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Sabahi F, Banihashemi Z, de Sain M, Rep M. Genome sequences of 38 Fusarium oxysporum strains. BMC Res Notes 2022; 15:229. [PMID: 35761299 PMCID: PMC9235281 DOI: 10.1186/s13104-022-06112-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 06/15/2022] [Indexed: 11/11/2022] Open
Abstract
Objective Wilt caused by Fusarium oxysporum f. sp. melonis (Fom) is one of the most widespread and destructive melon diseases worldwide. Whole-genome sequencing data of a diverse set of Fom strains, as well as several non-pathogenic strains isolated from melon from different parts of the world are described here. These data shed light on the genetic diversity, population structure and the potential evolutionary trajectories which have led to the emergence of different Fom races, and will facilitate identification of avirulence genes which will be helpful to develop resistant melon cultivars. Data description Genomic DNA was extracted from mycelium of 38 Fusarium oxysporum (Fo) strains collected from different parts of the world including Belgium, China, France, Iran, Israel, Japan, Mexico, New Zealand, Spain, the Netherlands, and the United States. The genomes were sequenced to ≈ 20 × coverage using the Illumina Hiseq Xten system, resulting in paired-end reads of 151 bp and assemblies of 1675 (Fom-18L) to 4472 (Fom-R12-13) scaffolds. The genome sequences are available in the National Center for Biotechnology Information (NCBI) and the Sequence Read Archive (SRA) under Project number PRJNA596396 and PRJNA596396, respectively. The presented data set can be useful to identify the genes associated with pathogenic strategies.
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Affiliation(s)
- Fatemeh Sabahi
- Department of Plant Protection, College of Agriculture, Shiraz University, Shiraz, Iran.,Molecular Plant Pathology, University of Amsterdam, Amsterdam, 1098 XH, The Netherlands
| | - Zia Banihashemi
- Department of Plant Protection, College of Agriculture, Shiraz University, Shiraz, Iran
| | - Mara de Sain
- Molecular Plant Pathology, University of Amsterdam, Amsterdam, 1098 XH, The Netherlands
| | - Martijn Rep
- Molecular Plant Pathology, University of Amsterdam, Amsterdam, 1098 XH, The Netherlands.
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Rivedal HM, Tabima JF, Stone AG, Johnson KB. Identity and Pathogenicity of Fungi Associated with Root, Crown, and Vascular Symptoms Related to Winter Squash Yield Decline. Plant Dis 2022; 106:1660-1668. [PMID: 34854760 DOI: 10.1094/pdis-09-20-2090-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Winter squash (Cucurbita maxima cultivar Golden Delicious) produced in Oregon's Willamette Valley for edible seed production has experienced significant yield losses because of a soilborne disease. The symptoms associated with this disease problem include root rot, crown rot, and vascular discoloration in the stems, leading to a severe late season wilt and plant collapse. Through field surveys, Fusarium oxysporum, F. solani, F. culmorum-like fungi, Plectosphaerella cucumerina, and Setophoma terrestris were identified to be associated with diseased tissues, and each produced symptoms of root rot, crown rot, or stem discoloration in preliminary pathogenicity trials. In this study, 219 isolates of these species were characterized by molecular identity analyses using BLAST of the internal transcribed spacer and translation elongation factor 1 alpha genomic regions and by pathogenicity testing in outdoor, large-container trials. Molecular identity analyses confirmed the identity of isolates at 99 to 100% similarity to reference isolates in the database. In pathogenicity experiments, F. solani produced the most severe symptoms, followed by F. culmorum-like fungi, F. oxysporum, P. cucumerina, and S. terrestris. Some treatments of mixed-species inoculum produced symptom severity greater than what was expected from individual species. In particular, the mixture of F. culmorum-like fungi, F. oxysporum, and P. cucumerina and the mixture of F. culmorum-like fungi, F. solani, and S. terrestris had symptom ratings as high as that of F. solani by itself. Results indicate that this soilborne disease is caused primarily by Fusarium solani, but interactions between the complex of F. solani, F. culmorum-like fungi, F. oxysporum, and P. cucumerina can exacerbate disease severity.
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Affiliation(s)
- Hannah M Rivedal
- Forage Seed and Cereal Research Unit, U.S. Department of Agriculture Agricultural Research Service, Corvallis, OR 97331
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331
| | - Javier F Tabima
- Department of Biology, Clark University, Worcester, MA 01610
| | - Alexandra G Stone
- Department of Horticulture, Oregon State University, Corvallis, OR 97331
| | - Kenneth B Johnson
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331
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Abstract
Indicator species analysis (ISA) uses indices of an organism's relative abundance and occurrence to estimate the strength of its associations with a priori groups of interest and a simple randomization test to evaluate the probability of association. Because ISA values tend to be greatest when a species is both relatively more abundant than other species in a particular group and it occurs more frequently in that same group (the expectations of a causal agent in diseased plants), ISA should be useful for identifying and narrowing the list of potential causal agents from a pool of pathogens in both emerging plant diseases and when the causal agent is unclear. Recent ISA plant disease applications suggests it may either directly identify a single causal agent from a pool of potential pathogens or narrow the pool of pathogens as candidates for pathogenicity tests in the process of fulfilling Koch's postulates. In this letter, we explain the underpinnings of ISA, summarize the known applications to plant pathosystems, offer caveats about the analysis, and suggest scenarios where ISA may be broadly applicable for plant disease studies.
