Affiliation:
1. Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
Abstract
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
.
IMPORTANCE
Pathogenic strains of
Fusarium oxysporum
are differentiated into
formae speciales
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
formae speciales
. This hinders accurate and rapid pathogen detection through molecular methods. In our research, we compared the genomes of 88 strains of
F. oxysporum
with each other, specifically targeting virulence-related genes that are typically highly similar within each
forma specialis
. Using this approach, we identified marker sequences that allow the discrimination of
F. oxysporum
strains affecting various cucurbit plant species through different PCR-based methods.
Funder
Netherlands Genomics Initiative
Publisher
American Society for Microbiology
Subject
Ecology,Applied Microbiology and Biotechnology,Food Science,Biotechnology
Cited by
59 articles.
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