MLSA phylogeny of 40 Agrobacterium spp.

For this MLSA of 40 Agrobacterium spp. strains, we extracted the CDS alignments of parE, gyrB, recA, and rpoB from the Pantagruel pangenome database and concatenated into a multi-locus alignment, totaling 9,968 positions. ML Phylogenies were 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.Separate and concatenated alignments of the 4 marker gene families are provided. The correspondance between genome code (prefix of locus tags) and organism name is provided in 'organism_code.tab'. Sequence similarity matrices for each locus are also provided.