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Affiliation(s)
- Paul M Severns
- Department of Plant Pathology, University of Georgia, Athens, GA 30602
| | - Emily M Sykes
- Department of Plant Pathology, University of Georgia, Athens, GA 30602
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Branham SE, Levi A, Katawczik M, Fei Z, Wechter WP. Construction of a genome-anchored, high-density genetic map for melon (Cucumis melo L.) and identification of Fusarium oxysporum f. sp. melonis race 1 resistance QTL. Theor Appl Genet 2018; 131:829-837. [PMID: 29372283 DOI: 10.1007/s00122-017-3039-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 12/11/2017] [Indexed: 05/22/2023]
Abstract
Four QTLs and an epistatic interaction were associated with disease severity in response to inoculation with Fusarium oxysporum f. sp. melonis race 1 in a recombinant inbred line population of melon. The USDA Cucumis melo inbred line, MR-1, harbors a wealth of alleles associated with resistance to several major diseases of melon, including powdery mildew, downy mildew, Alternaria leaf blight, and Fusarium wilt. MR-1 was crossed to an Israeli cultivar, Ananas Yok'neam, which is susceptible to all of these diseases, to generate a recombinant inbred line (RIL) population of 172 lines. In this study, the RIL population was genotyped to construct an ultra-dense genetic linkage map with 5663 binned SNPs anchored to the C. melo genome and exhibits the overall high quality of the assembly. The utility of the densely genotyped population was demonstrated through QTL mapping of a well-studied trait, resistance to Fusarium wilt caused by Fusarium oxysporum f. sp. melonis (Fom) race 1. A major QTL co-located with the previously validated resistance gene Fom-2. In addition, three minor QTLs and an epistatic interaction contributing to Fom race 1 resistance were identified. The MR-1 × AY RIL population provides a valuable resource for future QTL mapping studies and marker-assisted selection of disease resistance in melon.
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Affiliation(s)
- Sandra E Branham
- USDA, ARS, US Vegetable Laboratory, 2700 Savannah Highway, Charleston, SC, 29414, USA
| | - Amnon Levi
- USDA, ARS, US Vegetable Laboratory, 2700 Savannah Highway, Charleston, SC, 29414, USA
| | - Melanie Katawczik
- USDA, ARS, US Vegetable Laboratory, 2700 Savannah Highway, Charleston, SC, 29414, USA
| | - Zhangjun Fei
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
| | - W Patrick Wechter
- USDA, ARS, US Vegetable Laboratory, 2700 Savannah Highway, Charleston, SC, 29414, USA.
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Silvia Sebastiani M, Bagnaresi P, Sestili S, Biselli C, Zechini A, Orrù L, Cattivelli L, Ficcadenti N. Transcriptome Analysis of the Melon- Fusarium oxysporum f. sp. melonis Race 1.2 Pathosystem in Susceptible and Resistant Plants. Front Plant Sci 2017; 8:362. [PMID: 28367157 PMCID: PMC5356040 DOI: 10.3389/fpls.2017.00362] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Accepted: 03/01/2017] [Indexed: 05/20/2023]
Abstract
Fusarium oxysporum f. sp. melonis Snyd. & Hans race 1.2 (FOM1.2) is the most virulent and yield-limiting pathogen of melon (Cucumis melo L.) worldwide. Current information suggest that the resistance to race 1.2 is controlled by multiple recessive genes and strongly affected by the environment. RNA-Seq analysis was used to identify candidate resistance genes and to dissect the early molecular processes deployed during melon-FOM1.2 interaction in the resistant doubled haploid line NAD and in the susceptible genotype Charentais-T (CHT) at 24 and 48 h post-inoculation (hpi). The transcriptome analysis of the NAD-FOM1.2 interaction identified 2,461 and 821 differentially expressed genes (DEGs) at 24 hpi and at 48 hpi, respectively, while in susceptible combination CHT-FOM1.2, 882 and 2,237 DEGs were recovered at 24 hpi and at 48 hpi, respectively. The overall expression profile suggests a prompt activation of the defense responses in NAD due to its basal defense-related machinery that allows an early pathogen recognition. Gene Ontology (GO) enrichment analyses revealed a total of 57 GO terms shared by both genotypes and consistent with response to fungal infection. GO classes named "chitinase activity," "cellulase activity," "defense response, incompatible interaction," "auxin polar transport" emerged as major factors of resistance to FOM1.2. The data indicated that NAD reacts to FOM1.2 with a fine regulation of Ca2+-mediated signaling pathways, cell wall reorganization, and hormone crosstalk (jasmonate and ethylene, auxin and abscissic acid). Several unannotated transcripts were recovered providing a basis for a further exploration of the melon resistance genes. DEGs belonging to the FOM1.2 genome were also detected in planta as a resource for the identification of potential pathogenicity factors. This work provides a broader view of the dynamic changes of the melon transcriptome triggered by FOM1.2 and highlights that the resistance response of NAD is mainly signaled by jasmonic acid and ethylene pathways mediated by ABA and auxin. The role of candidate plant and fungal responsive genes involved in the resistance is discussed.
