Type-Strain-Anchored Phylogenomics Reveals Taxonomic Discordance and Functional Variation in Agrobacterium

Species names deposited for Agrobacterium genomes do not always correspond to genomic lineages, complicating taxonomy and functional comparisons. We analyzed 432 genome records, including 400 assigned to Agrobacterium, using ANI, AAI, type-strain dDDH comparisons, and phylogenies based on 120 bacterial markers and 42 ribosomal proteins. ANI clustering at 95% identified 29 Agrobacterium groups, including five highlighted candidate species-level lineages. Both phylogenies supported a genus-level clade, although one ANI group showed discordance between the ribosomal-protein ML topology and bootstrap consensus. Type-strain dDDH supported conspecificity of A. fabacearum and A. tumefaciens (86.0%), whereas A. leguminum and A. deltae were below the conventional species boundary (66.7%). Pan-genome analysis of 31 representatives revealed extensive gene-content variation. Across 400 Agrobacterium records, 148 of 342 KEGG modules reached the reconstruction threshold in at least one genome, and 58 did so in all genomes. In the full 432-record dataset, 174 genomes had Ti-associated and seven had Ri-associated marker profiles; catB1 and tet(30) were detected in 243 and 29 genomes, respectively. These results identify taxonomic assignments requiring reassessment and link genomic grouping to variation in predicted functional repertoires.