Molecular identification of formae specialis and racial identity in Iranian strains of Fusarium oxysporum f. sp. lycopersici: detection of avirulence genes

2017 ◽  
Vol 6 (1) ◽  
pp. 67-77
Author(s):  
Elahe Rabiei-Motlagh ◽  
◽  
Hamid Rouhani ◽  
Farhad Shokouhifar ◽  
Mahrokh Falahati Rastegar ◽  
...  
Keyword(s):  
Racial Identity ◽  
Fusarium Oxysporum ◽  
Molecular Identification ◽  
Avirulence Genes

scholarly journals Multiple Evolutionary Trajectories Have Led to the Emergence of Races in Fusarium oxysporum f. sp. lycopersici

2016 ◽  
Vol 83 (4) ◽  
Author(s):  
V. Chellappan Biju ◽  
Like Fokkens ◽  
Petra M. Houterman ◽  
Martijn Rep ◽  
Ben J. C. Cornelissen
Keyword(s):  
Transposable Elements ◽  
Fusarium Oxysporum ◽  
Resistance Genes ◽  
Pcr Analysis ◽  
Genomic Fragment ◽  
Avirulence Genes ◽  
Content Type ◽  
Race 1 ◽  
Tomato Cultivars ◽  
Race 2

ABSTRACT Race 1 isolates of Fusarium oxysporum f. sp. lycopersici (FOL) are characterized by the presence of AVR1 in their genomes. The product of this gene, Avr1, triggers resistance in tomato cultivars carrying resistance gene I. In FOL race 2 and race 3 isolates, AVR1 is absent, and hence they are virulent on tomato cultivars carrying I. In this study, we analyzed an approximately 100-kb genomic fragment containing the AVR1 locus of FOL race 1 isolate 004 (FOL004) and compared it to the sequenced genome of FOL race 2 isolate 4287 (FOL4287). A genomic fragment of 31 kb containing AVR1 was found to be missing in FOL4287. Further analysis suggests that race 2 evolved from race 1 by deletion of this 31-kb fragment due to a recombination event between two transposable elements bordering the fragment. A worldwide collection of 71 FOL isolates representing races 1, 2, and 3, all known vegetative compatibility groups (VCGs), and five continents was subjected to PCR analysis of the AVR1 locus, including the two bordering transposable elements. Based on phylogenetic analysis using the EF1-α gene, five evolutionary lineages for FOL that correlate well with VCGs were identified. More importantly, we show that FOL races evolved in a stepwise manner within each VCG by the loss of function of avirulence genes in a number of alternative ways. IMPORTANCE Plant-pathogenic microorganisms frequently mutate to overcome disease resistance genes that have been introduced in crops. For the fungus Fusarium oxysporum f. sp. lycopersici, the causal agent of Fusarium wilt in tomato, we have identified the nature of the mutations that have led to the overcoming of the I and I-2 resistance genes in all five known clonal lineages, which include a newly discovered lineage. Five different deletion events, at least several of which are caused by recombination between transposable elements, have led to loss of AVR1 and overcoming of I. Two new events affecting AVR2 that led to overcoming of I-2 have been identified. We propose a reconstruction of the evolution of races in FOL, in which the same mutations in AVR2 and AVR3 have occurred in different lineages and the FOL pathogenicity chromosome has been transferred to new lineages several times.

scholarly journals Molecular Identification of Two Vegetative Compatibility Groups of Fusarium oxysporum f. sp. cepae

2012 ◽  
Vol 102 (2) ◽  
pp. 204-213 ◽  
Author(s):  
Michael J. Southwood ◽  
Altus Viljoen ◽  
Glaudina Mostert ◽  
Adéle McLeod
Keyword(s):  
South Africa ◽  
Fusarium Oxysporum ◽  
Molecular Identification ◽  
Random Amplified Polymorphic Dna ◽  
Polymerase Chain Reaction Method ◽  
Vegetative Compatibility ◽  
Molecular Characteristics ◽  
Scar Markers ◽  
Vegetative Compatibility Groups ◽  
Sequence Characterized Amplified Region

