Incongruence between multi-locus sequence analysis (MLSA) and whole-genome-based phylogenies:Pseudomonas syringaepathovarpisias a cautionary tale

Summary Previous phylogenies, built using a subset of genomic loci, split P seudomonas syringae pv. pisi into two well‐supported clades and implied convergence in host range for these lineages. The analysis of phenotypic and genotypic data within the context of this phylogenetic relationship implied further convergence at the level of virulence gene loss and acquisition. We generate draft genome assemblies for two additional P . syringae strains, isolated from diseased pea plants, and demonstrate incongruence between phylogenies created from a subset of the data compared with the whole genomes. Our whole‐genome analysis demonstrates that strains classified as pv. pisi actually form a coherent monophyletic clade, so that apparent convergence is actually the product of shared ancestry. We use this example to urge caution when making evolutionary inferences across closely related strains of P . syringae .