Population structure and adaptation of a bacterial pathogen in California grapevines

Abstract

Summary Xylella fastidiosa subsp. fastidiosa causes Pierce's disease of grapevine (PD) and has been present in California for over a century. A singly introduced genotype spread across the state causing large outbreaks and damaging the grapevine industry. This study presents 122 X. fastidiosa subsp. fastidiosa genomes from symptomatic grapevines, and explores pathogen genetic diversity associated with PD in California. A total of 5218 single‐nucleotide polymorphisms (SNPs) were found in the dataset. Strong population genetic structure was found; isolates split into five genetic clusters divided into two lineages. The core/soft‐core genome constituted 41.2% of the total genome, emphasizing the high genetic variability of X. fastidiosa genomes. An ecological niche model was performed to estimate the environmental niche of the pathogen within California and to identify key climatic factors involved in dispersal. A landscape genomic approach was undertaken aiming to link local adaptation to climatic factors. A total of 18 non‐synonymous polymorphisms found to be under selective pressures were correlated with at least one environmental variable highlighting the role of temperature, precipitation and elevation on X. fastidiosa adaptation to grapevines in California. Finally, the contribution to virulence of three of the genes under positive selective pressure and of one recombinant gene was studied by reverse genetics.

Phylogenetic inference enables reconstruction of a long-overlooked outbreak of almond leaf scorch disease (Xylella fastidiosa) in Europe

“…Thus, we calculated the time of the most recent common ancestor for the Majorcan clade to be around 2004 (95% highest posterior density, HPD: 1982-2015). The average substitution rate calculated was 7.71 × 10 −7 substitutions nucleotide-site −1 year −1 (95% HPD: 1.20 × 10 −7 -1.69 × 10 −6 ), almost identical to that reported previously 12,53 , and corresponding to ∼1.3 SNPs core-genome −1 year −1 .…”

Impacts of local population history and ecology on the evolution of a globally dispersed pathogen

“…Specifically, Vanhove et al (2019) incorporated isolates from populations of diverse geographical origins, while Costa Rica represents a single geographic point. When both datasets are combined with Vanhove et al (2020) and Sicard et al (2020), the raw number of core and soft-core genes changed; however, the combined estimates for both categories remain roughly the same. This suggests that both subspecies have a largely stable core genome with most gain/loss events being limited to the accessory genome.…”

“…The nucleotide diversity values obtained here are lower than those previously reported for both subsp. fastidiosa [9] and uniquely California [8]. In addition, the r/m estimates for subsp.…”

“…However, despite the existence of numerous ecologically and economically important bacterial plant pathogens [6], similar studies are often not performed with such depth or scope. Recent studies have described the evolutionary history and ecology of diverse Xylella fastidiosa populations worldwide [7][8][9][10][11][12]. Each population has a unique evolutionary relationship as well as being subjected to distinct ecological forces.…”

“…Strong evidence shows that subsp. fastidiosa was introduced to the USA approximately 150 years ago [8,11]. Likewise, subsp.…”