Genome-Wide Analysis Provides Evidence on the Genetic Relatedness of the Emergent Xylella fastidiosa Genotype in Italy to Isolates from Central America

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.

Philaenus spumarius: when an old acquaintance becomes a new threat to European agriculture

“…This first detection was followed by findings of several subspecies and strains of X. fastidiosa in Corsica, mainland France, Germany and Spain (Denance et al 2017;Olmo et al 2017). The introduction is supposed to be related with trade of infected plant materials (Loconsole et al 2016;Giampetruzzi et al 2017). X. fastidiosa is transmitted exclusively by xylem sap-sucking insects (Frazier 1965).…”

Xylella fastidiosa: Insights into an Emerging Plant Pathogen

“…sandyi is still debated (4); recent genomic data suggest that this clade clusters within subsp. fastidiosa (60,87,89). Applying a phylogenetically representative genome sequence data set to X. fastidiosa taxonomy will likely clarify pending questions and lead to a revision of the group.…”

“…Applying a phylogenetically representative genome sequence data set to X. fastidiosa taxonomy will likely clarify pending questions and lead to a revision of the group. As diversity is not a goal of this review, we direct readers to recent work on the topic (28,60,89).…”

“…pauca isolates highlights their importance. Studies (60,87,90) have shown that all isolates from olive trees in Italy belong to the same ST that also contains Costa Rican isolates infecting oleander and coffee plants. Given the small number of SNPs that differentiate strains infecting olive trees from those infecting oleander or coffee, adaptation to this new host in Apulia likely results from a few mutations under selective pressure.…”

Coffee bacterial diseases: a plethora of scientific opportunities

“…In addition, some strains that cause CVC and CLS can also cause disease symptoms in several commercial grapevine cultivars (Li et al, 2002). Subspecies pauca was also associated with disease symptoms in Prunus persica and Quercus ilex in France (Denanc e et al, 2017) and in olive trees in Italy (Giampetruzzi et al, 2017).…”