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Gabriel, D.W. et al.

Gabriel, Allen, Schell, Denny, Greenberg, Duan, Flores-Cruz, Huang, Clifford, Presting, González, Reddy, Elphinstone, Swanson, Yao, Mulholland, Liu, Farmerie, Patnaikuni, Balogh, Norman, Alvarez, Castillo, Jones, Saddler, Walunas, Zhukov, Mikhailova,

Identification of open reading frames unique to a select agent: Ralstonia solanacearum race 3 biovar 2.

An 8x draft genome was obtained and annotated for Ralstonia solanacearum race 3 biovar 2 (R3B2) strain UW551, a United States Department of Agriculture Select Agent isolated from geranium. The draft UW551 genome consisted of 80,169 reads resulting in 582 contigs containing 5,925,491 base pairs, with an average 64.5% GC content. Annotation revealed a predicted 4,454 protein coding open reading frames (ORFs), 43 tRNAs, and 5 rRNAs; 2,793 (or 62%) of the ORFs had a functional assignment. The UW551 genome was compared with the published genome of R. solanacearum race 1 biovar 3 tropical tomato strain GMI1000. The two phylogenetically distinct strains were at least 71% syntenic in gene organization. Most genes encoding known pathogenicity determinants, including predicted type III secreted effectors, appeared to be common to both strains. A total of 402 unique UW551 ORFs were identified, none of which had a best hit or >45% amino acid sequence identity with any R. solanacearum predicted protein; 16 had strong (E < 10(-13)) best hits to ORFs found in other bacterial plant pathogens. Many of the 402 unique genes were clustered, including 5 found in the hrp region and 38 contiguous, potential prophage genes. Conservation of some UW551 unique genes among R3B2 strains was examined by polymerase chain reaction among a group of 58 strains from different races and biovars, resulting in the identification of genes that may be potentially useful for diagnostic detection and identification of R3B2 strains. One 22-kb region that appears to be present in GMI1000 as a result of horizontal gene transfer is absent from UW551 and encodes enzymes that likely are essential for utilization of the three sugar alcohols that distinguish biovars 3 and 4 from biovars 1 and 2.[1]

References

Identification of open reading frames unique to a select agent: Ralstonia solanacearum race 3 biovar 2. Gabriel, D.W., Allen, C., Schell, M., Denny, T.P., Greenberg, J.T., Duan, Y.P., Flores-Cruz, Z., Huang, Q., Clifford, J.M., Presting, G., González, E.T., Reddy, J., Elphinstone, J., Swanson, J., Yao, J., Mulholland, V., Liu, L., Farmerie, W., Patnaikuni, M., Balogh, B., Norman, D., Alvarez, A., Castillo, J.A., Jones, J., Saddler, G., Walunas, T., Zhukov, A., Mikhailova, N. Mol. Plant Microbe Interact. (2006) [Pubmed]

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