The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000

C. Robin Buell; Vinita Joardar; Magdalen Lindeberg; Jeremy Selengut; Ian T. Paulsen; Michelle L. Gwinn; Robert J. Dodson; Robert T. Deboy; A. Scott Durkin; James F. Kolonay; Ramana Madupu; Sean Daugherty; Lauren Brinkac; Maureen J. Beanan; Daniel H. Haft; William C. Nelson; Tanja Davidsen; Nikhat Zafar; Liwei Zhou; Jia Liu; Qiaoping Yuan; Hoda Khouri; Nadia Fedorova; Bao Tran; Daniel Russell; Kristi Berry; Teresa Utterback; Susan E. Van Aken; Tamara V. Feldblyum; Mark D'Ascenzo; Wen Ling Deng; Adela R. Ramos; James R. Alfano; Samuel Cartinhour; Arun K. Chatterjee; Terrence P. Delaney; Sondra G. Lazarowitz; Gregory B. Martin; David J. Schneider; Xiaoyan Tang; Carol L. Bender; Owen White; Claire M. Fraser; Alan Collmer

doi:10.1073/pnas.1731982100

The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000

C. Robin Buell, Vinita Joardar, Magdalen Lindeberg, Jeremy Selengut, Ian T. Paulsen, Michelle L. Gwinn, Robert J. Dodson, Robert T. Deboy, A. Scott Durkin, James F. Kolonay, Ramana Madupu, Sean Daugherty, Lauren Brinkac, Maureen J. Beanan, Daniel H. Haft, William C. Nelson, Tanja Davidsen, Nikhat Zafar, Liwei Zhou, Jia LiuQiaoping Yuan, Hoda Khouri, Nadia Fedorova, Bao Tran, Daniel Russell, Kristi Berry, Teresa Utterback, Susan E. Van Aken, Tamara V. Feldblyum, Mark D'Ascenzo, Wen Ling Deng, Adela R. Ramos, James R. Alfano, Samuel Cartinhour, Arun K. Chatterjee, Terrence P. Delaney, Sondra G. Lazarowitz, Gregory B. Martin, David J. Schneider, Xiaoyan Tang, Carol L. Bender, Owen White, Claire M. Fraser, Alan Collmer

Plant Pathology

Research output: Contribution to journal › Article › peer-review

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Abstract

We report the complete genome sequence of the model bacterial pathogen Pseudomonas syringae pathovar tomato DC3000 (DC3000), which is pathogenic on tomato and Arabidopsis thaliana. The DC3000 genome (6.5 megabases) contains a circular chromosome and two plasmids, which collectively encode 5,763 ORFs. We identified 298 established and putative virulence genes, including several clusters of genes encoding 31 confirmed and 19 predicted type III secretion system effector proteins. Many of the virulence genes were members of paralogous families and also were proximal to mobile elements, which collectively comprise 7% of the DC3000 genome. The bacterium possesses a large repertoire of transporters for the acquisition of nutrients, particularly sugars, as well as genes implicated in attachment to plant surfaces. Over 12% of the genes are dedicated to regulation, which may reflect the need for rapid adaptation to the diverse environments encountered during epiphytic growth and pathogenesis. Comparative analyses confirmed a high degree of similarity with two sequenced pseudomonads, Pseudomonas putida and Pseudomonas aeruginosa, yet revealed 1,159 genes unique to DC3000, of which 811 lack a known function.

Original language	English (US)
Pages (from-to)	10181-10186
Number of pages	6
Journal	Proceedings of the National Academy of Sciences of the United States of America
Volume	100
Issue number	18
DOIs	https://doi.org/10.1073/pnas.1731982100
State	Published - Sep 2 2003

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Buell, C. R., Joardar, V., Lindeberg, M., Selengut, J., Paulsen, I. T., Gwinn, M. L., Dodson, R. J., Deboy, R. T., Durkin, A. S., Kolonay, J. F., Madupu, R., Daugherty, S., Brinkac, L., Beanan, M. J., Haft, D. H., Nelson, W. C., Davidsen, T., Zafar, N., Zhou, L., ... Collmer, A. (2003). The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000. Proceedings of the National Academy of Sciences of the United States of America, 100(18), 10181-10186. https://doi.org/10.1073/pnas.1731982100

