Identification of open reading frames unique to a select agent: Ralstonia solanacearum race 3 biovar 2

Dean W. Gabriel, Caitilyn Allen, Mark Schell, Timothy P. Denny, Jean T. Greenberg, Yong Ping Duan, Zomary Flores-Cruz, Qi Huang, Jennifer M. Clifford, Gernot Presting, Enid T. González, Joseph Reddy, John Elphinstone, Jill Swanson, Jian Yao, Vincent Mulholland, Li Liu, William Farmerie, Manjeera Patnaikuni, Botond Balogh & 8 others David Norman, Anne Alvarez, Jose A. Castillo, Jeffrey Jones, Gerry Saddler, Theresa Walunas, Aleksey Zhukov, Natalia Mikhailova

Research output: Contribution to journalArticle

  • 83 Citations

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.

LanguageEnglish (US)
Pages69-79
Number of pages11
JournalMolecular Plant-Microbe Interactions
Volume19
Issue number1
DOIs
StatePublished - Jan 1 2006

Fingerprint

Ralstonia solanacearum
Open Reading Frames
open reading frames
Genome
Genes
genome
genes
Geranium
Sugar Alcohols
Prophages
Horizontal Gene Transfer
United States Department of Agriculture
sugar alcohols
Base Composition
Lycopersicon esculentum
Transfer RNA
Base Pairing
Virulence
Amino Acid Sequence
USDA

Keywords

  • Bacterial wilt
  • Comparative genomics

ASJC Scopus subject areas

  • Physiology
  • Agronomy and Crop Science

Cite this

Gabriel, D. W., Allen, C., Schell, M., Denny, T. P., Greenberg, J. T., Duan, Y. P., ... Mikhailova, N. (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. DOI: 10.1094/MPMI-19-0069
Gabriel, Dean W. ; Allen, Caitilyn ; Schell, Mark ; Denny, Timothy P. ; Greenberg, Jean T. ; Duan, Yong Ping ; Flores-Cruz, Zomary ; Huang, Qi ; Clifford, Jennifer M. ; Presting, Gernot ; González, Enid T. ; Reddy, Joseph ; Elphinstone, John ; Swanson, Jill ; Yao, Jian ; Mulholland, Vincent ; Liu, Li ; Farmerie, William ; Patnaikuni, Manjeera ; Balogh, Botond ; Norman, David ; Alvarez, Anne ; Castillo, Jose A. ; Jones, Jeffrey ; Saddler, Gerry ; Walunas, Theresa ; Zhukov, Aleksey ; Mikhailova, Natalia. / Identification of open reading frames unique to a select agent : Ralstonia solanacearum race 3 biovar 2. In: Molecular Plant-Microbe Interactions. 2006 ; Vol. 19, No. 1. pp. 69-79
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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.",
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Gabriel, DW, Allen, C, Schell, M, Denny, TP, Greenberg, JT, Duan, YP, Flores-Cruz, Z, Huang, Q, Clifford, JM, Presting, G, González, ET, Reddy, J, Elphinstone, J, Swanson, J, Yao, J, Mulholland, V, Liu, L, Farmerie, W, Patnaikuni, M, Balogh, B, Norman, D, Alvarez, A, Castillo, JA, Jones, J, Saddler, G, Walunas, T, Zhukov, A & Mikhailova, N 2006, 'Identification of open reading frames unique to a select agent: Ralstonia solanacearum race 3 biovar 2' Molecular Plant-Microbe Interactions, vol. 19, no. 1, pp. 69-79. DOI: 10.1094/MPMI-19-0069

Identification of open reading frames unique to a select agent : Ralstonia solanacearum race 3 biovar 2. / Gabriel, Dean W.; Allen, Caitilyn; Schell, Mark; Denny, Timothy P.; Greenberg, Jean T.; Duan, Yong Ping; Flores-Cruz, Zomary; Huang, Qi; Clifford, Jennifer M.; Presting, Gernot; González, Enid T.; Reddy, Joseph; Elphinstone, John; Swanson, Jill; Yao, Jian; Mulholland, Vincent; Liu, Li; Farmerie, William; Patnaikuni, Manjeera; Balogh, Botond; Norman, David; Alvarez, Anne; Castillo, Jose A.; Jones, Jeffrey; Saddler, Gerry; Walunas, Theresa; Zhukov, Aleksey; Mikhailova, Natalia.

In: Molecular Plant-Microbe Interactions, Vol. 19, No. 1, 01.01.2006, p. 69-79.

Research output: Contribution to journalArticle

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T1 - Identification of open reading frames unique to a select agent

T2 - Molecular Plant-Microbe Interactions

AU - Gabriel,Dean W.

AU - Allen,Caitilyn

AU - Schell,Mark

AU - Denny,Timothy P.

AU - Greenberg,Jean T.

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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 - 2006/1/1

Y1 - 2006/1/1

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.

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Gabriel DW, Allen C, Schell M, Denny TP, Greenberg JT, Duan YP et al. Identification of open reading frames unique to a select agent: Ralstonia solanacearum race 3 biovar 2. Molecular Plant-Microbe Interactions. 2006 Jan 1;19(1):69-79. Available from, DOI: 10.1094/MPMI-19-0069