Use of Comparative Genomics-Based Markers for Discrimination of Host Specificity in Fusarium oxysporum

• Published in: Applied and environmental microbiology 2018-01, Vol.84 (1)
• Main Authors: van Dam, Peter, de Sain, Mara, Ter Horst, Anneliek, van der Gragt, Michelle, Rep, Martijn
• Format: Article
• Language: English
• Subjects: Comparative analysis; Cucurbitaceae; Cucurbitaceae - microbiology; Deoxyribonucleic acid; DNA; Fungi; Fusarium; Fusarium - classification; Fusarium - genetics; Fusarium - isolation & purification; Fusarium oxysporum; Genes; Genome, Fungal; Genomics; Host range; Host Specificity; Markers; Pathogenicity; Pathogens; Phylogeny; Plant Diseases - classification; Plant Diseases - microbiology; Plant Microbiology; Whole Genome Sequencing
• ISSN: 0099-2240; 1098-5336
• DOI: 10.1128/AEM.01868-17

The polyphyletic nature of many of 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 , 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 When tested on a collection of strains encompassing different clonal lineages of these , nonpathogenic strains, and strains of other , they allowed clear recognition of the host range of each evaluated strain. Within f. sp. more genetic variability exists than anticipated, resulting in three f. sp. marker patterns that partially overlapped with the cucurbit-infecting f. sp. , f. sp. , f. sp. , and/or f. sp. For f. sp. , 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 pathogens. Additionally, the method can be applied to find markers distinguishing other host-specific forms of Pathogenic strains of are differentiated into based on their host range, which is normally restricted to only one or a few plant species. However, horizontal gene transfer between strains in the species complex has resulted in a polyphyletic origin of host specificity in many of these This hinders accurate and rapid pathogen detection through molecular methods. In our research, we compared the genomes of 88 strains of with each other, specifically targeting virulence-related genes that are typically highly similar within each Using this approach, we identified marker sequences that allow the discrimination of strains affecting various cucurbit plant species through different PCR-based methods.