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. 2022 Jan 13;20:16. doi: 10.1186/s12915-021-01221-y

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© The Author(s) 2022

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 1 — Relationships among representatives of the Agrobacterium tumefaciens species complex. The sister species Agrobacterium larrymoorei (A. l.) is included as the outgroup. A Maximum likelihood phylogeny based on a concatenated alignment of 2093 single-copy genes shared by all 35 genomes (635,594 aligned amino acid sites). Bootstrap support values in the range of 60–80% are labeled. Strains with complete genome assemblies are highlighted with an asterisk (“*”). The genomospecies assignments (i.e., G1-G9, G13, and G21-G22) are labeled to the right of strain names. The three A. tumefaciens supergroups are indicated by the colored background of the genomospecies assignments. Information to the right of the genomospecies assignments shows the grouping of genomes according to different cutoff values of genome-wide average nucleotide identity (ANI), the presence/absence of type VI secretion system (T6SS)-encoding gene cluster (green: present; white: absent), copy number of vgrG (white background: absent), number of plasmids, and the tumor-inducing plasmid (pTi) type based on k-mer profile (white background: absent). B Pairwise genome similarities based on the percentages of genomic segments mapped and the ANI values