Development of a new MLST scheme for differentiation of Fusarium solani Species Complex (FSSC) isolates

Debourgogne, Anne; Gueidan, Cécile; Hennequin, Christophe; Contet‐Audonneau, N.; Hoog, Sybren de; Machouart, M.

doi:10.1016/j.mimet.2010.07.008

Cited by 32 publications

(28 citation statements)

References 22 publications

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“…This index is based on the probability that two unrelated strains sampled from a test population are placed into different typing groups. This index was calculated for the O'Donnell et al (2008) three-gene scheme, the Debourgogne et al (2010) five-gene scheme, and the new consensus method.…”

Section: Discriminatory Powermentioning

confidence: 99%

“…These markers have been used for phylogenetic and population studies and have led to new species delimitations within the FSSC as well as to a new haplotype nomenclature system (Zhang et al, 2006;O'Donnell et al, 2008). More recently, a MLST scheme based on polymorphisms was proposed for the FSSC, which employed the five following housekeeping genes: ACC (acetylCoenzyme A carboxylase), ICL (isocitrate lyase), GDP (glyceraldehyde 3P dehydrogenase), MDP (mannitol 1P dehydrogenase) and SOD (superoxyde dismutase) (Debourgogne et al, 2010).…”

Section: Introductionmentioning

confidence: 99%

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Comparison of two DNA sequence-based typing schemes for the Fusarium solani Species Complex and proposal of a new consensus method

Debourgogne

Gueidan

Hoog

et al. 2012

Journal of Microbiological Methods

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Section: Discriminatory Powermentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Comparison of two DNA sequence-based typing schemes for the Fusarium solani Species Complex and proposal of a new consensus method

Debourgogne

Gueidan

Hoog

et al. 2012

Journal of Microbiological Methods

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“…As such, nomenclature systems based on multilocus sequence typing (MLST) schemes incorporating sequence analysis of 2 to 5 genetic loci have been developed to classify a number of Fusarium species complexes according to genotype or haplotype (7,9,12,15,23,24,27). This approach has further revealed the necessity of developing species and sequence type (ST) nomenclatures to designate cryptic speciation within the FSSC (2,9,20,24,27,42), F. oxysporum species complex (FOSC) (22,26,27), Gibberella (Fusarium) fujikuroi species complex (GFSC) (21,27), F. dimerum species complex (FDSC) (23,27,33), F. chlamydosporum species complex (FCSC) and F. incarnatum-F. equiseti species complex (FIESC) (25,27), F. sambucinum species complex (FSAMSC), and F. tricinctum species complex (FTSC) (27). Recently, O'Donnell et al evaluated a new 3-locus MLST scheme incorporating the partial translation elongation factor 1 alpha gene (EF-1␣), the largest subunit of the RNA polymerase gene (RPB1), and the second largest subunit of the RNA polymerase gene (RPB2) loci to identify with good discriminatory capacity 69 Fusarium species within the FCSC, FDSC, FIESC, FOSC, FSAMSC, FSSC, and GFSC (27).…”

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confidence: 99%

Accurate and Practical Identification of 20 Fusarium Species by Seven-Locus Sequence Analysis and Reverse Line Blot Hybridization, and an In Vitro Antifungal Susceptibility Study

Xiao

Kong

et al. 2011

J Clin Microbiol

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Eleven reference and 25 clinical isolates of Fusarium were subject to multilocus DNA sequence analysis to determine the species and haplotypes of the fusarial isolates from Beijing and Shandong, China. Seven loci were analyzed: the translation elongation factor 1 alpha gene (EF-1␣); the nuclear rRNA internal transcribed spacer (ITS), large subunit (LSU), and intergenic spacer (IGS) regions; the second largest subunit of the RNA polymerase gene (RPB2); the calmodulin gene (CAM); and the mitochondrial small subunit (mtSSU) rRNA gene. We also evaluated an IGS-targeted PCR/reverse line blot (RLB) assay for species/haplotype identification of Fusarium. Twenty Fusarium species and seven species complexes were identified. Of 25 clinical isolates (10 species), the Gibberella (Fusarium) fujikuroi species complex was the commonest (40%) and was followed by the Fusarium solani species complex (FSSC) (36%) and the F. incarnatum-F. equiseti species complex (12%). Six FSSC isolates were identified to the species level as FSSC-3؉4, and three as FSSC-5. Twenty-nine IGS, 27 EF-1␣, 26 RPB2, 24 CAM, 18 ITS, 19 LSU, and 18 mtSSU haplotypes were identified; 29 were unique, and haplotypes for 24 clinical strains were novel. By parsimony informative character analysis, the IGS locus was the most phylogenetically informative, and the rRNA gene regions were the least. Results by RLB were concordant with multilocus sequence analysis for all isolates. Amphotericin B was the most active drug against all species. Voriconazole MICs were high (>8 g/ml) for 15 (42%) isolates, including FSSC. Analysis of larger numbers of isolates is required to determine the clinical utility of the seven-locus sequence analysis and RLB assay in species classification of fusaria.

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“…We attempted to amplify DNA from 16 genomic regions by using the following primer pairs: for housekeeping genes identified in the G. morbida genome; for those developed for Fusarium solani MLST analysis [34]; for the rRNA internal transcribed spacer (ITS) region [35]; and for the b-tubulin (BT) gene [36], to obtain a MLST-based analysis of G. morbida (Table A4.2).…”

Section: Isolation and Identification Of Mlst Sequencesmentioning

confidence: 99%

“…From the set of 16 pairs of primers tested with G. morbida DNA as template (Table A4.2) all eight based on the Fusarium solani genome [34] failed to amplify a single well-defined band.…”

Section: Isolation and Identification Of Mlst Sequencesmentioning

confidence: 99%

Transcriptome and secretome of two Pythium species during infection and saprophytic growth

Caballero

Tisserat

2017

Physiological and Molecular Plant Pathology

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TRANSCRIPTOME AND SECRETOME OF TWO PYTHIUM SPECIES DURING INFECTION AND SAPROPHYTIC GROWTHIn the first part of this dissertation, I describe how we obtained and analyzed the full complement of transcripts -the transcriptome-and the set of secreted proteins -the secretomeof Pythium irregulare and Pythium iwayamai isolates when they were infecting plant hosts and when they were growing saprophytically. Additionally, these two treatments were performed at two different temperatures (4˚ and 19˚C). The assembled transcriptomes were annotated, and a closer analysis of the expression profiles of transcripts coding for pathogenicity-related proteins is shown. Secreted proteins were semi-quantified and their likely functions were determined based on the annotation of the corresponding transcripts.

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Development of a new MLST scheme for differentiation of Fusarium solani Species Complex (FSSC) isolates

Cited by 32 publications

References 22 publications

Comparison of two DNA sequence-based typing schemes for the Fusarium solani Species Complex and proposal of a new consensus method

Comparison of two DNA sequence-based typing schemes for the Fusarium solani Species Complex and proposal of a new consensus method

Accurate and Practical Identification of 20 Fusarium Species by Seven-Locus Sequence Analysis and Reverse Line Blot Hybridization, and an In Vitro Antifungal Susceptibility Study

Transcriptome and secretome of two Pythium species during infection and saprophytic growth

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