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We tested the qPCR assays on 39 target and 30 non-target strains, as well as on 13 different plant species spiked with strains of the different subspecies of X. We designed primers and probes using SkIf, a bioinformatics tool based on k-mers, to detect specific signatures of the species and subspecies from a data set of 58 genome sequences representative of X. fastidiosa detection and subspecies identification in planta in a single reaction. Thus, we developed various tetraplex and triplex quantitative PCR (qPCR) assays for X. fastidiosa outbreaks in Europe depends on the identification of the subspecies, accurate determination of the subspecies in infected plants as early as possible is of major interest. Initially limited to the Americas, Xf has been detected in Europe since 2013. Five subspecies of the pathogen with different but overlapping host ranges have been described, but only three subspecies are widely accepted, namely subspecies fastidiosa, multiplex, and pauca. This plant pathogen has a broad host range estimated to 560 plant species. Xylella fastidiosa ( Xf) is an insect-borne bacterium confined to the xylem vessels of plants.
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2French Agency for Food, Environmental and Occupational Health & Safety, Plant Health Laboratory, Angers, France.1IRHS, Agrocampus-Ouest, INRA, University of Angers, SFR 4207 QuaSaV, Beaucouzé, France.Enora Dupas 1,2, Martial Briand 1, Marie-Agnès Jacques 1* and Sophie Cesbron 1*