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

Kuzmanović, Nemanja; Biondi, Enrico; Overmann, Jörg; Puławska, Joanna; Verbarg, Susanne; Smalla, Kornelia; Lassalle, Florent

doi:10.1186/s12864-022-08662-x

Cited by 20 publications

(15 citation statements)

References 90 publications

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“…Core‐genome‐ and pan‐genome‐based phylogenies were inferred using GET_HOMOLOGUES Version 11042019 (Contreras‐Moreira & Vinuesa, 2013) and GET_PHYLOMARKERS Version 2.2.8_18Nov2018 (Vinuesa et al, 2018) as described before (Kuzmanović, Biondi, et al, 2022). For core‐genome‐based phylogenetic analyses, the latter pipeline was run using both DNA and protein sequences, thus generating core‐genome and core‐proteome phylogenies, respectively.…”

Section: Methodsmentioning

confidence: 99%

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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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Section: Methodsmentioning

confidence: 99%

“…The data set included two R. tumorigenes strains (1078 T and 932) and 12 strains comprising the new species R. rhododendri (see below; Table A1, https://doi.org/10.6084/m9.figshare.22193809). The analysis was performed using the GET_HOMOLOGUES software and its auxiliary scripts as described before (Kuzmanović, Biondi et al, 2022).…”

Section: Methodsmentioning

confidence: 99%

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

et al. 2023

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“…Core-genome- and pan-genome-based phylogenies were inferred using GET_HOMOLOGUES Version 11042019 (Contreras-Moreira and Vinuesa 2013) and GET_PHYLOMARKERS Version 2.2.8_18Nov2018 (Vinuesa et al 2018) as described before (Kuzmanović et al 2022b). For core-genome-based phylogenetic analyses, the latter pipeline was run using both DNA and protein sequences, thus generating core-genome and core-proteome phylogenies, respectively.…”

Section: Methodsmentioning

confidence: 99%

“…Nevertheless, based on the available genomes, the majority of species-specific genes are encoded on putative chromids and megaplasmids, which is in line with previous studies analyzing the A. tumefaciens species complex (Lassalle et al 2017) and All. vitis species complex (Kuzmanović et al 2022b) strains. Although most of the species-specific genes are annotated as encoding hypothetical or poorly described proteins, we could determine putative functions for several genes and gene clusters.…”

Section: Diversification Of "Tumorigenes" Cladementioning

confidence: 99%

Genomics of the “tumorigenes” clade of the familyRhizobiaceaeand description ofRhizobium rhododendrisp. nov.

Kuzmanović

diCenzo

Bunk

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 agricultural 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, 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 USA, 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 ecological diversification of R. rhododendri and R. tumorigenes were predicted and discussed.

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“…Core-genome phylogeny was inferred using the GET_HOMOLOGUES Version 11042019 ( Contreras-Moreira and Vinuesa, 2013 ) and GET_PHYLOMARKERS Version 2.2.8_18Nov2018 ( Vinuesa et al., 2018 ) software packages as described before ( Kuzmanović et al., 2022 ). The dataset contained two strains studied (KBI 423 T and KBI 447), as well as reference strains of Brenneria (14 strains), Dickeya (3 strains), Lonsdalea (3 strains) and Pectobacterium (3 strains).…”

Section: Methodsmentioning

confidence: 99%

Polyphasic study of phytopathogenic bacterial strains associated with deep bark canker of walnut in Serbia revealed a new species, Brenneria izbisi sp. nov

2022

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Serious outbreaks of walnut deep bark canker were observed on young walnut trees (Juglans regia L.) in two localities in the northern part of Serbia during 2020. From the symptomatic walnut tissues, two types of bacterial colonies were isolated, predominantly, light cream, circular and smooth colonies, as well as small, yellowish, mucoid and convex ones. PCR analysis and phenotypic assays suggested that the former group belongs to Brenneria spp., while the latter isolates were identified as Xanthomonas arboricola pv. juglandis. Within the Brenneria group, two strains were identified as Brenneria nigrifluens, while other 15 strains did not belong to any Brenneria species described so far. Therefore, we selected four representative strains of the unknown Brenneria sp. and subjected them to polyphasic analysis. As expected, in a phylogenetic tree based on partial 16S rDNA sequences, four novel strains grouped with other Brenneria representatives, and showed close phylogenetic relationship to Brenneria salicis. Furthermore, multilocus sequence analysis (MLSA) based on the partial sequences of atpD, gyrB, infB and rpoB housekeeping genes and core-genome phylogeny indicated that the studied strains form a novel and a clearly separate Brenneria lineage. Overall genome relatedness indices showed that they represent a new Brenneria species. The new species can be differentiated from the other Brenneria spp. infecting walnut and closely related B. salicis strains based on phenotypic characteristics, as well. Moreover, the pathogenicity tests on two-year-old walnut plants proved the ability of strains to cause necrosis and longitudinal black lesions and cracks on the trunk and branches of walnut trees. Overall, polyphasic characterization showed that the studied strains isolated from walnut with symptoms of deep bark canker represent a novel species of the genus Brenneria for which the name Brenneria izbisi sp. nov. is proposed. The type strain of B. izbisi is KBI 423T (= CFBP 9035T = LMG 32479T). To facilitate rapid identification of newly described species, a conventional PCR protocol and primers targeting the putative gene hrpP, were developed. Further study should reveal the potential role of each pathogen isolated from symptomatic walnut in disease development as well as possible interaction between them.

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

Cited by 20 publications

References 90 publications

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

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

Genomics of the “tumorigenes” clade of the familyRhizobiaceaeand description ofRhizobium rhododendrisp. nov.

Polyphasic study of phytopathogenic bacterial strains associated with deep bark canker of walnut in Serbia revealed a new species, Brenneria izbisi sp. nov

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