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.
Gabriel
Dean W
DW
Plant Pathology Department, University of Florida, Gainesville, USA. gabriel@biotech.ufl.edu
Allen
Caitilyn
C
Schell
Mark
M
Denny
Timothy P
TP
Greenberg
Jean T
JT
Duan
Yong Ping
YP
Flores-Cruz
Zomary
Z
Huang
Qi
Q
Clifford
Jennifer M
JM
Presting
Gernot
G
González
Enid T
ET
Reddy
Joseph
J
Elphinstone
John
J
Swanson
Jill
J
Yao
Jian
J
Mulholland
Vincent
V
Liu
Li
L
Farmerie
William
W
Patnaikuni
Manjeera
M
Balogh
Botond
B
Norman
David
D
Alvarez
Anne
A
Castillo
Jose A
JA
Jones
Jeffrey
J
Saddler
Gerry
G
Walunas
Theresa
T
Zhukov
Aleksey
A
Mikhailova
Natalia
N
D001120:Arginine; D005798:Genes, Bacterial; D016680:Genome, Bacterial / Q000235:genetics; D005810:Multigene Family; D016366:Open Reading Frames / Q000235:genetics*; D011401:Promoter Regions, Genetic; D039002:Prophages; D021381:Protein Transport; D043368:Ralstonia solanacearum / Q000145:classification* / Q000235:genetics* / Q000472:pathogenicity; D017422:Sequence Analysis, DNA; D013045:Species Specificity; D037521:Virulence Factors
D037521:Virulence Factors; D001120:Arginine