Comparison of Fusarium oxysporum fsp lycopersici races 1, 2 and 3, and f.sp radicis lycopersici based on the sequences of fragments of the ribosomal DNA intergenic spacer region

Nonpathogenic Fusarium oxysporum endophytes from healthy banana roots were evaluated for their ability to reduce Fusarium wilt of banana (Panama disease). Isolates were identified morphologically and by using species-specific primers. Pathogenicity was confirmed by inoculating banana plantlets in the greenhouse. Nonpathogenic F. oxysporum isolates were grouped into 14 haplotype groups by polymerase chain reaction restriction fragment length polymorphism analysis of the intergenic spacer region, and representative isolates evaluated for biocontrol of F. oxysporum f. sp. cubense. In the greenhouse, 10 nonpathogenic F. oxysporum isolates were able to significantly reduce Fusarium wilt of banana. The isolate that protected banana plantlets best in the greenhouse, a nonpathogenic F. oxysporum from the root rhizosphere, and Pseudomonas fluorescens WCS 417 were then field tested. When the putative biological control organisms were tested in the field, neither the nonpathogenic F. oxysporum, P. fluorescens, nor combinations thereof reduced Fusarium wilt development significantly. A number of factors could contribute to the lack of field protection, including soil microbial and chemical composition and reduced survival of biocontrol organisms in banana roots. A lack of knowledge regarding the etiology of Fusarium wilt of ‘Cavendish’ banana in the subtropics and the effect of F. oxysporum f. sp. cubense race and banana cultivar in protection of banana by biocontrol organisms should be further investigated.

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Genetic Diversity and Population Structure of Races of Fusarium oxysporum Causing Cotton Wilt

G3 Genes|Genome|Genetics ◽

10.1534/g3.120.401187 ◽

2020 ◽

Vol 10 (9) ◽

pp. 3261-3269

Author(s):

Hannah C Halpern ◽

Peng Qi ◽

Robert C Kemerait ◽

Marin T Brewer

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Fusarium Oxysporum ◽

Principal Components ◽

Phylogenetic Trees ◽

Elongation Factor ◽

Intergenic Spacer ◽

Pathogenic Fungi ◽

The United States ◽

Intergenic Spacer Region

Abstract To better understand the evolution of virulence we are interested in identifying the genetic basis of this trait in pathogenic fungi and in developing tools for the rapid characterization of variation in virulence among populations associated with epidemics. Fusarium oxysporum f. sp. vasinfectum (FOV) is a haploid fungus that causes devastating outbreaks of Fusarium wilt of cotton wherever it is grown. In the United States, six nominal races and eleven genotypes of FOV have been characterized based on the translation elongation factor (EF-1α) gene and intergenic spacer region (IGS), but it is unclear how race or genotype based on these regions relates to population structure or virulence. We used genotyping-by-sequencing to identify SNPs and determine genetic diversity and population structure among 86 diverse FOV isolates. Six individuals of Fusarium oxysporum closely related to FOV were genotyped and included in some analyses. Between 193 and 354 SNPs were identified and included in the analyses depending on the pipeline and filtering criteria used. Phylogenetic trees, minimum spanning networks (MSNs), principal components analysis (PCA), and discriminant analysis of principal components (DAPC) demonstrated that races and genotypes of FOV are generally not structured by EF-1α genotype, nor are they monophyletic groups with the exception of race 4 isolates, which are distinct. Furthermore, DAPC identified between 11 and 14 genetically distinct clusters of FOV, whereas only eight EF-1α genotypes were represented among isolates; suggesting that FOV, especially isolates within the widely distributed and common race 1 genotype, is more genetically diverse than currently recognized.

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Host Selectivity and Genetic Variation of Discula umbrinella Isolates from Two Oak Species: Analyses of Intergenic Spacer Region Sequences of Ribosomal DNA

Microbial Ecology ◽

10.1007/s00248-006-9073-5 ◽

2006 ◽

Vol 52 (3) ◽

pp. 463-469 ◽

Cited By ~ 12

Author(s):

Susan D. Cohen

Keyword(s):

Genetic Variation ◽

Ribosomal Dna ◽

Intergenic Spacer ◽

Intergenic Spacer Region ◽

Host Selectivity

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Genetic Diversity of Fusarium oxysporum f. sp. cubense in East and Central Africa

Plant Disease ◽

10.1094/pdis-02-17-0282-re ◽

2018 ◽

Vol 102 (3) ◽

pp. 552-560 ◽

Cited By ~ 9

Author(s):

Patrick Karangwa ◽

Diane Mostert ◽

Privat Ndayihanzamaso ◽

Thomas Dubois ◽

Björn Niere ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Disease Management ◽

