Fig. 2.

Maximum likelihood phylogeny of the core genome alignment of 13 strains of X. fastidiosa in vitro recombinants and their donor and recipient parental strains before (a) and after (b) recombination filtering. Population structure was inferred using nested clustering implemented in hierBAPS. For (b), recombinant regions detected by BratNextGen in the genomes were excluded to build a recombination-free phylogenetic tree. The overall topology remained similar, but the phylogenetic distance decreased among the genomes after recombination filtering. The phylogenetic tree was mid-point rooted, representing an increasing order of nodes. Bootstrap support was >98% for all nodes, except where otherwise indicated