The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000. / Buell, C. Robin; Joardar, Vinita; Lindeberg, Magdalen; Selengut, Jeremy; Paulsen, Ian T.; Gwinn, Michelle L.; Dodson, Robert J.; Deboy, Robert T.; Durkin, A. Scott; Kolonay, James F.; Madupu, Ramana; Daugherty, Sean; Brinkac, Lauren; Beanan, Maureen J.; Haft, Daniel H.; Nelson, William C.; Davidsen, Tanja; Zafar, Nikhat; Zhou, Liwei; Liu, Jia; Yuan, Qiaoping; Khouri, Hoda; Fedorova, Nadia; Tran, Bao; Russell, Daniel; Berry, Kristi; Utterback, Teresa; Van Aken, Susan E.; Feldblyum, Tamara V.; D'Ascenzo, Mark; Deng, Wen Ling; Ramos, Adela R.; Alfano, James R.; Cartinhour, Samuel; Chatterjee, Arun K.; Delaney, Terrence P.; Lazarowitz, Sondra G.; Martin, Gregory B.; Schneider, David J.; Tang, Xiaoyan; Bender, Carol L.; White, Owen; Fraser, Claire M.; Collmer, Alan.

In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 100, No. 18, 02.09.2003, p. 10181-10186.

Research output: Contribution to journal › Article › peer-review

Buell, CR, Joardar, V, Lindeberg, M, Selengut, J, Paulsen, IT, Gwinn, ML, Dodson, RJ, Deboy, RT, Durkin, AS, Kolonay, JF, Madupu, R, Daugherty, S, Brinkac, L, Beanan, MJ, Haft, DH, Nelson, WC, Davidsen, T, Zafar, N, Zhou, L, Liu, J, Yuan, Q, Khouri, H, Fedorova, N, Tran, B, Russell, D, Berry, K, Utterback, T, Van Aken, SE, Feldblyum, TV, D'Ascenzo, M, Deng, WL, Ramos, AR, Alfano, JR, Cartinhour, S, Chatterjee, AK, Delaney, TP, Lazarowitz, SG, Martin, GB, Schneider, DJ, Tang, X, Bender, CL, White, O, Fraser, CM & Collmer, A 2003, 'The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000', Proceedings of the National Academy of Sciences of the United States of America, vol. 100, no. 18, pp. 10181-10186. https://doi.org/10.1073/pnas.1731982100

Buell, C. Robin ; Joardar, Vinita ; Lindeberg, Magdalen ; Selengut, Jeremy ; Paulsen, Ian T. ; Gwinn, Michelle L. ; Dodson, Robert J. ; Deboy, Robert T. ; Durkin, A. Scott ; Kolonay, James F. ; Madupu, Ramana ; Daugherty, Sean ; Brinkac, Lauren ; Beanan, Maureen J. ; Haft, Daniel H. ; Nelson, William C. ; Davidsen, Tanja ; Zafar, Nikhat ; Zhou, Liwei ; Liu, Jia ; Yuan, Qiaoping ; Khouri, Hoda ; Fedorova, Nadia ; Tran, Bao ; Russell, Daniel ; Berry, Kristi ; Utterback, Teresa ; Van Aken, Susan E. ; Feldblyum, Tamara V. ; D'Ascenzo, Mark ; Deng, Wen Ling ; Ramos, Adela R. ; Alfano, James R. ; Cartinhour, Samuel ; Chatterjee, Arun K. ; Delaney, Terrence P. ; Lazarowitz, Sondra G. ; Martin, Gregory B. ; Schneider, David J. ; Tang, Xiaoyan ; Bender, Carol L. ; White, Owen ; Fraser, Claire M. ; Collmer, Alan. / The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000. In: Proceedings of the National Academy of Sciences of the United States of America. 2003 ; Vol. 100, No. 18. pp. 10181-10186.

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title = "The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000",

abstract = "We report the complete genome sequence of the model bacterial pathogen Pseudomonas syringae pathovar tomato DC3000 (DC3000), which is pathogenic on tomato and Arabidopsis thaliana. The DC3000 genome (6.5 megabases) contains a circular chromosome and two plasmids, which collectively encode 5,763 ORFs. We identified 298 established and putative virulence genes, including several clusters of genes encoding 31 confirmed and 19 predicted type III secretion system effector proteins. Many of the virulence genes were members of paralogous families and also were proximal to mobile elements, which collectively comprise 7% of the DC3000 genome. The bacterium possesses a large repertoire of transporters for the acquisition of nutrients, particularly sugars, as well as genes implicated in attachment to plant surfaces. Over 12% of the genes are dedicated to regulation, which may reflect the need for rapid adaptation to the diverse environments encountered during epiphytic growth and pathogenesis. Comparative analyses confirmed a high degree of similarity with two sequenced pseudomonads, Pseudomonas putida and Pseudomonas aeruginosa, yet revealed 1,159 genes unique to DC3000, of which 811 lack a known function.",