Fusarium Oxysporum ◽

Fusarium Wilt ◽

Management Practices ◽

Management Strategies ◽

Central Africa ◽

Elongation Factor ◽

Intergenic Spacer ◽

Intergenic Spacer Region

Banana Fusarium wilt is a major production constraint globally and a significant threat to the livelihoods of millions of people in East and Central Africa (ECA). A proper understanding of the diversity and population dynamics of the causal agent, Fusarium oxysporum f. sp. cubense (Foc), could be useful for the development of sustainable disease management strategies for the pathogen. The current study investigated the diversity of Foc in ECA using vegetative compatibility group (VCG) analysis, PCR-RFLPs of the ribosomal DNA’s intergenic spacer region, as well as phylogenetic analysis of the elongation factor-1α gene. Six VCGs (0124, 0125, 0128, 01212, 01220, and 01222), which all belong to one lineage (Foc lineage VI), were widely distributed throughout the region. VCGs 0128 and 01220 are reported for the first time in Burundi, the Democratic Republic of Congo (DRC), Rwanda, Tanzania, and Uganda, while VCG 01212 is reported in the DRC and Rwanda. Isolates that did not belong to any of the known VCGs were identified as Foc lineage VI members by phylogenetic analysis and may represent novel VCGs. CAV 2734, a banana pathogen collected in Rwanda, clustered with nonpathogenic F. oxysporum isolates in lineage VIII. Results from this study will contribute significantly toward the implementation of banana Fusarium wilt disease management practices in the region, such as the restricted movement of infected planting material and the selective planting of resistant banana varieties.

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Bartonella vinsonii subsp.berkhoffii as an Agent of Afebrile Blood Culture-Negative Endocarditis in a Human

Journal of Clinical Microbiology ◽

10.1128/jcm.38.4.1698-1700.2000 ◽

2000 ◽

Vol 38 (4) ◽

pp. 1698-1700 ◽

Cited By ~ 103

Author(s):

Véronique Roux ◽

Susannah J. Eykyn ◽

Sarah Wyllie ◽

Didier Raoult

Keyword(s):

Blood Culture ◽

Ribosomal Dna ◽

Citrate Synthase ◽

Pcr Amplification ◽

Intergenic Spacer ◽

Bacterial Identification ◽

Gene Encoding ◽

Intergenic Spacer Region ◽

16S Ribosomal Dna ◽

Culture Negative

We report a case of endocarditis in a human infected withBartonella vinsonii subsp. berkhoffii, which causes bacteremia and endocarditis in dogs. Bacterial identification was established by PCR amplification and sequencing of an intergenic spacer region (ITS1), 16S ribosomal DNA, and a gene encoding citrate synthase (gltA). Bartonella antibodies were detected by immunofluorescence.

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Simple species identification of Trichinella isolates by amplification and sequencing of the 5S ribosomal DNA intergenic spacer region

Veterinary Parasitology ◽

10.1016/j.vetpar.2005.05.026 ◽

2005 ◽

Vol 132 (1-2) ◽

pp. 57-61 ◽

Cited By ~ 14

Author(s):

Aymeric De Bruyne ◽

Hélène Yera ◽

Franck Le Guerhier ◽

Pascal Boireau ◽

Jean Dupouy-Camet

Keyword(s):

Species Identification ◽

Ribosomal Dna ◽

Intergenic Spacer ◽

Intergenic Spacer Region

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PCR amplification and characterization of the intergenic spacer region of the ribosomal DNA in Pyrenophora graminea

FEMS Microbiology Letters ◽

10.1111/j.1574-6968.1998.tb13178.x ◽

1998 ◽

Vol 166 (1) ◽

pp. 21-27 ◽

Cited By ~ 13

Author(s):

Susanna Pecchia ◽

Elisabetta Mercatelli ◽

Giovanni Vannacci

Keyword(s):

Ribosomal Dna ◽

Pcr Amplification ◽

Intergenic Spacer ◽

Intergenic Spacer Region ◽

Pyrenophora Graminea

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Conventional and real-time PCR assays for specific detection and quantification of Fusarium oxysporum f. sp. ciceris in plants using intergenic spacer region-based marker

Biologia ◽

10.1515/biolog-2015-0041 ◽

2015 ◽

Vol 70 (3) ◽

Cited By ~ 1

Author(s):

Kumari Priyanka ◽

Sunil C. Dubey ◽

Arun K. Singh

Keyword(s):

Fusarium Oxysporum ◽

Host Plant ◽

Real Time ◽

Real Time Pcr ◽

Infected Plant ◽

Intergenic Spacer ◽

Infected Host ◽

Pcr Assay ◽

Intergenic Spacer Region ◽

Plant Samples

AbstractFusarium wilt of chickpea, caused by Fusarium oxysporum f. sp. ciceris (Foc) is one of the most important fungal diseases worldwide. The detection of the pathogen at reasonable time period is of great importance, which requires rapid and sensitive detection methods. The intraspecific divergence sequences found in the intergenic spacer region (IGS) were selected and utilized with the aim to develop a molecular marker specifically to identify the Foc. A marker set, ISR52 F1 and R1 developed, was tested for their specificity as well as sensitivity using conventional as well as real-time polymerase chain reaction (PCR). The specificity of the marker was tested against Foc, other Fusarium species which are closely related to Foc as well as with artificially infected host plant samples. The detection limits of conventional PCR assay was up to 100 pg of infected plant DNA. It proved possible to amplify the IGS region in different portion of a Foc infected host plant by this PCR method. Furthermore, the real-time assay showed more sensitivity and was able to detect the pathogen in infected chickpea plant samples at the DNA concentration of 5 pg. A single melting peak obtained at 87.5°C showed the specificity of the marker towards Foc. Thus, real-time PCR assay proved their potentiality for same-day diagnosis of fungal infection and can be used as a rapid and effective procedure for routine detection and identification of Foc in chickpea samples.

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