Tracing the Origin of Xylella fastidiosa subspecies pauca ST53 Strains in France Using Comparative Genomics Approaches

Xylella fastidiosa is a plant-pathogenic bacterium native to the Americas. It has a wide host range and causes significant diseases in economically important crops, including grapevine, citrus, and olive trees. Since 2013, this bacterium has been identified in Europe and other countries of the Mediterranean basin, with the detection of several subspecies (multiplex, fastidiosa and pauca) and sequence types (ST) in various plant species in Italy, France, the Balearic Islands, Spain, Portugal, Israel and Lebanon. This study focuses on the genomic analyses of the pauca subspecies ST53 strains detected in France. Indeed, ST53 was identified (i) on intercepted coffee plants in Pays-de-la-Loire region and (ii) on two infected host plant collected in Menton in the PACA region in 2015 and 2019. As an efficient and promising alternative, the targeted enrichment method developed specifically to capture X. fastidiosa gDNA was applied to obtain whole genome. Phylogenetic and genomic comparisons were carried out to compare the French ST53 genomic sequences to a range of X. fastidiosa subspecies pauca genomic sequences from public database, including ST53 from Italy and Costa Rica. The results obtained from these different approaches revealed a link between these strains. A tip-dating analysis and transmission tree were performed, highlighting the hypothesis that French ST53 strains were related to the Italian and Costa Rican strains.