High-Quality Draft Genome Sequence of the Type Strain of Allorhizobium vitis, the Primary Causal Agent of Grapevine Crown Gall

Gan, Han Ming; Lee, Melvin Vun Jye; Savka, Michael A.

doi:10.1128/mra.01045-18

Cited by 7 publications

(9 citation statements)

References 15 publications

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“…We re-sequenced the genome of Agrobacterium radiobacter type strain using strain directly obtained from NCPPB. The assembled Agrobacterium radiobacter genome reported in this study exhibits assembly statistics that are consistent with a high-quality draft genome such as high genome completeness and contiguity, near-zero contamination/duplication and comparable genome size to other closely related strains (Gan, Lee & Savka, 2018; Parks et al, 2015). Furthermore, given the improved contiguity and dramatic reduction in the number of contigs of this newly assembled draft genome, we recommend using this genome in place of the previously published draft genome for future Agrobacterium comparative studies.…”

Section: Discussionsupporting

confidence: 71%

Improved genome ofAgrobacterium radiobactertype strain provides new taxonomic insight intoAgrobacteriumgenomospecies 4

Gan

Lee

Savka

2019

PeerJ

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The reported Agrobacterium radiobacter DSM 30174T genome is highly fragmented, hindering robust comparative genomics and genome-based taxonomic analysis. We re-sequenced the Agrobacterium radiobacter type strain, generating a dramatically improved genome with high contiguity. In addition, we sequenced the genome of Agrobacterium tumefaciens B6T, enabling for the first time, a proper comparative genomics of these contentious Agrobacterium species. We provide concrete evidence that the previously reported Agrobacterium radiobacter type strain genome (Accession Number: ) is contaminated which explains its abnormally large genome size and fragmented assembly. We propose that Agrobacterium tumefaciens be reclassified as Agrobacterium radiobacter subsp. tumefaciens and that Agrobacterium radiobacter retains it species status with the proposed name of Agrobacterium radiobacter subsp. radiobacter. This proposal is based, first on the high pairwise genome-scale average nucleotide identity supporting the amalgamation of both Agrobacterium radiobacter and Agrobacterium tumefaciens into a single species. Second, maximum likelihood tree construction based on the concatenated alignment of shared genes (core genes) among related strains indicates that Agrobacterium radiobacter NCPPB3001 is sufficiently divergent from Agrobacterium tumefaciens to propose two independent sub-clades. Third, Agrobacterium tumefaciens demonstrates the genomic potential to synthesize the L configuration of fucose in its lipid polysaccharide, fostering its ability to colonize plant cells more effectively than Agrobacterium radiobacter.

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Section: Discussionsupporting

confidence: 71%

Improved genome ofAgrobacterium radiobactertype strain provides new taxonomic insight intoAgrobacteriumgenomospecies 4

Gan

Lee

Savka

2019

PeerJ

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“…After assembly by Flye, four contigs were produced that had a combined length of 5.79 Mb and a GC content of 57.5% ( Table 1 ). The K306 genome size and GC content are similar to those of the draft genome of A. vitis K309 and the completely assembled A. vitis S4 genome ( 7 , 8 ). The A. vitis S4 genome has two circular chromosomes and five plasmids, including the tumor-inducing plasmid pTiS4.…”

Section: Announcementmentioning

confidence: 56%

“…The A. vitis strain known as K306 is of the OL type, i.e., catabolizes octopine and has a large TA (T-DNA) region ( 4 ), and strains of this type catabolize octopine as a sole carbon and nitrogen source ( 5 , 6 ). To date, only two A. vitis genome sequences are available, namely, a complete genome sequence of strain S4 ( 7 ) and a draft genome sequence of the type strain K309 (NCPPB 3554) ( 8 ).…”

Section: Announcementmentioning

confidence: 99%

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Complete Genome Sequence of Allorhizobium vitis Strain K306, the Causal Agent of Grapevine Crown Gall

Ryder

Searle

2020

Microbiol Resour Announc

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“…The causal agent of CG tumor disease is commonly referred to as Agrobacterium vitis which was recently reclassified to the genus Allorhizobium based on whole genome phylogeny (Mousavi et al, 2014; Gan et al, 2018). Although less common, some strains of tumor-inducing (Ti) plasmid-harboring Agrobacterium tumefaciens can also cause CG (Pu and Goodman, 1992; Abdellatif et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

Insight Into the Microbial Co-occurrence and Diversity of 73 Grapevine (Vitis vinifera) Crown Galls Collected Across the Northern Hemisphere

et al. 2019

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Crown gall (CG) is a globally distributed and economically important disease of grapevine and other important crop plants. The causal agent of CG is Agrobacterium or Allorhizobium strains that harbor a tumor-inducing plasmid (pTi). The microbial community within the CG tumor has not been widely elucidated and it is not known if certain members of this microbial community promote or inhibit CG. This study investigated the microbiotas of grapevine CG tumor tissues from seven infected vineyards located in Hungary, Japan, Tunisia, and the United States. Heavy co-amplification of grapevine chloroplast and mitochondrial ribosomal RNA genes was observed with the widely used Illumina V3–V4 16S rRNA gene primers, requiring the design of a new reverse primer to enrich for bacterial 16S rRNA from CG tumors. The operational taxonomic unit (OTU) clustering approach is not suitable for CG microbiota analysis as it collapsed several ecologically distinct Agrobacterium species into a single OTU due to low interspecies genetic divergence. The CG microbial community assemblages were significantly different across sampling sites (ANOSIM global R = 0.63, p- value = 0.001) with evidence of site-specific differentially abundant ASVs. The presence of Allorhizobium vitis in the CG microbiota is almost always accompanied by Xanthomonas and Novosphingobium , the latter may promote the spread of pTi plasmid by way of acyl-homoserine lactone signal production, whereas the former may take advantage of the presence of substrates associated with plant cell wall growth and repair. The technical and biological insights gained from this study will contribute to the understanding of complex interaction between the grapevine and its microbial community and may facilitate better management of CG disease in the future.

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High-Quality Draft Genome Sequence of the Type Strain of Allorhizobium vitis, the Primary Causal Agent of Grapevine Crown Gall

Cited by 7 publications

References 15 publications

Improved genome ofAgrobacterium radiobactertype strain provides new taxonomic insight intoAgrobacteriumgenomospecies 4

Improved genome ofAgrobacterium radiobactertype strain provides new taxonomic insight intoAgrobacteriumgenomospecies 4

Complete Genome Sequence of Allorhizobium vitis Strain K306, the Causal Agent of Grapevine Crown Gall

Insight Into the Microbial Co-occurrence and Diversity of 73 Grapevine (Vitis vinifera) Crown Galls Collected Across the Northern Hemisphere

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