Xylella fastidiosa strain:CFBP8073 Genome sequencing and assembly

Xylella fastidiosa is a xylem-limited phytopathogenic bacterium endemic to the Americas, but that recently emerged in Asia and Europe. Albeit it is a quarantine organism for the European Union, importation of plant material from contaminated areas and latent infection in asymptomatic plants rendered its introduction inevitable. In 2012, four coffee plants (Coffea arabica and C. canephora) with leaf scorch symptoms growing in a confined glasshouse were detected in France. After identification of the causal agent, this outbreak was eradicated. Three X. fastidiosa strains were isolated from these plants confirming a preliminary diagnostic based on immunofluorescence. The strains were characterized by multiplex PCR and by multilocus sequence analysis / typing (MLSA-MLST) based on seven housekeeping genes. One strain, CFBP 8073, which was isolated from C. canephora imported from Mexico was assigned to X. fastidiosa subsp. fastidiosa/sandyi and presented a novel sequence type (ST) with novel alleles at two loci. The two other strains, CFBP 8072 and 8074, isolated from C. arabica imported from Ecuador were allocated to X. fastidiosa subsp. pauca. These two strains presented an identical novel ST with novel alleles at two loci. These MLST profiles evidenced recombination events. We provided genome sequences for CFBP 8072 and 8073 strains. Comparative analyses of the two new X. fastidiosa genome sequences with publicly available data, including the Italian strain CoDiRO, confirmed these phylogenetic positions and provided candidate alleles for coffee adaptation. This study confirms the global diversity of X. fastidiosa and highlights the diversity of strains isolated from coffee.