and Environmental Sciences, Faculty of Agriculture, Yamaguchi University, Yamaguchi, 753-8515, Japan
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Suga H, Hirayama Y, Morishima M, Suzuki T, Kageyama K, Hyakumachi M. Development of PCR Primers to Identify Fusarium oxysporum f. sp. fragariae. PLANT DISEASE 2013; 97:619-625. [PMID: 30722188 DOI: 10.1094/pdis-07-12-0663-re] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Fusarium oxysporum f. sp. fragariae is a fungal pathogen causing Fusarium wilt on strawberry. Polymerase chain reaction (PCR) primers that can discriminate F. oxysporum f. sp. fragariae from nonpathogenic F. oxysporum would greatly assist pathogen identification. In order to develop a molecular diagnostic tool for this pathogen, transposable elements in the pathogen were characterized and used for designing a specific set of PCR primers. Portions of the transposable elements Fot3, Han, Hop, Hornet1, and Skippy were detected in all 33 strains of F. oxysporum f. sp. fragariae tested by PCR, whereas Foxy was detected in 32 strains and Impala sequences were detected in 30 strains. Two types of sequences were detected for Hop, two types for Impala, and three types for Skippy. The genomic region between Han and Skippy was amplified by an inter-retrotransposon amplified polymorphism technique, and PCR primers (FofraF and FofraR) to specifically identify F. oxysporum f. sp. fragariae were designed from this region. The developed PCR primers discriminated F. oxysporum f. sp. fragariae strains from nonpathogenic F. oxysporum strains and five other formae speciales. Conidia of F. oxysporum f. sp. fragariae could be detected in brown lowland-type soil by PCR using the primers. After preculturing the soil sample on FoG2 medium, 1 × 102 conidia/g of soil could be detected; without preculturing, 1 × 103 conidia/g of soil were detected.
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Affiliation(s)
- H Suga
- Life Science Research Center, Gifu University, Gifu 501-1193, Japan
| | - Y Hirayama
- Nara Prefectural Experiment Station, Nara 634-0813, Japan
| | - M Morishima
- Tochigi Prefectural Agricultural Experiment Station, Tochigi 320-0002 Japan
| | - T Suzuki
- Chiba Prefectural Agriculture and Forestry Research Center, Chiba 266-0006 Japan
| | - K Kageyama
- River Basin Research Center, Gifu University, 501-1193, Gifu, Japan
| | - M Hyakumachi
- Faculty of Applied Biological Science, Gifu University, 501-1193, Gifu, Japan
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Southwood MJ, Viljoen A, Mostert L, Rose LJ, McLeod A. Phylogenetic and Biological Characterization of Fusarium oxysporum Isolates Associated with Onion in South Africa. PLANT DISEASE 2012; 96:1250-1261. [PMID: 30727153 DOI: 10.1094/pdis-10-11-0820-re] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Fusarium oxysporum f. sp. cepae causes Fusarium basal rot of onion, a disease of worldwide importance. Limited information is available on the phylogenetic diversity, vegetative compatibility groups (VCGs), mating type idiomorphs, and virulence of F. oxysporum isolates associated with onion. Therefore, these characteristics were investigated in 19 F. oxysporum f. sp. cepae isolates from Colorado, 27 F. oxysporum f. sp. cepae and 33 F. oxysporum isolates nonpathogenic to onion from South Africa. Six F. oxysporum f. sp. cepae VCGs (0421 to 0426) were identified, of which three were new. The dominant VCGs in Colorado and South Africa were VCG 0421 (47% of isolates) and VCG 0425 (74%), respectively. VCG 0423 was the only VCG that was shared between the two regions. Molecular phylogenies (intergenic spacer region of the rDNA, elongation factor 1α, and mitochondrial small-subunit) confirmed the polyphyletic nature of F. oxysporum f. sp. cepae and showed that some F. oxysporum f. sp. cepae and nonpathogenic F. oxysporum isolates were genetically related. Most F. oxysporum f. sp. cepae isolates clustered into two distinct, well-supported clades. The largest clade only contained highly virulent isolates, including the two main VCGs (0421 and 0425), whereas the basal clade mostly contained moderately virulent isolates. These groupings along with the VCG data provide an important basis for selection of isolates for use in breeding programs, and for the development of molecular makers to identify VCGs. Mating type genotyping revealed the distribution of both mating type (MAT1-1 and MAT1-2) idiomorphs across phylogenetic clades, and the fact that several isolates contained both idiomorphs.
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Affiliation(s)
- Michael J Southwood
- Department of Plant Pathology, Stellenbosch University, Private Bag X1, Matieland, 7600, South Africa
| | - Altus Viljoen
- Department of Plant Pathology, Stellenbosch University, Private Bag X1, Matieland, 7600, South Africa
| | - Lizel Mostert
- Department of Plant Pathology, Stellenbosch University, Private Bag X1, Matieland, 7600, South Africa
| | - Lindy J Rose
- Department of Plant Pathology, Stellenbosch University, Private Bag X1, Matieland, 7600, South Africa
| | - Adéle McLeod
- Department of Plant Pathology, Stellenbosch University, Private Bag X1, Matieland, 7600, South Africa
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