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Population structure and adaptation of a bacterial pathogen in California grapevines
Author(s) -
Vanhove Mathieu,
Sicard Anne,
Ezennia Jeffery,
Leviten Nina,
Almeida Rodrigo P.P.
Publication year - 2020
Publication title -
environmental microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.954
H-Index - 188
eISSN - 1462-2920
pISSN - 1462-2912
DOI - 10.1111/1462-2920.14965
Subject(s) - biology , xylella fastidiosa , adaptation (eye) , genetic diversity , biological dispersal , genome , population , niche , local adaptation , ecological niche , genotype , outbreak , genetics , single nucleotide polymorphism , genetic structure , genetic variation , ecology , gene , virology , bacteria , demography , neuroscience , sociology , habitat
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.