Insights into the genome of the De Donno strain of Xylella fastidiosa

Genetic studies showed that the genotype of the olive-infecting strain of X. fastidiosa (Xf-
De Donno) belongs to the sequence type ST53 within subspecies pauca, already reported to occur in
Costa Rica. The analysis of single nucleotide polymorphisms (SNPs) and the study of the pan-genome
of 27 available whole genomes were performed to determine the phylogenetic placement of Xf-De
Donno. Maximum-parsimony and maximum likelihood trees constructed using the SNPs and the pangenome
data distinguished the subsp. fastidiosa, multiplex, pauca, sandyi, and morus and groups the
Italian and three Costa Rican ST53 isolates in a compact clade that diverges from the South American
pauca isolates. These findings were supported by the characterization of a conjugative plasmid shared
by the four ST53 isolates and by the identification of a gene encoding a putative histidine kinase-like
ATPase, which is not present in isolates from the subsp. multiplex, sandyi and pauca, but was
detected in the four ST53 and ST21 isolates of the subspecies fastidiosa from Costa Rica. These data
support the common and recent origin of the ST53 isolates. The complete and annotated genome
sequence of the strain De Donno of X. fastidiosa was obtained by a combined Illumina and PacBio
sequencing. This strain, recovered from an olive tree affected by Olive Quick Decline Syndrome
(OQDS), when mechanically inoculated in different olive cultivars, caused symptoms identical to those
observed in contaminated olive groves.