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Draft Genome Sequence of Ralstonia solanacearum Race 4 Biovar 4 Strain SD54.

ABSTRACT: Ralstonia solanacearum is an important etiological agent that can cause serious bacterial wilt in a very wide range of potential host plants, including ginger. Here, we report the complete genome sequence of R. solanacearum SD54, a race 4 biovar 4 (R4B4) strain from a diseased ginger plant in China.

SUBMITTER: Shan W

PROVIDER: S-EPMC3868847 | biostudies-literature | 2013 Dec

REPOSITORIES: biostudies-literature

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Draft Genome Sequence of Ralstonia solanacearum Race 4 Biovar 4 Strain SD54.

Shan Weiwei W Yang Xiaohui X Ma Weiqing W Yang Yu Y Guo Xiao X Guo Jianhua J Zheng Huajun H Li Guangcun G Xie Bingyan B

Genome announcements 20131219 6

Ralstonia solanacearum is an important etiological agent that can cause serious bacterial wilt in a very wide range of potential host plants, including ginger. Here, we report the complete genome sequence of R. solanacearum SD54, a race 4 biovar 4 (R4B4) strain from a diseased ginger plant in China. ...[more]

PMID: 24356823

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Project description:A filamentous bacteriophage, designated ϕRs551, was isolated and purified from the quarantine and select agent phytopathogen Ralstonia solanacearum race 3 biovar 2 strain UW551 (phylotype IIB sequevar 1) grown under normal culture conditions. Electron microscopy suggested that ϕRs551 is a member of the family Inoviridae, and is about 1200 nm long and 7 nm wide. ϕRs551 has a genome of 7929 nucleotides containing 14 open reading frames, and is the first isolated virion that contains a resolvase (ORF13) and putative type-2 phage repressor (ORF14). Unlike other R. solanacearum phages isolated from soil, the genome sequence of ϕRs551 is not only 100% identical to its prophage sequence in the deposited genome of R. solanacearum strain UW551 from which the phage was isolated, but is also surprisingly found with 100% identity in the deposited genomes of 10 other phylotype II sequevar 1 strains of R. solanacearum. Furthermore, it is homologous to genome RS-09-161, resulting in the identification of a new prophage, designated RSM10, in a R. solanacearum strain from India. When ORF13 and a core attP site of ϕRs551 were either deleted individually or in combination, phage integration was not observed, suggesting that similar to other filamentous R. solanacearum ϕRSM phages, ϕRs551 relies on its resolvase and the core att sequence for site-directed integration into its susceptible R. solanacearum strain. The integration occurred four hours after phage infection. Infection of a susceptible R. solanacearum strain RUN302 by ϕRs551 resulted in less fluidal colonies and EPS production, and reduced motilities of the bacterium. Interestingly, infection of RUN302 by ϕRs551 also resulted in reduced virulence, rather than enhanced or loss of virulence caused by other ϕRSM phages. Study of bacteriophages of R. solanacearum would contribute to a better understanding of the phage-bacterium-environment interactions in order to develop integrated management strategies to combat R. solanacearum.

Project description:BackgroundBacterial wilt caused by Ralstonia solanacearum species complex is an important soil-borne disease worldwide that affects more than 450 plant species, including peanut, leading to great yield and quality losses. However, there are no effective measures to control bacterial wilt. The reason is the lack of research on the pathogenic mechanism of bacterial wilt.ResultsHere, we report the complete genome of a toxic Ralstonia solanacearum species complex strain, Rs-P.362200, a peanut pathogen, with a total genome size of 5.86 Mb, encoding 5056 genes and the average G + C content of 67%. Among the coding genes, 75 type III effector proteins and 12 pseudogenes were predicted. Phylogenetic analysis of 41 strains including Rs-P.362200 shows that genetic distance mainly depended on geographic origins then phylotypes and host species, which associated with the complexity of the strain. The distribution and numbers of effectors and other virulence factors changed among different strains. Comparative genomic analysis showed that 29 families of 113 genes were unique to this strain compared with the other four pathogenic strains. Through the analysis of specific genes, two homologous genes (gene ID: 2_657 and 3_83), encoding virulence protein (such as RipP1) may be associated with the host range of the Rs-P.362200 strain. It was found that the bacteria contained 30 pathogenicity islands and 6 prophages containing 378 genes, 7 effectors and 363 genes, 8 effectors, respectively, which may be related to the mechanism of horizontal gene transfer and pathogenicity evaluation. Although the hosts of HA4-1 and Rs-P.362200 strains are the same, they have specific genes to their own genomes. The number of genomic islands and prophages in HA4-1 genome is more than that in Rs-P.36220, indicating a rapid change of the bacterial wilt pathogens.ConclusionThe complete genome sequence analysis of peanut bacterial wilt pathogen enhanced the information of R. solanacearum genome. This research lays a theoretical foundation for future research on the interaction between Ralstonia solanacearum and peanut.

Dataset Information

Draft Genome Sequence of Ralstonia solanacearum Race 4 Biovar 4 Strain SD54.

Publications

Draft Genome Sequence of Ralstonia solanacearum Race 4 Biovar 4 Strain SD54.

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