title: Identification of open reading frames unique to a select agent: Ralstonia solanacearum race 3 biovar 2.
abstract: 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.
authors.affiliation: Plant Pathology Department, University of Florida, Gainesville, USA. gabriel@biotech.ufl.edu
authors.forename: Dean W
authors.initials: DW
authors.lastname: Gabriel
authors.forename: Caitilyn
authors.initials: C
authors.lastname: Allen
authors.forename: Mark
authors.initials: M
authors.lastname: Schell
authors.forename: Timothy P
authors.initials: TP
authors.lastname: Denny
authors.forename: Jean T
authors.initials: JT
authors.lastname: Greenberg
authors.forename: Yong Ping
authors.initials: YP
authors.lastname: Duan
authors.forename: Zomary
authors.initials: Z
authors.lastname: Flores-Cruz
authors.forename: Qi
authors.initials: Q
authors.lastname: Huang
authors.forename: Jennifer M
authors.initials: JM
authors.lastname: Clifford
authors.forename: Gernot
authors.initials: G
authors.lastname: Presting
authors.forename: Enid T
authors.initials: ET
authors.lastname: González
authors.forename: Joseph
authors.initials: J
authors.lastname: Reddy
authors.forename: John
authors.initials: J
authors.lastname: Elphinstone
authors.forename: Jill
authors.initials: J
authors.lastname: Swanson
authors.forename: Jian
authors.initials: J
authors.lastname: Yao
authors.forename: Vincent
authors.initials: V
authors.lastname: Mulholland
authors.forename: Li
authors.initials: L
authors.lastname: Liu
authors.forename: William
authors.initials: W
authors.lastname: Farmerie
authors.forename: Manjeera
authors.initials: M
authors.lastname: Patnaikuni
authors.forename: Botond
authors.initials: B
authors.lastname: Balogh
authors.forename: David
authors.initials: D
authors.lastname: Norman
authors.forename: Anne
authors.initials: A
authors.lastname: Alvarez
authors.forename: Jose A
authors.initials: JA
authors.lastname: Castillo
authors.forename: Jeffrey
authors.initials: J
authors.lastname: Jones
authors.forename: Gerry
authors.initials: G
authors.lastname: Saddler
authors.forename: Theresa
authors.initials: T
authors.lastname: Walunas
authors.forename: Aleksey
authors.initials: A
authors.lastname: Zhukov
authors.forename: Natalia
authors.initials: N
authors.lastname: Mikhailova
mesh_terms: 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
chemical_list: D037521:Virulence Factors; D001120:Arginine