Molecular Plant-Microbe Interactions (2006) 19, 69-79

D.W. Gabriel, C. Allen, M. Schell, T.P. Denny, J.T. Greenberg, Y.P. Duan, Z. Flores-Cruz, Q. Huang, J.M. Clifford, G. Presting, E.T. González, J. Reddy, J. Elphinstone, J. Swanson, J. Yao, V. Mulholland, L. Liu, W. Farmerie, Manjeera Patnaikuni, Botond Balogh, David Norman, Anne Alvarez, Jose A. Castillo, Jeffrey Jones, Gerry Saddler, Theresa Walunas, Aleksey Zhukov and Natalia Mikhailova (2006)
Identification of open reading frames unique to a select agent: Ralstonia solanacearum race 3 biovar 2
Molecular Plant-Microbe Interactions 19 (1), 69-79
Abstract: An 8× 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.
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Link to article at publishers website
Database assignments for author(s): Dean W. Gabriel, Caitilyn Allen, John Elphinstone

Research topic(s) for pests/diseases/weeds:
molecular biology - genes

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Pest and/or beneficial records:

Beneficial	Pest/Disease/Weed	Crop/Product	Country	Quarant.
	Ralstonia solanacearum	Geranium (crop)