Genomics informed design of a suite of real‐time PCR assays for the specific detection of each <i>Xylella fastidiosa</i> subspecies

Aims Existing methods for the identification of subspecies Xylella fastidiosa are time-consuming which can lead to delays in diagnosis and associated plant health response outbreaks interceptions. Methods Results Diagnostic markers were identified using a comparative genomics approach allow fine differentiation very closely related subspecies. Five qPCR assays designed specific detection X. subsp. fastidiosa, multiplex, pauca, morus sandyi. All validated according European Mediterranean Plant Protection Organisation (EPPO) standard PM7/98(2). Conclusions shown be target all could used detect femtogram quantities DNA. Significance Impact Study At present, diagnosing requires multiple conventional PCR (although only available three five subspecies) or multi-locus sequence typing takes several days. By comparison, new provide substantial reduction turnaround time direct level as little 75 min.