Applied and Environmental Microbiology (2018) 84 (1 - e01868-17)

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Peter van Dam, Mara de Sain, Anneliek ter Horst, Michelle van der Gragt and Martijn Rep (2018)
Use of comparative genomics-based markers for discrimination of host specificity in Fusarium oxysporum
Applied and Environmental Microbiology 84 (1 - e01868-17)
Abstract: The polyphyletic nature of many formae speciales of Fusarium oxysporum prevents molecular identification of newly encountered strains based on conserved, vertically inherited genes. Alternative molecular detection methods that could replace labor- and time-intensive disease assays are therefore highly desired. Effectors are functional elements in the pathogen-host interaction and have been found to show very limited sequence diversity between strains of the same forma specialis, which makes them potential markers for host-specific pathogenicity. We therefore compared candidate effector genes extracted from 60 existing and 22 newly generated genome assemblies, specifically targeting strains affecting cucurbit plant species. Based on these candidate effector genes, a total of 18 PCR primer pairs were designed to discriminate between each of the seven Cucurbitaceae-affecting formae speciales. When tested on a collection of strains encompassing different clonal lineages of these formae speciales, nonpathogenic strains, and strains of other formae speciales, they allowed clear recognition of the host range of each evaluated strain. Within Fusarium oxysporum f. sp. melonis more genetic variability exists than anticipated, resulting in three F. oxysporum f. sp. melonis marker patterns that partially overlapped with the cucurbit-infecting Fusarium oxysporum f. sp. cucumerinum, Fusarium oxysporum f. sp. niveum, Fusarium oxysporum f. sp. momordicae, and/or Fusarium oxysporum f. sp. lagenariae. For F. oxysporum f. sp. niveum, a multiplex TaqMan assay was evaluated and was shown to allow quantitative and specific detection of template DNA quantities as low as 2.5 pg. These results provide ready-to-use marker sequences for the mentioned F. oxysporum pathogens. Additionally, the method can be applied to find markers distinguishing other host-specific forms of F. oxysporum.
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Research topic(s) for pests/diseases/weeds:
identification/taxonomy
surveys/sampling/distribution


Pest and/or beneficial records:

Beneficial Pest/Disease/Weed Crop/Product Country Quarant.
Fusarium oxysporum f.sp. niveum
Fusarium oxysporum f.sp. cucumerinum
Fusarium oxysporum f.sp. melonis
Fusarium oxysporum f.sp. momordicae
Fusarium oxysporum f.sp. lagenariae