16S phylogeny of 40 Agrobacterium spp.

We searched the 16S rRNA 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.Another version of the tree has beenmade adding to the alignment the 16S ribosomal RNA gene sequence from <i>Rhizobium leguminosarum</i> type strain USDA 2370 (GenBank accession: U29386.1).