Genetic relatedness and recombination analysis of<i>Allorhizobium vitis</i>strains associated with grapevine crown gall outbreaks in Europe

Kuzmanović, Nemanja; Biondi, Enrico; Bertaccini, Assunta; Obradović, Aleksa

doi:10.1111/jam.12858

Cited by 11 publications

(20 citation statements)

References 47 publications

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“…vitis strains used in this study were isolated from crown gall tumors on grapevine originating from different geographical areas (Table 1). These strains were predominantly representatives of the two main phylogenetic groups (C and D) delineated in our previous study (Kuzmanovid et al, 2015).…”

Section: Methodsmentioning

confidence: 79%

“…Our previous study based on the analysis of several housekeeping gene sequences suggested the existence of several phylogenetic groups within All. vitis species complex (Kuzmanovid et al, 2015). The present study focused on two phylogenetic groups defined in the previous study, the first comprises the type strain of All.…”

Section: Discussionmentioning

confidence: 99%

“…vitis genomic species based on OGRIs (e.g. ANI and isDDH) and core-genome phylogeny, as well as by analysis of sequences of housekeeping genes (Kuzmanovid et al, 2015). Furthermore, All.…”

Section: Description Of Allorhizobium Ampelinum Sp Novmentioning

confidence: 99%

“…Thus, our previous study analyzing a representative collection of All. vitis strains originating from several European countries, Africa, North America, and Australia using MLSA indicated a high genetic diversity between strains, which clustered into four main phylogenetic groups (Kuzmanovid et al, 2015). These data suggested that All.…”

Section: Introductionmentioning

confidence: 99%

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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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Section: Methodsmentioning

confidence: 79%

Section: Discussionmentioning

confidence: 99%

“…vitis genomic species based on OGRIs (e.g. ANI and isDDH) and core-genome phylogeny, as well as by analysis of sequences of housekeeping genes (Kuzmanovid et al, 2015). Furthermore, All.…”

Section: Description Of Allorhizobium Ampelinum Sp Novmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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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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“…vitis harboured a circular chromid, supporting the distinction into different genera (Ram ırez-Bahena et al 2014). In the same way, recent phylogenetic and genomic analyses proposed that Agrobacterium must be retained as a valid genus gathering Agrobacterium rubi, Agrobacterium larrymoorei and agrobacteria of the so-called biovar 1 (Ram ırez-Bahena et al 2014;Kuzmanovi c et al 2015;Mousavi et al 2015). The appellation 'biovar 1' comprises several genomic species (or genomospecies), called G1 to G9, G13 and G14, among which some received a Latin epithet, such as 'Agrobacterium fabrum' for G8 (Lassalle et al 2011;Shams et al 2013).…”

Section: Introductionmentioning

confidence: 99%

Characterization and phylogenetic diversity of Allorhizobium vitis isolated from grapevine in Morocco

et al. 2019

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Aims Crown gall, a phytobacteriosis characterized by the formation of tumours on plant roots was observed in recently planted vineyards of the Meknes region (Morocco). The objective of this research was to analyse the diversity of pathogenic agrobacteria isolated from grapevine in Morocco. Methods and Results Eighty‐two isolates from 11 affected vineyards were characterized by recA sequencing and were found to belong to Agrobacterium tumefaciens genomospecies G1, G4 or G7, Rhizobium rhizogenes, and to Allorhizobium vitis. Only the All. vitis isolates appeared to be pathogenic on tomato and multilocus sequence analysis phylogenetic analyses revealed a weak genetic diversity, with the definition of only four genomic groups. Definition of the All. vitis genomic groups correlated with specific pathogenic traits: indeed, genomic groups differed with respect to the severity of hypersensitive response symptoms on tobacco leaves, the intensity of necrotic response on grapevine explants and opine profiles. Both vitopine and octopine were detected by UHPLC in tumours induced by isolates of three genomic groups, an opine signature scarcely ever reported. Conclusions Allorhizobium vitis is the only causative agent of crown gall on grape in Morocco, pathogenic isolates can be separated into four genomic groups. Significance and Impact of the Study This study of recently crown‐gall‐infested vineyards demonstrated that All. vitis is the only causative agent and revealed the presence of nonpathogenic Agrobacterium strain within tumours. Moreover, as the genetic diversity of the All. vitis isolates is relatively narrow, this study lays the basis for further analyses on the evolution of the disease, on the dissemination of the pTi and more globally on the fate of the different genomic groups in this newly colonized environment.

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Genomics of the “tumorigenes” clade of the family Rhizobiaceae and description of Rhizobium rhododendri sp. nov.

et al. 2023

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Tumorigenic members of the family Rhizobiaceae, known as agrobacteria, are responsible for crown and cane gall diseases of various crops worldwide. Tumorigenic agrobacteria are commonly found in the genera Agrobacterium, Allorhizobium, and Rhizobium. In this study, we analyzed a distinct “tumorigenes” clade of the genus Rhizobium, which includes the tumorigenic species Rhizobium tumorigenes, as well as strains causing crown gall disease on rhododendron. Here, high‐quality, closed genomes of representatives of the “tumorigenes” clade were generated, followed by comparative genomic and phylogenomic analyses. Additionally, the phenotypic characteristics of representatives of the “tumorigenes” clade were analyzed. Our results showed that the tumorigenic strains isolated from rhododendron represent a novel species of the genus Rhizobium for which the name Rhizobium rhododendri sp. nov. is proposed. This species also includes additional strains originating from blueberry and Himalayan blackberry in the United States, whose genome sequences were retrieved from GenBank. Both R. tumorigenes and R. rhododendri contain multipartite genomes, including a chromosome, putative chromids, and megaplasmids. Synteny and phylogenetic analyses indicated that a large putative chromid of R. rhododendri resulted from the cointegration of an ancestral megaplasmid and two putative chromids, following its divergence from R. tumorigenes. Moreover, gene clusters specific for both species of the “tumorigenes” clade were identified, and their biological functions and roles in the ecological diversification of R. rhododendri and R. tumorigenes were predicted and discussed.

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Genetic relatedness and recombination analysis ofAllorhizobium vitisstrains associated with grapevine crown gall outbreaks in Europe

Abstract: We demonstrated clear epidemiological relationship between majority of strains studied, suggesting a need for more stringent phytosanitary measures in international trade. Moreover, this is the first study to report recombination in A. vitis.

Cited by 11 publications

References 47 publications

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

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

Characterization and phylogenetic diversity of Allorhizobium vitis isolated from grapevine in Morocco

Genomics of the “tumorigenes” clade of the family Rhizobiaceae and description of Rhizobium rhododendri sp. nov.

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