TY - JOUR
T1 - Identification of open reading frames unique to a select agent
T2 - Ralstonia solanacearum race 3 biovar 2
AU - Gabriel, Dean W.
AU - Allen, Caitilyn
AU - Schell, Mark
AU - Denny, Timothy P.
AU - Greenberg, Jean T.
AU - Duan, Yong Ping
AU - Flores-Cruz, Zomary
AU - Huang, Qi
AU - Clifford, Jennifer M.
AU - Presting, Gernot
AU - González, Enid T.
AU - Reddy, Joseph
AU - Elphinstone, John
AU - Swanson, Jill
AU - Yao, Jian
AU - Mulholland, Vincent
AU - Liu, Li
AU - Farmerie, William
AU - Patnaikuni, Manjeera
AU - Balogh, Botond
AU - Norman, David
AU - Alvarez, Anne
AU - Castillo, Jose A.
AU - Jones, Jeffrey
AU - Saddler, Gerry
AU - Walunas, Theresa
AU - Zhukov, Aleksey
AU - Mikhailova, Natalia
PY - 2006/1
Y1 - 2006/1
N2 - 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.
AB - 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.
KW - Bacterial wilt
KW - Comparative genomics
UR - http://www.scopus.com/inward/record.url?scp=29444453684&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=29444453684&partnerID=8YFLogxK
U2 - 10.1094/MPMI-19-0069
DO - 10.1094/MPMI-19-0069
M3 - Article
C2 - 16404955
AN - SCOPUS:29444453684
SN - 0894-0282
VL - 19
SP - 69
EP - 79
JO - Molecular Plant-Microbe Interactions
JF - Molecular Plant-Microbe Interactions
IS - 1
ER -