Fig. 1

Maximum-likelihood core-genome phylogeny of 69 strains belonging to the genus Allorhizobium and other Rhizobiaceae members (collapsed branches). The tree was estimated with IQ-TREE from the concatenated alignment of 344 top-ranked genes selected using GET_PHYLOMARKERS software. The numbers on the nodes indicate the approximate Bayesian posterior probabilities support values (first value) and ultra-fast bootstrap values (second value), as implemented in IQ-TREE. The tree was rooted using the Mesorhizobium spp. sequences as the outgroup. The scale bar represents the number of expected substitutions per site under the best-fitting GTR + F + ASC + R6 model. All. vitis species complex clade is collapsed on the left tree and shown expanded on the right. The matrix represents the distribution of ANI blast (ANIb) values for the genomic sequences of the clade corresponding to the All. vitis species complex, relative to the typical species delimitation threshold of 95%. The same tree, but without collapsed clades, is presented in the Figure S1