Abstract
Ralstonia pseudosolanacearum causes bacterial wilt in ginger, reducing ginger production worldwide. We sequenced the whole genome of a highly virulent phylotype I, race 4, biovar 3 Ralstonia pseudosolanacearum strain GRsMep isolated from a severely infected ginger field in India. R. pseudosolanacearum GRsMep genome is organised into two replicons: chromosome and megaplasmid with a total genome size of 5,810,605 bp. This strain encodes approximately 72 effectors which include a combination of core effectors as well as highly variable, diverse repertoire of type III effectors. Comparative genome analysis with GMI1000 identified conservation in the genes involved in the general virulence mechanism. Our analysis identified type III effectors, RipBJ and RipBO as present in GRsMep but absent in the reported genomes of other strains infecting Zingiberaceae family. GRsMep contains 126 unique genes when compared to the pangenome of the Ralstonia strains that infect the Zingiberaceae family. The whole-genome data of R. pseudosolanacearum strain will serve as a resource for exploring the evolutionary processes that structure and regulate the virulence determinants of the strain. Pathogenicity testing of the transposon insertional mutant library of GRsMep through virulence assay on ginger plants identified a few candidate virulence determinants specific to bacterial wilt in ginger.
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Data availability
The whole genome of R.pseudosolanacearum GRsMep has been deposited in NCBI under Bioproject accession number PRJNA772165. The Biosample accession number is SAMN22367847.
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Acknowledgements
The work is supported by National Post-Doctoral Fellowship (PDF/2016/003228/LS), awarded to Suraby E. J. by Science, Engineering and Research Board (SERB), India and Central University of Kerala (internal funding) to Ginny Antony. The authors acknowledge the Director, ICAR-Indian Institute of Spices Research for providing the R. pseudosolanacearum cultures.
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438_2022_1925_MOESM9_ESM.jpg
Supplementary file9 Fig. S1. The distribution of genomic islands and prophages in GRsMep genome a) Chromosome, b) Megaplasmid. The regions in different colours indicate GIs predicted by different prediction methods such as integrated (red), IslandPath-DIMOB (blue), SIGI-HMM (orange) and Island Pick (green) (JPG 737 KB)
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Supplementary file10 Fig. S2. KEGG distribution of core, accessory, and unique genes of Ralstonia strains infecting members of Zingiberaceae family. The bar diagram represents the distribution of core, accessory and unique genes in a) major category and b) sub-category (JPG 959 KB)
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Supplementary file11 Fig. S3. Phylogenetic tree comparing GRsMep with Ralstonia strains from other phylotypes based on OrthoANI values. The heat map was generated with orthoANI values calculated from OAT software. Ralstonia strains used in the analysis is detailed in Table 1. All the strains used for the comparison based on OrthoANI values are non-pathogenic to ginger. (JPG 478 KB)
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Suraby, E.J., Sruthi, K.B. & Antony, G. Genome-wide identification of type III effectors and other virulence factors in Ralstonia pseudosolanacearum causing bacterial wilt in ginger (Zingiber officinale). Mol Genet Genomics 297, 1371–1388 (2022). https://doi.org/10.1007/s00438-022-01925-y
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DOI: https://doi.org/10.1007/s00438-022-01925-y