Abstract
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 that 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 pan-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 subspecies multiplex, sandyi, and pauca, 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.
Highlights
Xylella fastidiosa is a plant-pathogenic bacterium widely distributed in the Americas, where it is associated with a number of plant diseases and relevant losses in commercially important crops (Almeida and Nunney 2015)
The wholegenome SNP approach agrees with the known X. fastidiosa phylogeny, depicting a more complex scenario with the inclusion of the recently acquired genomes described in Costa Rica or intercepted in Europe
Obtained MP and maximum likelihood (ML) phylogenetic trees using data from SNP analysis basically overlaps except for the placement of the new isolate CO33 (Giampetruzzi et al 2015b), which clusters with isolate sandyi Ann 1 in the subsp. sandyi in ML
Summary
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, distinct from the recently described coffee isolate CFBP8072 imported into Europe from Ecuador. These findings were supported by the gene characterization of a conjugative plasmid shared by all the four ST53 isolates. 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 subspecies multiplex, sandyi, and pauca, but was detected in ST21 isolates of the subspecies fastidiosa from Costa Rica. X. fastidiosa populations appeared to have historically remained largely isolated due to geographical barriers, recent human-mediated invasions are responsible for important plant diseases driven by bacterial introductions in new areas
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