Fusarium oxysporum f. sp. cepae, which causes basal rot of onion, consists of seven vegetative compatibility groups (VCGs 0420 to 0426) and several single-member VCGs (SMVs). F. oxysporum f. sp. cepae populations in South Africa and Colorado each consist of one main VCG (namely, VCG 0425 and 0421, respectively). The aim of this study was to develop sequence-characterized amplified region (SCAR) markers for the identification of VCGs 0425 and 0421, using 79 previously characterized F. oxysporum isolates. A second aim was to investigate the prevalence of VCG 0425 among 88 uncharacterized South African onion F. oxysporum isolates using (i) the developed SCAR markers and (ii) inter-retrotransposon (IR)- and random amplified polymorphic DNA (RAPD) fingerprinting. Only two RAPD primers provided informative fingerprints for VCG 0425 isolates but these could not be developed into SCAR markers, although they provided diagnostic fragments for differentiation of VCG 0425 from VCG 0421. IR fingerprinting data were used to develop a multiplex IR-SCAR polymerase chain reaction method for the identification of VCG 0421, VCG 0425, and SMV 4 isolates as a group. Molecular identification of the uncharacterized collection of 88 F. oxysporum isolates (65 F. oxysporum f. sp. cepae and 23 F. oxysporum isolates nonpathogenic to onion) confirmed that VCG 0425 is the main VCG in South Africa, with all but 3 of the 65 F. oxysporum f. sp. cepae isolates having the molecular characteristics of this VCG. Genotyping and VCG testing showed that two of the three aforementioned isolates were new SMVs (SMV 6 and SMV 7), whereas the third (previously known as SMV 3) now belongs to VGC 0247.

scholarly journals Molecular Identification of Mating Type Genes in Asexually Reproducing Fusarium Oxysporum and F. Culmorum

2011 ◽  
Vol 51 (4) ◽  
pp. 405-409 ◽  
Author(s):  
Lidia Irzykowska ◽  
Tomasz Kosiada
Keyword(s):  
Fusarium Oxysporum ◽  
Mating Type ◽  
Molecular Identification ◽  
Dna Sequences ◽  
Control Strategies ◽  
Sexual Stage ◽  
Reproduction Mode ◽  
Successful Control ◽  
Mating Type Genes

Molecular Identification of Mating Type Genes in Asexually ReproducingFusarium OxysporumandF. CulmorumSexually (homothallic and heterothallic) and asexually reproducing species belong to theFusariumgenus. So far, there is no known sexual stage of theF. oxysporumSchlechtend.: Fr. andF. culmorum(W.G. Smith) Sacc. Knowing the reproduction mode is important for the design of successful control strategies, since they are different for clonally and sexually reproducing organisms. In examined sets of asexualF. oxysporumandF. culmorumisolates, the DNA sequences of mating type genes (idiomorphsMAT-1andMAT-2) were identified.MAT-1sequence was detected for 33 and 40% ofF. oxysporumandF. culmorumisolates, respectively. For the remaining isolates a sequence specific forMAT-2was amplified.

Molecular Determination of Mixed Infections of Dermatophytes and Nondermatophyte Molds in Individuals with Onychomycosis

2014 ◽  
Vol 104 (4) ◽  
pp. 330-336 ◽  
Author(s):  
Aditya K. Gupta ◽  
Kerry-Ann Nakrieko
Keyword(s):  
Fusarium Oxysporum ◽  
Molecular Identification ◽  
Mixed Infection ◽  
Traditional Culture ◽  
Mixed Infections ◽  
Molecular Analyses ◽  
Scopulariopsis Brevicaulis ◽  
Infecting Organisms ◽  
Molecular Determination

Background Reports of mixed infections with nondermatophyte molds (NDMs) and dermatophytes in onychomycosis are rare, possibly owing to the inhibition of NDM growth during traditional culture. We sought to determine the prevalence of mixed infections in onychomycosis using molecular identification. Methods Molecular analyses were used to identify infecting organisms directly from at least two serial great toenail samples from each of the 44 patients. Results Mixed infections were present in 41% of the patients (18 of 44). A single coinfecting NDM was the most common mixed infection and was detected in 34% of patients with onychomycosis (15 of 44), with Fusarium oxysporum present in 14% (6 of 44), Scopulariopsis brevicaulis in 9% (4 of 44), Acremonium spp in 2% (1 of 44), Aspergillus spp in 4.5% (2 of 44), and Scytalidium spp in 4.5% (2 of 44). Mixed infections with two NDMs were found in 7% of patients (3 of 44). Conclusions Mixed onychomycosis infections may be more prevalent than previously reported.

scholarly journals First Report of Fusarium oxysporum on Sweet Pepper Seedlings in Almería, Spain

