gyrB phylogeny of 40 Agrobacterium spp.

We searched the gyrB gene sequences in 40 Agrobacterium spp. genomes using BLASTN, extracted them using a custom Python script and then aligned with ClustalOmega.A ML phylogeny was then inferred based on these alignments with RAxML-NG 1.0.0 with the options ‘--model GTR+G4 --all’, implying the use of the model GTR+FO+G4m, and that 20 independent inferences were run, starting with 10 random trees and 10 parsimony-optimized tree, and retaining the the best ML tree from these 20 inferences. Branch supports were estimated with 200 Felsentein bootstrap trees.