Type-Strain-Anchored Phylogenomics Reveals Taxonomic Discordance and Functional Variation in Agrobacterium
4 affiliations
- 1Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16/10, 117997 Moscow, Russia
- 2Nelyubin Institute of Pharmacy, Sechenov First Moscow State Medical University (Sechenov University), Trubetskaya Str. 8, bldg. 2, 119991 Moscow, Russia
- 3Pirogov Russian National Research Medical University, Ostrovityanova Str. 1, 117997 Moscow, Russia
- 4Agrobiotechnology Department, Agrarian and Technological Institute, RUDN University, Miklukho-Maklaya Str. 6, 117198 Moscow, Russia
Abstract
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.
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BibTeX
@article{filatova2026typestrainanchored,
title = {{Type-Strain-Anchored Phylogenomics Reveals Taxonomic Discordance and Functional Variation in Agrobacterium}},
author = {Maria S. Filatova and Peter V. Evseev and Alexander N. Ignatov and Polina V. Asmaeva and Andrey V. Chaplin and Konstantin A. Miroshnikov},
journal = {International Journal of Molecular Sciences},
year = {2026},
month = oct,
doi = {10.3390/ijms27209210},
url = {https://www.mdpi.com/1422-0067/27/20/9210},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Type-Strain-Anchored Phylogenomics Reveals Taxonomic Discordance and Functional Variation in Agrobacterium
AU - Maria S. Filatova
AU - Peter V. Evseev
AU - Alexander N. Ignatov
AU - Polina V. Asmaeva
AU - Andrey V. Chaplin
AU - Konstantin A. Miroshnikov
PY - 2026
DA - 2026/10/01
JO - International Journal of Molecular Sciences
DO - 10.3390/ijms27209210
UR - https://www.mdpi.com/1422-0067/27/20/9210
AB - 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.
SN - 1422-0067
ER -