Fot 1 insertions in the Fusarium oxysporum f. sp. albedinis genome provide diagnostic PCR targets for detection of the date palm pathogen

Populations of #Fusarium oxysporum$ f. sp. #albedinis$, the causal agent of Bayoud disease of date palm, are derivatives of a single clonal lineage and exhibit very similar Fot 1 hybridization patterns. In order to develop a sensitive diagnostic tool for #F. oxysporum$ f. sp. #albedinis$ detection, we isolated several DNA clones containing a copy of the transposable element Fot 1 from a genomic library of the date palm pathogen. Regions flanking the insertion sites were sequenced, and these sequences were used to design PCR primers that amplify the DNA regions at several Fot 1 insertion sites. When tested on a large sample of #Fusarium$ isolates, including 286 #F. oxysporum$ f. sp. #albedinis$ isolates, 17 other special forms, nonpathogenic #F. oxysporum$ isolates from palm grove soils, and 8 other #Fusarium$ species, the primer pair TL3-FOA28 allowed amplification of a 400-bp fragment found only in #F. oxysporum$ f. sp. #albedinis$. Sequence analysis showed that one of the Fot 1 copies was truncated, lacking 182 bp at its 3' terminus. The primer pair BI03-FOA1 amplified a 204-bp fragment which overlapped the Fot 1 truncated copy and its 3' site of insertion in the #F. oxysporum$ f. sp. #albedinis$ genome and identified 95% of the isolates. The primer pairs BI03-FOA1 and TL3-FOA28 used in PCR assays thus provide a useful diagnostic tool for #F. oxysporum$ f. sp. #albedinis$ isolates. (Résumé d'auteur