Genetic Assessment Of Xylella Fastidiosa Recovered In The Salento Peninsula

Xylella fastidiosa is a plant pathogenic bacterium, recently introduced in Europe that is causing a decline in olive trees in the South of Italy. Preliminary genetic studies using Multi Locus Sequence Typing (MLST) analysis revealed that the bacterial genotype recovered from the infected olive trees belongs to the sequence type “ST53” within subspecies pauca. This genotype has also been reported to occur in Costa Rica, and more recently in France. Extensive MLST analyses coupled with next generation sequencing (NGS) approaches have been conducted to assess the population genomics of the isolates occurring in the epidemic area of the Salento peninsula. All the different tested susceptible hosts and all the olive trees sampled in the most recently reported outbreaks show to harbor the same sequence type ST53. NGS using complementary approaches based on Illumina and PacBio technologies was used to reconstruct the genome of the selected reference isolate “De Donno”, being the first sequenced olive strain. Indeed, the draft genomes of two additional olive isolates were obtained both from the pure culture and total plant DNA. The sequence dataset of these novel reconstructed genomes was inferred with the recently sequenced draft genomes of the Costa Rican ST53 genotypes to assess their phylogenetic relatedness. Comparative analysis based on single nucleotide polymorphisms and the study of the pan-genome of these whole genome sequences along with those currently available for X. fastidiosa, confirmed that within the subsp. pauca the Italian and Costa Rican ST53 isolates formed a distinct phylotype in a clade divergent from the South American pauca isolates. The clustering and distinctiveness of the ST53 isolates support the hypothesis of their common origin, and the limited genetic diversity among these isolates suggests this is an emerging clade.