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Affiliation(s)
- M. Silvia Sebastiani
- Research Unit for Vegetable Crops in Central Areas, Council for Agricultural Research and EconomicsAscoli Piceno, Italy
| | - Paolo Bagnaresi
- Genomics Research Centre, Council for Agricultural Research and EconomicsPiacenza, Italy
| | - Sara Sestili
- Research Unit for Vegetable Crops in Central Areas, Council for Agricultural Research and EconomicsAscoli Piceno, Italy
| | - Chiara Biselli
- Genomics Research Centre, Council for Agricultural Research and EconomicsPiacenza, Italy
| | - Antonella Zechini
- Genomics Research Centre, Council for Agricultural Research and EconomicsPiacenza, Italy
| | - Luigi Orrù
- Genomics Research Centre, Council for Agricultural Research and EconomicsPiacenza, Italy
| | - Luigi Cattivelli
- Genomics Research Centre, Council for Agricultural Research and EconomicsPiacenza, Italy
| | - Nadia Ficcadenti
- Research Unit for Vegetable Crops in Central Areas, Council for Agricultural Research and EconomicsAscoli Piceno, Italy
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Pryor SW, Gibson DM, Bergstrom GC, Walker LP. Minimization of between-well sample variance of antifungal activity using a high-throughput screening microplate bioassay. Biotechniques 2007; 42:168, 170, 172. [PMID: 17373480 DOI: 10.2144/000112328] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Ficcadenti N, Sestili S, Annibali S, Campanelli G, Belisario A, Maccaroni M, Corazza L. Resistance to Fusarium oxysporum f. sp. melonis Race 1,2 in Muskmelon Lines Nad-1 and Nad-2. Plant Dis 2002; 86:897-900. [PMID: 30818645 DOI: 10.1094/pdis.2002.86.8.897] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Of seven doubled-haploid melon lines parthenogenetically originated using irradiated pollen, two lines, Nad-1 and Nad-2, were selected for resistance to Fusarium wilt after successive inoculations with F. oxysporum f. sp. melonis race 1,2w virulent isolate. Nad-1 and Nad-2 were compared with the commercial hybrids and with the parent cvs. Isabelle and Giallo di Paceco. Evaluation of germplasm extended over a 2-year period showed a higher resistance of Nad-1 and Nad-2 plants to Fusarium oxysporum f. sp. melonis race 1,2 than other genotypes tested in this study. The resistance expressed in the two doubled-haploid lines could be due to their homozygous state that maximizes the expression of the genes for resistance already present in the parental line Isabelle. The use of this source of resistance may be exploited commercially either in rootstocks or to facilitate breeding for F1 hybrids. Future research will concentrate on the identification of genetic markers associated with resistance to race 1,2 using these doubledhaploid lines.
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Affiliation(s)
- N Ficcadenti
- Research Institute for Vegetable Crops, Via Salaria 1, 63030, Monsampolo del Tronto, Ascoli Piceno, Italy
| | - S Sestili
- Research Institute for Vegetable Crops, Via Salaria 1, 63030, Monsampolo del Tronto, Ascoli Piceno, Italy
| | - S Annibali
- Research Institute for Vegetable Crops, Via Salaria 1, 63030, Monsampolo del Tronto, Ascoli Piceno, Italy
| | - G Campanelli
- Research Institute for Vegetable Crops, Via Salaria 1, 63030, Monsampolo del Tronto, Ascoli Piceno, Italy
| | - A Belisario
- Plant Pathology Research Institute, Via C. G. Bertero 22, 00156, Rome, Italy
| | - M Maccaroni
- Plant Pathology Research Institute, Via C. G. Bertero 22, 00156, Rome, Italy
| | - L Corazza
- Plant Pathology Research Institute, Via C. G. Bertero 22, 00156, Rome, Italy
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