Phylogeny of <i>Fusarium oxysporum</i> f. sp. <i>lactucae</i> Inferred from Mitochondrial Small Subunit, Elongation Factor 1-α, and Nuclear Ribosomal Intergenic Spacer Sequence Data

Mbofung, Gladys Y.; Hong, Soon Gyu; Pryor, Barry M.

doi:10.1094/phyto-97-0087

Cited by 82 publications

(74 citation statements)

References 29 publications

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“…IGS sequence polymorphisms contained much useful data for phylogenetic reconstruction and for inferring species limits with high discriminatory power within Fusarium as also previously noted by O'Donnell et al (22). The IGS has become one of the more popular loci for investigating genetic diversity or haplotypes nested within the FOSC (5,11,14) and, more recently, within the GFSC and other Fusaria spp. (16, 32).…”

Section: Vol 49 2011 Seven-locus Sequence Analysis Of Fusarium 1895mentioning

confidence: 73%

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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Section: Vol 49 2011 Seven-locus Sequence Analysis Of Fusarium 1895mentioning

confidence: 73%

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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“…This suggests that each VCG represents a clonal population (28,31,32). To determine further phylogenetic relationships within and among formae speciales of F. oxysporum DNA sequences of the mitochondrial small-subunit (mtSSU) rRNA gene, the ribosomal DNA (rDNA) intergenic spacer (IGS) region and the translation elongation factor (EF1-␣) gene have been used (33)(34)(35). Such studies confirmed multiple evolutionary origins for many formae speciales of F. oxysporum.…”

mentioning

confidence: 94%

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

Biju

Fokkens

Houterman

et al. 2017

Appl Environ Microbiol

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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-␣ 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.

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“…The tests are, however, time consuming, labor intensive and subject to varying environmental or culture growth conditions during the experiments (Mbofung et al 2007;Woo et al 1996). Molecular techniques, such as restriction fragment analysis of PCR-amplified ribosomal intergenic spacers (IGS), can help to rapidly characterize large F. oxysporum populations (Edel et al 1995).…”

Section: Introductionmentioning

confidence: 99%

“…Of the relatively small number of genes that have been used for phylogenetic studies within the Fusarium genus (e.g. IGS rDNA, elongation factor-1α, polygalacturonases, mitochondrial small subunit ribosomal RNA, phosphate permease, β-tubulin, nitrate reductase, MAT 1 and MAT2), the EF-1α (Amatulli et al 2010) and IGS rDNA genes (Mbofung et al 2007) seem adept for such application (O'Donnell et al 2009). The IGS region, which separates rDNA repeat units, is particularly suitable for studying intraspecific relationships (Appel and Gordon 1996;Mbofung et al 2007).…”

Section: Introductionmentioning

confidence: 99%

“…IGS rDNA, elongation factor-1α, polygalacturonases, mitochondrial small subunit ribosomal RNA, phosphate permease, β-tubulin, nitrate reductase, MAT 1 and MAT2), the EF-1α (Amatulli et al 2010) and IGS rDNA genes (Mbofung et al 2007) seem adept for such application (O'Donnell et al 2009). The IGS region, which separates rDNA repeat units, is particularly suitable for studying intraspecific relationships (Appel and Gordon 1996;Mbofung et al 2007). Phylogenetic analysis of the IGS region sequence is very useful for studying the composition of F. oxysporum populations (Dissanayake et al 2009;Enya et al 2008;Kawabe et al 2005Kawabe et al , 2007Srinivasan et al 2010).…”

Section: Introductionmentioning

confidence: 99%

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Genetic diversity and pathogenicity of Fusarium oxysporum isolated from wilted rocket plants in Italy

et al. 2011

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Thirty-six isolates of Fusarium oxysporum originated from Eruca vesicaria and Diplotaxis tenuifolia together with eight reference strains belonging to the formae speciales raphani, matthioli and conglutinans, typical on the Brassicaceae family, were tested for pathogenicity on two species of rocket plants (E. vesicaria L., syn. E. sativa, cv. 'Rucola coltivata'; and D. tenuifolia cv. 'Winter') cultivated in the glasshouse. The results showed that different isolates were slightly, moderately or highly virulent.

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Phylogeny of Fusarium oxysporum f. sp. lactucae Inferred from Mitochondrial Small Subunit, Elongation Factor 1-α, and Nuclear Ribosomal Intergenic Spacer Sequence Data

Cited by 82 publications

References 29 publications

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

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

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

Genetic diversity and pathogenicity of Fusarium oxysporum isolated from wilted rocket plants in Italy

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