Xylella fastidiosa subsp. fastidiosa in Californian Grapevines

Xylella fastidiosa (Xf) subsp. fastidiosa, the etiological agent of Pierce’s disease, has been present in California for more than a century. The singly-introduced genotype spread across the state causing large outbreaks and damaging the vine industry. The study presents 122 Xf. subsp. fastidiosa genomes and explore the genetic diversity associated with Pierce’s disease in California. A total of 5,218 single-nucleotide polymorphisms (SNPs) was uncovered in the present dataset. Strong genetic architecture was found within subsp. fastidiosa. Isolates split into five genetic clusters divided into two lineages. The core/soft-core genome constituted 41.2% of the genome emphasizing the high genetic variability and adaptability of bacterial genomes. Recombination analyses confirmed the ability of bacterial plant-pathogen to acquire new genetic elements and the essential role of inter-subspecific homologous recombination in the pathogen adaptation. Additionally, footprints of selective sweeps within each of the identified genetic clusters were uncovered. Signs of isolation by distance (Mantel r test = 0.392, p ≤ 0;001) confirmed that genetic disparities were present over the landscape. An ecological niche model was performed to estimate the environmental niche of the pathogen within California and to identify key climatic factors involved in the pathogen dispersal. Finally, a landscape genomic approach was undertaken aiming to link local adaptation to the climatic factors. A total of 18 non-synonymous polymorphisms (NSY) present in genes found to be under selective pressures were correlated with at least one environmental variable highlighting the role of temperature, precipitation and elevation on Xylella fastidiosa subsp. fastidiosa adaptation.