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Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A
Steven L Salzberg, Daniel D Sommer, Michael C Schatz, Adam M Phillippy, Pablo D Rabinowicz, Seiji Tsuge, Ayako Furutani, Hirokazu Ochiai, Arthur L Delcher, David Kelley, Ramana Madupu, Daniela Puiu, Diana Radune, Martin Shumway, Cole Trapnell, Gudlur Aparna, Gopaljee Jha, Alok Pandey, Prabhu B Patil, Hiromichi Ishihara, Damien F Meyer, Boris Szurek, Valerie Verdier, Ralf Koebnik, J Maxwell Dow, Robert P Ryan, Hisae Hirata, Shinji Tsuyumu, Sang Won Lee, Pamela C Ronald, Ramesh V Sonti, Marie-Anne Van Sluys, Jan E Leach, Frank F White, Adam J Bogdanove
BMC Genomics. 2008; 9: 204. Published online 2008 May 1. doi: 10.1186/1471-2164-9-204
Correction in:
BMC Genomics. 2008; 9: 534.
PMCID:
PMC2432079
Abstract Full Text PDF–943K Supplementary Material Correction

Is Cited by the Following 28 Articles in this Archive:

Genomes-based phylogeny of the genus Xanthomonas
Luis M Rodriguez-R, Alejandro Grajales, Mario L Arrieta-Ortiz, Camilo Salazar, Silvia Restrepo, Adriana Bernal
BMC Microbiol. 2012; 12: 43. Published online 2012 March 23. doi: 10.1186/1471-2180-12-43
PMCID:
PMC3359215
Abstract Full Text PDF–928K Supplementary Material
Fructose-Bisphophate Aldolase Exhibits Functional Roles between Carbon Metabolism and the hrp System in Rice Pathogen Xanthomonas oryzae pv. oryzicola
Wei Guo, Li-fang Zou, Yu-rong Li, Yi-ping Cui, Zhi-yuan Ji, Lu-lu Cai, Hua-song Zou, William C. Hutchins, Ching-hong Yang, Gong-you Chen
PLoS One. 2012; 7(2): e31855. Published online 2012 February 22. doi: 10.1371/journal.pone.0031855
PMCID:
PMC3285194
Abstract Full Text PDF–857K Supplementary Material
Type Three Effector Gene Distribution and Sequence Analysis Provide New Insights into the Pathogenicity of Plant-Pathogenic Xanthomonas arboricola
Ahmed Hajri, Joël F. Pothier, Marion Fischer-Le Saux, Sophie Bonneau, Stéphane Poussier, Tristan Boureau, Brion Duffy, Charles Manceau
Appl Environ Microbiol. 2012 January; 78(2): 371–384. doi: 10.1128/AEM.06119-11
PMCID:
PMC3255760
Free in PMC on 2012/07/01
Novel Roles of SoxR, a Transcriptional Regulator from Xanthomonas campestris, in Sensing Redox-Cycling Drugs and Regulating a Protective Gene That Have Overall Implications for Bacterial Stress Physiology and Virulence on a Host Plant
Aekkapol Mahavihakanont, Nisanart Charoenlap, Poommaree Namchaiw, Warawan Eiamphungporn, Sorayut Chattrakarn, Paiboon Vattanaviboon, Skorn Mongkolsuk
J Bacteriol. 2012 January; 194(2): 209–217. doi: 10.1128/JB.05603-11
PMCID:
PMC3256661
Free in PMC on 2012/07/01
KdgR, an IClR Family Transcriptional Regulator, Inhibits Virulence Mainly by Repression of hrp Genes in Xanthomonas oryzae pv. oryzae
Yao Lu, Islam M. Rashidul, Hisae Hirata, Shinji Tsuyumu
J Bacteriol. 2011 December; 193(23): 6674–6682. doi: 10.1128/JB.05714-11
PMCID:
PMC3232914
Free in PMC on 2012/06/01
Two New Complete Genome Sequences Offer Insight into Host and Tissue Specificity of Plant Pathogenic Xanthomonas spp.
