Agrobacterium cucumeris sp. nov. isolated from crazy roots on cucumber (Cucumis sativus)

Warabieda, Michał; Kuzmanović, Nemanja; Trzciński, Paweł; Puławska, Joanna

doi:10.1016/j.syapm.2023.126402

Cited by 4 publications

(2 citation statements)

References 52 publications

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“…Indeed, the MLSA-and WGS-based phylogeny showed that strains previously assigned to G3 were clearly divided in two separate subclades. While strains of subclade Atsc8 MLSA or Atsc5 WGS were assigned to A. tomkonis (G3), strains of the other subclade were reclassified into A. cucumeris [59]. This was also supported by the ANIb analysis that showed <94.0% identity among strains of both subclades.…”

Section: Discussionmentioning

confidence: 91%

Evaluation of sequence-based tools to gather more insight into the positioning of rhizogenic agrobacteria within the Agrobacterium tumefaciens species complex

Vargas Ribera,

Kim,

Venbrux

et al. 2024

Preprint

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Rhizogenic Agrobacterium, the causative agent of hairy root disease (HRD), is known for its high phenotypic and genetic diversity. The taxonomy of rhizogenic agrobacteria has undergone several changes in the past and is still somewhat controversial. While the classification of Agrobacterium strains was initially mainly based on phenotypic properties and the symptoms they induced on plants, more and more genetic information has been used along the years to infer Agrobacterium taxonomy. This has led to the definition of the so-called Agrobacteriumtumefaciens species complex (Atsc), which comprises several genomospecies. Interestingly, the rhizogenic Agrobacterium strains are found in several of these genomospecies. Nevertheless, even up until today Agrobacterium strains, and in particular rhizogenic agrobacteria, are prone to misclassification and considerable confusion in literature. In this study, we evaluated different phylogenetic analysis approaches for their use to improve Agrobacterium taxonomy and tried to gain more insight in the classification of strains into this complex genus, with a particular focus on rhizogenic agrobacteria. The genome sequence analysis of 579 assemblies, comprising Agrobacterium, Allorhizobium and Rhizobium strains demonstrated that phylogenies based on single marker genes, such as the commonly used 16S rRNA and recA gene, do not provide sufficient resolution for proper delineation of the different genomospecies within the Atsc. Our results revealed that (in silico) multi-locus sequences analysis (MLSA) in combination with average nucleotide identity (ANIb) at a 94.0% threshold delineates genomospecies accurately and efficiently. Additionally, this latter approach permitted the identification of two new candidate genomospecies.

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Section: Discussionmentioning

confidence: 91%

Evaluation of sequence-based tools to gather more insight into the positioning of rhizogenic agrobacteria within the Agrobacterium tumefaciens species complex

Vargas Ribera,

Kim,

Venbrux

et al. 2024

Preprint

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show abstract

“…Puławska mentioned a new publication in the taxonomy of agrobacteria that describes new species Agrobacterium cucumeris including bacteria causing crazy roots [7].…”

Section: Online Minute 15 Additional Recent Publicationsmentioning

confidence: 99%

International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Rhizobia and Agrobacteria: Minutes of the closed annual meeting, videoconference on 2 October 2023, followed by online discussion until 31 December 2023

Mousavi,

Young

2024

International Journal of Systematic and Evolutionary Microbiology

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Validation List no. 213. Valid publication of new names and new combinations effectively published outside the IJSEM

Oren,

Göker

2023

International Journal of Systematic and Evolutionary Microbiology

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Agrobacterium cucumeris sp. nov. isolated from crazy roots on cucumber (Cucumis sativus)

Cited by 4 publications

References 52 publications

Evaluation of sequence-based tools to gather more insight into the positioning of rhizogenic agrobacteria within the Agrobacterium tumefaciens species complex

Evaluation of sequence-based tools to gather more insight into the positioning of rhizogenic agrobacteria within the Agrobacterium tumefaciens species complex

International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Rhizobia and Agrobacteria: Minutes of the closed annual meeting, videoconference on 2 October 2023, followed by online discussion until 31 December 2023

Validation List no. 213. Valid publication of new names and new combinations effectively published outside the IJSEM

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