author = "Buell, {C. Robin} and Vinita Joardar and Magdalen Lindeberg and Jeremy Selengut and Paulsen, {Ian T.} and Gwinn, {Michelle L.} and Dodson, {Robert J.} and Deboy, {Robert T.} and Durkin, {A. Scott} and Kolonay, {James F.} and Ramana Madupu and Sean Daugherty and Lauren Brinkac and Beanan, {Maureen J.} and Haft, {Daniel H.} and Nelson, {William C.} and Tanja Davidsen and Nikhat Zafar and Liwei Zhou and Jia Liu and Qiaoping Yuan and Hoda Khouri and Nadia Fedorova and Bao Tran and Daniel Russell and Kristi Berry and Teresa Utterback and {Van Aken}, {Susan E.} and Feldblyum, {Tamara V.} and Mark D'Ascenzo and Deng, {Wen Ling} and Ramos, {Adela R.} and Alfano, {James R.} and Samuel Cartinhour and Chatterjee, {Arun K.} and Delaney, {Terrence P.} and Lazarowitz, {Sondra G.} and Martin, {Gregory B.} and Schneider, {David J.} and Xiaoyan Tang and Bender, {Carol L.} and Owen White and Fraser, {Claire M.} and Alan Collmer",

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T1 - The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000

AU - Buell, C. Robin

AU - Joardar, Vinita

AU - Lindeberg, Magdalen

AU - Selengut, Jeremy

AU - Paulsen, Ian T.

AU - Gwinn, Michelle L.

AU - Dodson, Robert J.

AU - Deboy, Robert T.

AU - Durkin, A. Scott

AU - Kolonay, James F.

AU - Madupu, Ramana

AU - Daugherty, Sean

AU - Brinkac, Lauren

AU - Beanan, Maureen J.

AU - Haft, Daniel H.

AU - Nelson, William C.

AU - Davidsen, Tanja

AU - Zafar, Nikhat

AU - Zhou, Liwei

AU - Liu, Jia

AU - Yuan, Qiaoping

AU - Khouri, Hoda

AU - Fedorova, Nadia

AU - Tran, Bao

AU - Russell, Daniel

AU - Berry, Kristi

AU - Utterback, Teresa

AU - Van Aken, Susan E.

AU - Feldblyum, Tamara V.

AU - D'Ascenzo, Mark

AU - Deng, Wen Ling

AU - Ramos, Adela R.

AU - Alfano, James R.

AU - Cartinhour, Samuel

AU - Chatterjee, Arun K.

AU - Delaney, Terrence P.

AU - Lazarowitz, Sondra G.

AU - Martin, Gregory B.

AU - Schneider, David J.

AU - Tang, Xiaoyan

AU - Bender, Carol L.

AU - White, Owen

AU - Fraser, Claire M.

AU - Collmer, Alan

PY - 2003/9/2

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N2 - We report the complete genome sequence of the model bacterial pathogen Pseudomonas syringae pathovar tomato DC3000 (DC3000), which is pathogenic on tomato and Arabidopsis thaliana. The DC3000 genome (6.5 megabases) contains a circular chromosome and two plasmids, which collectively encode 5,763 ORFs. We identified 298 established and putative virulence genes, including several clusters of genes encoding 31 confirmed and 19 predicted type III secretion system effector proteins. Many of the virulence genes were members of paralogous families and also were proximal to mobile elements, which collectively comprise 7% of the DC3000 genome. The bacterium possesses a large repertoire of transporters for the acquisition of nutrients, particularly sugars, as well as genes implicated in attachment to plant surfaces. Over 12% of the genes are dedicated to regulation, which may reflect the need for rapid adaptation to the diverse environments encountered during epiphytic growth and pathogenesis. Comparative analyses confirmed a high degree of similarity with two sequenced pseudomonads, Pseudomonas putida and Pseudomonas aeruginosa, yet revealed 1,159 genes unique to DC3000, of which 811 lack a known function.

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The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000

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