Plant Disease ◽  
2014 ◽  
Vol 98 (10) ◽  
pp. 1435-1435 ◽  
Author(s):  
T. Lomas-Cano ◽  
D. Palmero-Llamas ◽  
M. de Cara ◽  
C. García-Rodríguez ◽  
A. Boix-Ruiz ◽  
...  
Keyword(s):  
Fusarium Oxysporum ◽  
Molecular Identification ◽  
Citrullus Lanatus ◽  
Fusarium Species ◽  
Phytophthora Capsici ◽  
Petri Dish ◽  
Sweet Pepper ◽  
Crown Rot ◽  
Conidial Suspension ◽  
Pepper Plants

In March of 2013, new symptoms were observed in more than seven million nursery-grown sweet pepper (Capsicum annuum) plants in El Ejido, Almería (southern Spain). Symptoms included wilting without yellowing of leaves and stunting of plants. Plant crowns exhibited necrosis that advanced through the main root along with slight root rot. Xylem was not affected above or below the crown. Symptoms were thought to be caused by the well-known pepper pathogen Phytophthora capsici. However, sporodochia of Fusarium oxysporum were observed on plant crowns. Symptomatic seedlings (n = 200) were sampled and analyzed. Tissue from roots and epidermal crowns were plated on PDA, PARP, and Komada media, as well as stem discs on PDA and Komada. No Phytophthora sp. were observed and F. oxyporum was exclusively isolated from all 200 samples, from roots and crowns, but not from xylem. Pathogenicity of 60 of these F. oxysporum isolates was studied by inoculation onto sweet pepper plants (cv. del Piquillo) at the 2-true-leaf stage. Twelve plants per isolate, grown on autoclaved vermiculite, were inoculated by drenching with 20 ml of a conidial suspension (1 × 105 CFU/ml) of each isolate per plant. Each suspension was obtained by blending one PDA petri dish fully covered with one isolate. Non-inoculated plants served as control. Plants were maintained for 30 days in a growth chamber with a 14-h photoperiod (1.6 ×·104 lux) and temperatures at 23 to 26°C. The assay was conducted twice. Symptoms described above were reproduced on crown and roots of the inoculated plants with no symptoms in stem discs. No symptoms were observed on controls after 48 days. Host specificity was tested for 13 isolates to tomato (Solanum lycopersicum) cv. San Pedro, eggplant (S. melongena) cv. Alegria, cucumber (Cucumis sativus) cv. Marketmore, watermelon (Citrullus lanatus) cv. Sugar Baby, and Chinese cabbage (Brassica campestris subsp. condensa) cv. Kasumi (4). These plants were inoculated as previously described for pathogenicity tests (12 plants per species, repeated twice). None of the plants exhibited the characteristic symptoms after 60 days. Five isolates of F. oxysporum f. sp. radicis-cucumerinum and four isolates of F. o. f. sp radicis-lycopersici were also inoculated without any symptoms in any of the inoculated sweet pepper plants. Morphological identity of all isolates corresponded to F. oxysporum. The fungi were identified following the morphological keys and methodology provided by (1) and (2). Three isolates from the 60 tested were selected for molecular identification. Molecular identification was performed by sequencing partial TEF-1α gene (3). Subsequent database searches by BLASTn indicated that the resulting sequence of 659-bp had 100% identity with the corresponding gene sequence of F. oxysporum. The sequences were identical for the three isolates and were deposited on the EMBL Sequence Database (HG916993, HG916994, and HG916995). Results suggest that the pathogenic ability of the isolates varies from a vascular Fusarium wilt. F. oxysporum f. sp. capsici is a reported pathogen to sweet pepper (5), but the symptoms we have found are closer to those manifested by the formae speciales that causes root and crown rot of other plants. Consistent with the convention stablished for similar diseases we propose the name F. oxysporum f. sp. radicis-capsici f. sp. nov. References: (1) J. F. Leslie and B. A. Summerell. The Fusarium Laboratory Manual. Blackwell, Ames, IA, 2006. (2) P. E. Nelson et al. Fusarium species. An Ilustrated Manual for Identification. The Penn St. University Press, 1983. (3) K. O'Donnell et al. Proc. Nat. Acad. Sci. 95:2044, 1998.(4) L. M. Oelke and P. W. Bosland. Capsicum Eggplant Newsl. 20:86, 2001. (5) V. C. Rivelli. M.S. Thesis. Dep. Plant Pathol. and Crop Phys. Louisiana State Univ., Baton Rouge, 1989.

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