Genome Sequencing of Ralstonia solanacearum Biovar 3, Phylotype I, Strains Rs-09-161 and Rs-10-244, Isolated from Eggplant and Chili in India.

Ralstonia solanacearum Indian strains Rs-09-161 and Rs-10-244 were isolated from the coastal region of Goa and from the Andaman Islands. We report the draft genome sequences of these representative isolates infecting solanaceous vegetables in India.

GENOME ANNOUNCEMENT

Ralstonia solanacearum is a major plant-pathogenic bacterium that causes bacterial wilt disease in over 400 plant species (1). R. solanacearum strains from Africa, South America, North America, and the Caribbean have been sequenced (2). Phylotype I R. solanacearum strains from China have already been sequenced (3–5). Though bacterial wilt is severe in India (6), no genomic sequence is available as of yet. We sequenced the R. solanacearum strains Rs-09-161 and Rs-10-244, respectively isolated from eggplant (Solanum melongena) grown in the west coast region of India and chili (Capsicum annum) grown in the Andaman Islands, India. Both strains belong to biovar 3, phylotype I, historically classified as race 1. Endoglucanase (egl) gene sequence analysis of R. solanacearum isolates collected from India indicated that Rs-09-161 belongs to the major group found within the phylotype I strains and hence represents the R. solanacearum population infecting solanaceous vegetables from India. Based on the egl gene sequence analysis, Rs-10-244 is the representative R. solanacearum isolate from the other subgroup.

Using Illumina HiSeq 2000, we obtained the nucleotide sequences of the Rs-09-161 and Rs-10-244 genomes from a paired-end library with an average insert size of 300 to 500 bp. The trimmed reads were assembled into contigs by using SOAP de novo (1.05) and Velvet (1.2.07). Meta-assembly was done using progressiveMauve (2.3.1), with R. solanacearum strain GMI1000 as the reference genome. Structural annotation was carried out using EuGene-P (7), with R. solanacearum strain GMI1000 as the reference proteome.

The overall G+C content of the Rs-09-161 genome is 66.82%. It contains 5,215 predicted genes, similar to the species complex average of 5,213. The draft genome sequence consists of 5,185 protein-coding genes with a mean gene length of 974 bp and 30 non-protein-coding genes with a mean gene length of 534 bp. The overall G+C content of the Rs-10-244 genome is 66.98%. It contains 5,202 predicted genes. The draft genome sequence consists of 5,171 protein-coding genes with a mean gene length of 969 bp and 31 non-protein-coding genes with a mean gene length of 446 bp. Compared with the published R. solanacearum genomes, Rs-09-161 and Rs-10-244 are most closely related to phylotype I strains GMI 1000 and FQY_4.

Further, T3E genes present in these genomes are identified according to the latest nomenclature (2). 71 T3E genes are present in Rs-09-161, which includes two putative candidate T3E genes, and 76 T3E genes are present in Rs-10-244.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at GenBank under the accession numbers JHBO00000000 for strain Rs-09-161 and JHAM00000000 for strain Rs-10-244. The versions described in this paper are the first versions.