Complete genome sequence analysis of the peanut pathogen Ralstonia solanacearum strain Rs-P.362200

Abstract

Background: Bacterial 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.

Results: Here, 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.

Conclusion: The 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.

Keywords: Effector; Genome; Pathogenicity island; Peanut; Prophage; Ralstonia solanacearum.

Fig. 1

The circular maps of the RS-P362200 genome. The outermost circle indicates the size of the genome (0, 1, and 2 indicate the chromosome, the big plasmid and the small one, respectively, each scale is 0.1 Mb); the second and third circles are genes on the positive and negative strands of the genome, respectively. Different colors represent different COG functional classifications (for the detailed explanations of functional groups of each color, see the Fig. 2). The fourth circle is the repeat sequence; the fifth circle is the tRNA; the innermost layer is the GC content. The red bars of this layer indicates that the GC content in this area is higher than the average GC content of the genome. The blue bars indicates that the GC content in this region is lower than the average GC level of the genome

Fig. 2

Functional classification analysis in Rs-P.362200 genome. a COG classification statistics: Letters along the abscissa is the content of functional classification of COG, and the ordinate is the number of genes. b GO classification statistics: The abscissa is the name of each GO classification, the left of the ordinate is the percentage of the number of genes, and the right is the number of genes

Fig. 3

NR species distribution statistics. This map reflects the distribution of different homologous species genome annotated by NR. Different colors represent different homologous species

Fig. 4

Genetic relationship between Rs-P.362200 and other virulent strains. The evolutionary relationship was inferred using the Neighbor-Joining method. Phylogenetic tree based on the comparison of endoglucanase gene sequence from R. solanacearum strains. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches. The bottom 0.2 scale represents two nucleotide change per 100-nucleotide position

Fig. 5

Venn diagram showing the orthologous genes shared between or distinct to the indicated R. solanacearum strains Rs-P.362200, GMI1000, CMR15, Po82 and PSI07. There are 3400 common protein-coding gene clusters for these five types of strains and Rs-P.362200 contains more specific gene families