Genome-wide analysis provides evidence on the genetic relatedness of the emergent Xylella fastidiosa genotype in Italy to isolates from Central America

Xylella fastidiosa is a plant pathogenic bacterium recently introduced in Europe that is causing
decline in olive trees in the South of Italy. Genetic studies have consistently shown that the bacterial
genotype recovered from infected olive trees belongs to the sequence type ST53 within subspecies
pauca. This genotype, ST53, has also been reported to occur in Costa Rica. The ancestry of ST53 was
recently clarified, showing it contains alleles which are monophyletic with those of subsp. pauca in
South America. To more robustly determine the phylogenetic placement of ST53 within X. fastidiosa,
we performed a comparative analysis based on single nucleotide polymorphisms (SNPs) and the study of the pan-genome of the 27 currently public available whole genome sequences of X. fastidiosa. The
 resulting maximum-parsimony and maximum likelihood trees constructed using the SNPs and the pan31
genome analysis are consistent with previously described X. fastidiosa taxonomy, distinguishing the
subsp. fastidiosa, multiplex, pauca, sandyi, and morus. Within the subsp. pauca the Italian and three
Costa Rican isolates, all belonging to ST53, formed a compact phylotype in a clade divergent from the
South American pauca isolates, also distinct from the recently described coffee isolate CFBP8072
imported into Europe from Ecuador. These findings were also supported by the gene characterization
of a conjugative plasmid shared by all the four ST53 isolates. Furthermore, isolates of the ST53 clade
possess an exclusive locus encoding a putative ATP-binding protein belonging to the family of
histidine kinase-like ATPase gene, which is not present in isolates from the multiplex, sandyi and
pauca subspecies, but was detected in ST21 isolates of the subspecies fastidiosa from Costa Rica. The
clustering and distinctiveness of the ST53 isolates supports the hypothesis of their common origin, and
the limited genetic diversity among these isolates suggests this is an emerging clade within subsp. pauca.