LAUSR

Abstract While there are documented host shifts in many bacterial plant pathogens, the genetic foundation of host shifts is largely unknown. Xylella fastidiosa is a bacterial pathogen found in over 600 host plant species. Two parallel host shifts occurred—in Brazil and Italy—in which X. fastidiosa adapted to infect olive trees, whereas related strains infected coffee. Using 10 novel whole‐genome sequences from an olive‐infecting population in Brazil, we investigated whether these olive‐infecting strains diverged from closely related coffee‐infecting strains. Several single‐nucleotide polymorphisms, many derived from recombination events, and gene gain and loss events separated olive‐infecting strains from coffee‐infecting strains in this clade. The olive‐specific variation suggests that this event was a host jump with genetic isolation between coffee‐ and olive‐infecting X. fastidiosa populations. Next, we investigated the hypothesis of genetic convergence in the host shift from coffee to olive in both populations (Brazil and Italy). Each clade had multiple mutations and gene gain and loss events unique to olive, yet no overlap between clades. Using a genome‐wide association study technique, we did not find any plausible candidates for convergence. Overall, this work suggests that the two populations adapted to infect olive trees through independent genetic solutions.