Origin of Pathogens of Grapevine Crown Gall Disease in Hokkaido in Japan as Characterized by Molecular Epidemiology of Allorhizobium vitis Strains

Crown gall is a globally distributed and economically important disease of grapevine and other important crop plants. The causal agent of grapevine crown gall is tumorigenic Allorhizobium vitis (Ti) strains that harbor a tumor-inducing plasmid (pTi). The epidemic of grapevine crown gall has not been widely elucidated. In this study, we investigated the genetic diversity of 89 strains of Ti and nonpathogenic A. vitis to clarify their molecular epidemiology. Multi-locus sequence analysis (MLSA) of the partial nucleotide sequences of pyrG, recA, and rpoD was performed for molecular typing of A. vitis strains isolated from grapevines with crown gall symptoms grown in 30 different vineyards, five different countries, mainly in Japan, and seven genomic groups A to F were obtained. The results of MLSA and logistic regression indicated that the population of genetic group A was significantly related to a range of prefectures and that the epidemic of group A strains originated mainly in Hokkaido in Japan through soil infection. Moreover, group E strains could have been transported by infected nursery stocks. In conclusion, this study indicates that both soil infection and transporting of infected nursery stocks are working as infection source in Hokkaido.

Complete Genome Sequence Data of the Grapevine Crown Gall inhibiting bacteria Allorhizobium vitis Strain F2/5.

Crown gall disease in grapevine is caused by pathogenic strains of Allorhizobium vitis. A. vitis strain F2/5 is a non-pathogenic biocontrol agent that was previously shown to act as a biological control agent to crown gall disease and first isolated from South Africa. Here, we present the complete assembled genome and is 5.94 Mb in length with 5,414 predicted protein-coding sequences, has two circular chromosomes and five plasmids. The genome sequence has no detectable T-DNA border sequences and is missing key virulence genes which is consistent with the bacteria being non-pathogenic. The F2/5 genome sequence could contribute to understanding the molecular basis underlying the biocontrol activity.

Near-Complete Genome Assembly of the Grapevine Crown Gall Pathogen Allorhizobium vitis Strain K377

Here, we report the annotated, near-complete genome sequence of Allorhizobium vitis K377, a phytopathogenic Rhizobiales strain isolated from a grapevine in South Australia. The assembled genome sequence is 6.40 Mb long, with 5,855 predicted protein-coding sequences, 56 tRNAs, and 12 rRNAs, and contains ttuC (tartrate metabolism; chromosomal) and nopaline synthesis, uptake, and catabolic genes (tumor-inducing plasmid-encoded).

Establishment, maintenance and ordering of grapevine traits collections (Vitis vinifera L.)

Based on the grapevine genotypes of NSC “Tairov Research Institute of Viticulture and Wine-Making” analysis, traits collections have been created and registered, representing genotypes for breeding programs to obtain new varieties resistant to abiotic and biotic environmental factors (frost and phytopathogens) under conditions implementation of climate change scenarios, varieties with improved quality traits and seedless varieties. Genetic ordering of traits collections has begun on the basis of varieties molecular identification using microsatellite DNA markers (from 5 to 9 MC loci) and identification using DNA markers of genes of interest or gene complexes (primarily a trait of seedlessness). Microsatellite analysis made it possible to identify a total of about 80 genotypes, mainly the varieties breeded at the NSC “Tairov Research Institute of Viticulture and Wine-Making”, belonging to the traits collections of resistance and quality. Visual sanitary control of three traits collections showed a practical absence of virus diseases and grapevine crown gall disease symptoms. Sometimes symptoms similar to the phytoplasma infection manifestation were found. The data of virus diseases agents identification by ELISA showed the absence the most harmful viruses — grapevine fanleaf virus (GFLV) and grapevine leafroll virus 1 (GLRaV I) on 19 samples tested. From samples of resistance traits collection one sample was positive on grapevine leafroll virus 3 and two were positive on grapevine fleck virus (GfkV). These samples should be eliminated from further propagation and genetic material moving between germplasm repositories. The causative agent of grapevine crown gall disease (Agrobacterium vitis) was not detected on 14 samples of 3 traits collections tested by PCR. It has been determined that the sanitary status of grapevine traits collections practically corresponds to the European minimum sanitary requirements, genetic ordering of characteristic collections will be continued.

Characterization of Migration and Induced Resistance of Rhizobium Vitis Strain ARK-1, a Biological Control Agent Against Grapevine Crown Gall Disease

A nonpathogenic strain ARK-1 of Rhizobium vitis has an antagonistic activity toward tumorigenic (Ti) strain of R. vitis, a causal agent of grapevine crown gall disease, and works as a biocontrol agent. We have demonstrated that the gall formation was fully suppressed when ARK-1 was co-inoculated with Ti into the grapevine stem at a 1:1 ratio. For practical use of ARK-1 in agriculture, understanding the temporal dynamics of the bacterial habitat on host plants and the biocontrol property are needed in order to develop proper application methods. Here we demonstrated that the gall incidence by Ti was reduced to about 50% when ARK-1 was pre-inoculated at both upper and lower positions on the grapevine stem 3 cm away from the Ti-inoculation point 5 days before. The bacterial cell detection assay in the grapevine tissue revealed that ARK-1 could migrate at least 3 cm in 5 days. Inoculations of ARK-1 or Ti induced expression of marker genes for defense-related phytohormones such as salicylic acid, jasmonic acid, and ethylene in grapevine within 3 days but they were diminished by 6 days. Inoculation of Ti 5 days after ARK-1 pre-inoculation induced expression of the marker genes except for the LOX-9 gene in a basically similar way to those without the pre-inoculation, suggesting that ARK-1 did not induce typical acquired systemic resistance or induced systemic resistance in grapevine, while the transcript of LOX-9 was detected at 24 and 48 hours after the Ti inoculation when ARK-1 was pre-inoculated, unlike the un-inoculated condition. ARK-1 primed the induction of certain defense genes and it may take part in its biocontrol activity.

Complete Genome Sequence Data of Tumorigenic Rhizobium vitis Strain VAT03-9, a Causal Agent of Grapevine Crown Gall Disease

Rhizobium vitis strain VAT03-9 (MAFF 211676) is a causal agent of crown gall disease in grapevine. It is one of the pathogenic strains of R. vitis isolated from graft unions of grapevine in Okayama Prefecture, Japan. Inoculation tests verified its virulence for gall formation on grapevine, tomato, and sunflower. It harbors tumor-inducing plasmid. Here, we present the complete genome sequence with annotation of R. vitis VAR03-9 obtained by assembling reads from PacBio and Illumina-sequencers. This genome sequence should be useful for the analyses of pathogenicity and evolutionary lineage of the pathogens of crown gall disease. [Formula: see text] Copyright © 2020 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

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

ABSTRACT Here, we present the annotated complete genome sequence of Allorhizobium vitis K306, a phytopathogenic strain causing crown gall of grapevine. The A. vitis K306 genome is 5.79 Mb long with 5,199 predicted protein-coding genes and contains 2 circular chromosomes of 3.8 Mb and 1.1 Mb and 2 plasmids, namely, pTiK306 and pTrK306, that are 262 kb and 581 kb, respectively.

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

Using Illumina and Nanopore reads, we assembled a high-quality draft genome sequence of Allorhizobium vitis K309T (= ATCC 49767T, = NCPPB 3554T), a phytopathogenic strain isolated from a grapevine in Australia. The hybrid approach generated 50% fewer contigs and a 3-fold increase in the N 50 value compared with the previous Illumina-only assembly.