Construction of physical map and mapping of chromosomal virulence genes of the biovar 3 Agrobacterium (Rhizobium vitis) strain K-Ag-1

Tanaka, Katsuyuki; Urbanczyk, Henryk; Matsui, Hiroki; Sawada, Hiroyuki; Suzuki, K.

doi:10.1266/ggs.81.373

Cited by 7 publications

(5 citation statements)

References 30 publications

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“…A. tumefaciens has one circular and one linear chromosome (Goodner et al, 2001;Suzuki et al, 2001;Wood et al, 2001). A. vitis contains two circular chromosomes (Tanaka et al, 2006). A. rhizogenes harbors a circular chromosome and a chromosome-size plasmid (Urbanczyk et al, 2003).…”

Section: Discussionmentioning

confidence: 99%

Ability of Agrobacterium tumefaciens and A. rhizogenes strains, inability of A. vitis and A. rubi strains to adapt to salt-insufficient environment, and taxonomic significance of a simple salt requirement test in the pathogenic Agrobacterium species

Tanaka

Arafat

Urbanczyk

et al. 2009

J. Gen. Appl. Microbiol.

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Section: Discussionmentioning

confidence: 99%

Ability of Agrobacterium tumefaciens and A. rhizogenes strains, inability of A. vitis and A. rubi strains to adapt to salt-insufficient environment, and taxonomic significance of a simple salt requirement test in the pathogenic Agrobacterium species

Tanaka

Arafat

Urbanczyk

et al. 2009

J. Gen. Appl. Microbiol.

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“…In contrast to Agrobacterium , the All. vitis strains carry two circular chromosomes [ 18 , 20 , 21 ]. However, the smaller circular chromosome (named chromosome II) was later classified as a chromid in the fully sequenced strain All.…”

Section: Introductionmentioning

confidence: 99%

Genomic analysis provides novel insights into diversification and taxonomy of Allorhizobium vitis (i.e. Agrobacterium vitis)

et al. 2022

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Background Allorhizobium vitis (formerly named Agrobacterium vitis or Agrobacterium biovar 3) is the primary causative agent of crown gall disease of grapevine worldwide. We obtained and analyzed whole-genome sequences of diverse All. vitis strains to get insights into their diversification and taxonomy. Results Pairwise genome comparisons and phylogenomic analysis of various All. vitis strains clearly indicated that All. vitis is not a single species, but represents a species complex composed of several genomic species. Thus, we emended the description of All. vitis, which now refers to a restricted group of strains within the All. vitis species complex (i.e. All. vitis sensu stricto) and proposed a description of a novel species, All. ampelinum sp. nov. The type strain of All. vitis sensu stricto remains the current type strain of All. vitis, K309T. The type strain of All. ampelinum sp. nov. is S4T. We also identified sets of gene clusters specific to the All. vitis species complex, All. vitis sensu stricto and All. ampelinum, respectively, for which we predicted the biological function and infer the role in ecological diversification of these clades, including some we could experimentally validate. All. vitis species complex-specific genes confer tolerance to different stresses, including exposure to aromatic compounds. Similarly, All. vitis sensu stricto-specific genes confer the ability to degrade 4-hydroxyphenylacetate and a putative compound related to gentisic acid. All. ampelinum-specific genes have putative functions related to polyamine metabolism and nickel assimilation. Congruently with the genome-based classification, All. vitis sensu stricto and All. ampelinum were clearly delineated by MALDI-TOF MS analysis. Moreover, our genome-based analysis indicated that Allorhizobium is clearly separated from other genera of the family Rhizobiaceae. Conclusions Comparative genomics and phylogenomic analysis provided novel insights into the diversification and taxonomy of Allorhizobium vitis species complex, supporting our redefinition of All. vitis sensu stricto and description of All. ampelinum. Our pan-genome analyses suggest that these species have differentiated ecologies, each relying on specialized nutrient consumption or toxic compound degradation to adapt to their respective niche.

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“…In contrast to Agrobacterium , the All. vitis strains carry two circular chromosomes (18, 20, 21). However, the smaller circular chromosome (named chromosome II) was later classified as a chromid in the fully sequenced strain All.…”

Section: Introductionmentioning

confidence: 99%

Genomic analysis provides novel insights into diversification and taxonomy ofAllorhizobium vitis(i.e.Agrobacterium vitis)

Kuzmanović

Biondi

Overmann

et al. 2020

Preprint

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Allorhizobium vitis (formerly named Agrobacterium vitis or Agrobacterium biovar 3) is the primary causative agent of crown gall disease of grapevine worldwide. Whole-genome sequence comparisons and phylogenomic analysis of various All. vitis strains clearly indicated that All. vitis is not a single species, but represents a species complex composed of at least four genomic species. Thus, we amended the description of All. vitis which now refers to a restricted group of strains within the All. vitis complex (i.e. All. vitis sensu stricto) and proposed a description of a novel species All. ampelinum sp. nov. The type strain of All. vitis sensu stricto remains the existing type strain of All. vitis, K309T (= NCPPB 3554T =HAMBI 1817T = ATCC 49767T = CIP 105853T = ICMP 10752T = IFO 15140T = JCM 21033T = LMG 8750T = NBRC 15140T). The type strain of All. ampelinum sp. nov. is S4T (= DSM 112012T = ATCCBAA-846T). This genome-based classification was supported by differentiation of strains based on a MALDI-TOF MS analysis. We also identified gene clusters specific for All. vitis species complex, All. vitis sensu stricto and All. ampelinum, and attempted to predict their function and their role in ecological diversification of these clades, some of which were experimentally validated. Functions of All. vitis species complex-specific genes convergently indicate a role in adaptation to different stresses, including exposure to aromatic compounds. Similarly, All vitis sensu stricto-specific genes also confer the ability to degrade 4-hydroxyphenylacetate and a putative compound related to gentisic acid, while All. ampelinum-specific genes have putative functions related to polyamine metabolism and nickel assimilation. This suggests that these species have differentiated ecologies, each relying on specialized nutrient consumption or toxic compound degradation to adapt to their respective niche. Moreover, our genome-based analysis indicated that Allorhizobium and the “R. aggregatum complex” represent separate genera of the family Rhizobiaceae.

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Construction of physical map and mapping of chromosomal virulence genes of the biovar 3 Agrobacterium (Rhizobium vitis) strain K-Ag-1

Cited by 7 publications

References 30 publications

Ability of Agrobacterium tumefaciens and A. rhizogenes strains, inability of A. vitis and A. rubi strains to adapt to salt-insufficient environment, and taxonomic significance of a simple salt requirement test in the pathogenic Agrobacterium species

Ability of Agrobacterium tumefaciens and A. rhizogenes strains, inability of A. vitis and A. rubi strains to adapt to salt-insufficient environment, and taxonomic significance of a simple salt requirement test in the pathogenic Agrobacterium species

Genomic analysis provides novel insights into diversification and taxonomy of Allorhizobium vitis (i.e. Agrobacterium vitis)

Genomic analysis provides novel insights into diversification and taxonomy ofAllorhizobium vitis(i.e.Agrobacterium vitis)

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