Adam J. Bogdanove, Ralf Koebnik, Hong Lu, Ayako Furutani, Samuel V. Angiuoli, Prabhu B. Patil, Marie-Anne Van Sluys, Robert P. Ryan, Damien F. Meyer, Sang-Wook Han, Gudlur Aparna, Misha Rajaram, Arthur L. Delcher, Adam M. Phillippy, Daniela Puiu, Michael C. Schatz, Martin Shumway, Daniel D. Sommer, Cole Trapnell, Faiza Benahmed, George Dimitrov, Ramana Madupu, Diana Radune, Steven Sullivan, Gopaljee Jha, Hiromichi Ishihara, Sang-Won Lee, Alok Pandey, Vikas Sharma, Malinee Sriariyanun, Boris Szurek, Casiana M. Vera-Cruz, Karin S. Dorman, Pamela C. Ronald, Valérie Verdier, J. Maxwell Dow, Ramesh V. Sonti, Seiji Tsuge, Volker P. Brendel, Pablo D. Rabinowicz, Jan E. Leach, Frank F. White, Steven L. Salzberg
J Bacteriol. 2011 October; 193(19): 5450–5464. doi: 10.1128/JB.05262-11
PMCID:
PMC3187462
Abstract Full Text PDF–3.5M Supplementary Material
Mycobacterium tuberculosis Rv0899 defines a family of membrane proteins widespread in nitrogen-fixing bacteria
Francesca M. Marassi
Proteins. Author manuscript; available in PMC 2012 October 1.
Published in final edited form as: Proteins. 2011 October; 79(10): 2946–2955. Published online 2011 August 26. doi: 10.1002/prot.23151
PMCID:
PMC3172613
Free in PMC on 2012/10/01
A Novel Manganese Efflux System, YebN, Is Required for Virulence by Xanthomonas oryzae pv. oryzae
Chunxia Li, Jun Tao, Daqing Mao, Chaozu He
PLoS One. 2011; 6(7): e21983. Published online 2011 July 14. doi: 10.1371/journal.pone.0021983
PMCID:
PMC3136493
Abstract Full Text PDF–987K Supplementary Material
Genomic Analysis of Xanthomonas oryzae Isolates from Rice Grown in the United States Reveals Substantial Divergence from Known X. oryzae Pathovars
L. R. Triplett, J. P. Hamilton, C. R. Buell, N. A. Tisserat, V. Verdier, F. Zink, J. E. Leach
Appl Environ Microbiol. 2011 June; 77(12): 3930–3937. doi: 10.1128/AEM.00028-11
PMCID:
PMC3131649
Abstract Full Text PDF–534K Supplementary Material
A Component of the Xanthomonadaceae Type IV Secretion System Combines a VirB7 Motif with a N0 Domain Found in Outer Membrane Transport Proteins
Diorge P. Souza, Maxuel O. Andrade, Cristina E. Alvarez-Martinez, Guilherme M. Arantes, Chuck S. Farah, Roberto K. Salinas
PLoS Pathog. 2011 May; 7(5): e1002031. Published online 2011 May 12. doi: 10.1371/journal.ppat.1002031
PMCID:
PMC3093366
Abstract Full Text PDF–2.3M Supplementary Material
The influence of the accessory genome on bacterial pathogen evolution
Robert W Jackson, Boris Vinatzer, Dawn L Arnold, Steve Dorus, Jesús Murillo
Mob Genet Elements. 2011 May-Jun; 1(1): 55–65. Published online May-Jun 2011. doi: 10.4161/mge.1.1.16432
PMCID:
PMC3190274
Abstract Full Text PDF–3.8M
Identification and functional characterization of small non-coding RNAs in Xanthomonas oryzae pathovar oryzae
Hong Liang, Ying-Tao Zhao, Jie-Qiong Zhang, Xiu-Jie Wang, Rong-Xiang Fang, Yan-Tao Jia
BMC Genomics. 2011; 12: 87. Published online 2011 January 30. doi: 10.1186/1471-2164-12-87
PMCID:
PMC3039613
Abstract Full Text PDF–986K Supplementary Material
Analysis of streptococcal CRISPRs from human saliva reveals substantial sequence diversity within and between subjects over time
David T. Pride, Christine L. Sun, Julia Salzman, Nitya Rao, Peter Loomer, Gary C. Armitage, Jillian F. Banfield, David A. Relman
Genome Res. 2011 January; 21(1): 126–136. doi: 10.1101/gr.111732.110
PMCID:
PMC3012920
Abstract Full Text PDF–949K
Rice xa13 Recessive Resistance to Bacterial Blight Is Defeated by Induction of the Disease Susceptibility Gene Os-11N3
