|Duan, Yong Ping|
Submitted to: Molecular Plant-Microbe Interactions
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/5/2005
Publication Date: 1/6/2006
Citation: Gabriel, D.W., Allen, C.A., Schell, M., Denny, T., Greenberg, J., Duan, Y.P., Flores-Cruz, Z., Huang, Q., Clifford, J.M., Presting, G., Gonzelez, E.T., Reedy, J., Elphinstone, J., Swanson, J., Yao, J., Mulholand, V., Liu, L., Farmerie, W., Patnaikuni, M., Galogh, B., Norman, D., Alverez, A., Castillo, J., Saddler, G., Walunas, T., Zhukov, A. and Mikhailova, N. 2006. Molecular Plant-Microbe Interaction. Identification of open reading frames unique to a select agent: Ralstonia solanacearum race 3, biovar 2. 19:69-79.
Interpretive Summary: Ralstonia solanacearum causes bacterial wilt, a soilborne vascular disease that is distributed worldwide in tropical and warm temperate regions. The disease attacks over 450 plant species including ornamentals, and is the major constraint on production of many economically important crops including potato and tomato. R. solanacearum is generally classified into 5 races and 5 biovars based on host range and carbohydrate utilization. Race 3, biovar2 (R3B2) causes brown rot, which ranks among the most destructive diseases of potato in Africa, Asia, and Central and South America. R3B2 strains are listed as Select Agents in the United States and are quarantined pathogens in Europe and Canada. In this study, the genome of R3B2 was determined and the unique R3B2 genome components were identified in order to gain a better understanding of the pathogen and to develop race-specific detection method. Our work will be of value primarily to plant pathologists, as well as state and federal regulatory officials interested in diseases caused by R. solanacearum R3B2.
Technical Abstract: An 8X draft genome was obtained and annotated for Ralstonia solanacearum race 3 biovar 2 strain UW551, a USDA 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 83% 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 PCR 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 are likely essential for utilization of the three sugar alcohols that distinguish biovars 3 and 4 from biovars 1 and 2.