A New Real-Time PCR Assay for Detecting Fungi in Genus .

The genus contains several significant plant pathogens, causing wilt and canker disease on a wide range of plant species. There are >40 known species of , some of which are becoming increasingly important in agricultural or natural ecosystems. The diagnostic procedures for most species rely on time-consuming and labor-intensive culturing approaches. To provide more time-efficient and sensitive molecular diagnostic tools for , a generic TaqMan real-time PCR assay was developed using the ITS gene. This novel two-probe TaqMan assay amplified DNA from all tested species. Some nonspecific amplification of a few species from closely related genera was observed under certain conditions; however, these false-positive detections could be ruled out using the additional PCR primers developed for further sequence-based identification of the detected species. The assay was found to be highly sensitive, as it detected 0.2 pg/μl of DNA in water as well as in host DNA matrix. Further validation with artificially inoculated fig stem tissue demonstrated that the assay was also able to effectively detect the pathogen in infected asymptomatic stem tissue. This newly developed real-time PCR assay has practical applications in biosecurity, conservation, and agriculture; it will enable the detection of species directly from plant material to facilitate more sensitive screening of imported plant germplasm, and allow rapid tracking of pathogens in the case of disease outbreaks.