Phylogeny and molecular diagnosis of mycotoxigenic fungi

Seifert, Keith A.; Lévesque, C. André

doi:10.1007/978-1-4020-2285-2_1

Cited by 16 publications

(18 citation statements)

References 66 publications

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“…Array Designer version 1.1 (Premier Biosoft International) uses the polymorphism location to generate hybridization oligonucleotides of specific melting temperature while minimizing hairpins and dimers. Seifert & Lévesque (2004) described in detail how to perform sequential analyses to obtain oligonucleotides with various level of specificity. In the Penicillium COX1 neighbour‐joining (NJ) tree (Seifert et al .…”

Section: Methodsmentioning

confidence: 99%

A high density COX1 barcode oligonucleotide array for identification and detection of species of Penicillium subgenus Penicillium

Chen

Seifert

Lévesque

2009

Molecular Ecology Resources

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We developed a COX1 barcode oligonucleotide array based on 358 sequences, including 58 known and two new species of Penicillium subgenus Penicillium, and 12 allied species. The array was robotically spotted at near microarray density on membranes. Species and clade-specific oligonucleotides were selected using the computer programs SigOli and Array Designer. Robotic spotting allowed 768 spots with duplicate sets of perfect match and the corresponding mismatch and positive control oligonucleotides, to be printed on 2 × 6 cm 2 nylon membranes. The array was validated with hybridizations between the array and digoxigenin (DIG)-labelled COX1 polymerase chain reaction amplicons from 70 pure DNA samples, and directly from environmental samples (cheese and plants) without culturing. DNA hybridization conditions were optimized, but undesired cross-reactions were detected frequently, reflecting the relatively high sequence similarity of the COX1 gene among Penicillium species. Approximately 60% of the perfect match oligonucleotides were rejected because of low specificity and 76 delivered useful group-specific or species-specific reactions and could be used for detecting certain species of Penicillium in environmental samples. In practice, the presence of weak signals on arrays exposed to amplicons from environmental samples, which could have represented weak detections or weak cross reactions, made interpretation difficult for over half of the oligonucleotides. DNA regions with very few single nucleotide polymorphisms or lacking insertions/deletions among closely related species are not ideal for oligonucleotidebased diagnostics, and supplementing the COX1-based array with oligonucleotides derived from additional genes would result in a more robust hierarchical identification system.

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Section: Methodsmentioning

confidence: 99%

A high density COX1 barcode oligonucleotide array for identification and detection of species of Penicillium subgenus Penicillium

Chen

Seifert

Lévesque

2009

Molecular Ecology Resources

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“…Assays based on sequence-characterized amplified region (SCAR) markers for the differential detection of F. culmorum, F. graminearum, F. avenaceum, and F. poae have been developed (Nicholson et al 1998;Llorens et al 2006). Advances in the molecular characterization of genes from 'toxin clusters' had provided the potential to develop PCR assays based upon the mycotoxin biosynthetic gene sequences for the identification and characterization of fungal species and isolates (Edwards et al 2002;Seifert and Levesque 2004). In particular, the molecular characterization of the Tri-5 gene cluster, which contains most of the genes involved in trichothecene biosynthesis, has been exploited in the development of several PCR-based assays to target Fusarium species and chemotypes (Lee et al 2001;Ward et al 2002;Kimura et al 2003).…”

Section: Introductionmentioning

confidence: 99%

Assessment ofFusariuminfection in wheat heads using a quantitative polymerase chain reaction (qPCR) assay

Rossi

Terzi

Moggi

et al. 2007

Food Additives and Contaminants

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The accuracy of a quantitative polymerase chain reaction assay in quantifying the DNA of trichothecene-producing F. culmorum and F. graminearum within harvested wheat grains and head tissue was evaluated in comparison with incidences of infected kernels and deoxynivalenol levels. In a first experiment, six durum and bread wheat varieties were grown in randomized plots for a 2-year period, and inoculated with Fusarium macroconidia at six growth stages between heading and dough ripening, to obtain a wide range of Fusarium head blight incidences. There was a close relationship between fungal DNA and the amount of deoxynivalenol, and this relationship was consistent over Fusarium species, wheat species and varieties, and over a wide range of Fusarium head blight infection. In a second experiment potted wheat plants were grown under environmentally controlled conditions and inoculated with the two Fusarium species at full flowering; head samples were collected before inoculation and after 6 h to 12 days, and processed by the quantitative polymerase chain reaction assay. This assay made it possible to detect the dynamic of fungal invasion in planta after infection had occurred, and to single out the presence of infection before the onset of the disease symptoms: A robust detection of the infection occurred within 18-24 h for F. culmorum, and within 2-9 days for F. graminearum.

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“…Studies on Fusarium have shown that TEF‐1 α is a suitable genetic marker to distinguish between and within species groups (O'Donnell et al. ; Seifert and Levesque ). This gene appears to be consistently single‐copy in Fusarium , and it shows a high level of sequence polymorphism among closely related species even in comparison with the intron‐rich portions of other protein‐coding genes such as calmodulin, β ‐tubulin and histone H3 (Carbone and Kohn ; Skovgaard et al.…”

Section: Introductionmentioning

confidence: 99%

Genetic Diversity and Pathogenicity of Fusarium oxysporum f.sp. melonis Races from Different Areas of Italy

Luongo

Ferrarini

Haegi

et al. 2014

Journal of Phytopathology

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Fusarium wilt caused by Fusarium oxysporum f.sp. melonis (FOM) is a devastating disease of melon worldwide. Pathogenicity tests performed with F. oxysporum isolates obtained from Italian melon‐growing areas allowed to identify thirty‐four FOM isolates and the presence of all four races. The aims of this work were to examine genetic relatedness among FOM isolates by race determination and to perform phylogenetic analyses of identified FOM races including also other formae speciales of F. oxysporum of cucurbits. Results showed that FOM race 1,2 was the most numerous with a total of eighteen isolates, while six and nine isolates were identified as race 0 and 1, respectively, and just one isolate was assigned to race 2. Phylogenetic analysis was performed by random amplified polymorphic DNA (RAPD) profiling and by translation elongation factor‐1α (TEF‐1α) sequencing. The analysis of RAPD profiles separated FOM races into two distinct clades. Clade 1, which included races 0, 1 and 1,2, was further divided into ‘subclade a’ which grouped almost all race 1,2 isolates, and into ‘subclade b’ which included race 0 and 1 isolates. Clade 2 comprised only race 2 isolates. The phylogenetic analysis based on TEF‐1α separated FOM from the other formae speciales of F. oxysporum. Also with TEF‐1α analysis, FOM races 0, 1 and 1,2 isolates grouped in one single clade clearly separated from FOM race 2 isolates which grouped closer to F. oxysporum f.sp. cucumerinum. RAPD technique was more effective than TEF‐1α in differentiating FOM race 1,2 isolates from those belonging to the closely related races 0 and 1. Both phylogenetic analyses supported the close relationship between the three different FOM races which might imply the derivation from one another and the different origin of FOM race 2.

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Phylogeny and molecular diagnosis of mycotoxigenic fungi

Cited by 16 publications

References 66 publications

A high density COX1 barcode oligonucleotide array for identification and detection of species of Penicillium subgenus Penicillium

A high density COX1 barcode oligonucleotide array for identification and detection of species of Penicillium subgenus Penicillium

Assessment ofFusariuminfection in wheat heads using a quantitative polymerase chain reaction (qPCR) assay

Genetic Diversity and Pathogenicity of Fusarium oxysporum f.sp. melonis Races from Different Areas of Italy

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