Ginny Antony, Junhui Zhou, Sheng Huang, Ting Li, Bo Liu, Frank White, Bing Yang
Plant Cell. 2010 November; 22(11): 3864–3876. Published online 2010 November 23. doi: 10.1105/tpc.110.078964
PMCID:
PMC3015117
Abstract Full Text PDF–1.0M Supplementary Material
Interference with histidyl-tRNA synthetase by a CRISPR spacer sequence as a factor in the evolution of Pelobacter carbinolicus
Muktak Aklujkar, Derek R Lovley
BMC Evol Biol. 2010; 10: 230. Published online 2010 July 28. doi: 10.1186/1471-2148-10-230
PMCID:
PMC2923632
Abstract Full Text PDF–578K Supplementary Material
Rice bacterial blight pathogen Xanthomonas oryzae pv. oryzae produces multiple DSF-family signals in regulation of virulence factor production
Ya-Wen He, Ji'en Wu, Jae-Soon Cha, Lian-Hui Zhang
BMC Microbiol. 2010; 10: 187. Published online 2010 July 9. doi: 10.1186/1471-2180-10-187
PMCID:
PMC2909994
Abstract Full Text PDF–621K Supplementary Material
In planta gene expression analysis of Xanthomonas oryzae pathovar oryzae, African strain MAI1
Mauricio Soto-Suárez, Diana Bernal, Carolina González, Boris Szurek, Romain Guyot, Joe Tohme, Valérie Verdier
BMC Microbiol. 2010; 10: 170. Published online 2010 June 11. doi: 10.1186/1471-2180-10-170
PMCID:
PMC2893596
Abstract Full Text PDF–1.1M Supplementary Material
Assembly Algorithms for Next-Generation Sequencing Data
Jason R. Miller, Sergey Koren, Granger Sutton
Genomics. Author manuscript; available in PMC 2011 June 1.
Published in final edited form as: Genomics. 2010 June; 95(6): 315–327. Published online 2010 March 6. doi: 10.1016/j.ygeno.2010.03.001
PMCID:
PMC2874646
Abstract Full Text PDF–367K
Meeting report: a workshop on Best Practices in Genome Annotation
Ramana Madupu, Lauren M. Brinkac, Jennifer Harrow, Laurens G. Wilming, Ulrike Böhme, Philippe Lamesch, Linda I. Hannick
Database (Oxford) 2010; 2010: baq001. Published online 2010 February 18. doi: 10.1093/database/baq001
PMCID:
PMC2860899
Abstract Full Text PDF–1.8M
The complete genome sequence of Xanthomonas albilineans provides new insights into the reductive genome evolution of the xylem-limited Xanthomonadaceae
Isabelle Pieretti, Monique Royer, Valérie Barbe, Sébastien Carrere, Ralf Koebnik, Stéphane Cociancich, Arnaud Couloux, Armelle Darrasse, Jérôme Gouzy, Marie-Agnès Jacques, Emmanuelle Lauber, Charles Manceau, Sophie Mangenot, Stéphane Poussier, Béatrice Segurens, Boris Szurek, Valérie Verdier, Matthieu Arlat, Philippe Rott
BMC Genomics. 2009; 10: 616. Published online 2009 December 17. doi: 10.1186/1471-2164-10-616
PMCID:
PMC2810307
Abstract Full Text PDF–949K Supplementary Material
Inference of the impact of insertion sequence (IS) elements on bacterial genome diversification through analysis of small-size structural polymorphisms in Escherichia coli O157 genomes
Tadasuke Ooka, Yoshitoshi Ogura, Md Asadulghani, Makoto Ohnishi, Keisuke Nakayama, Jun Terajima, Haruo Watanabe, Tetsuya Hayashi
Genome Res. 2009 October; 19(10): 1809–1816. doi: 10.1101/gr.089615.108
PMCID:
PMC2765283
Abstract Full Text PDF–1008K
Legionella pneumophila Secretes an Endoglucanase That Belongs to the Family-5 of Glycosyl Hydrolases and Is Dependent upon Type II Secretion
Meghan M. Pearce, Nicholas P. Cianciotto
FEMS Microbiol Lett. Author manuscript; available in PMC 2010 November 1.
Published in final edited form as: FEMS Microbiol Lett. 2009 November; 300(2): 256–264. Published online 2009 September 21. doi: 10.1111/j.1574-6968.2009.01801.x
PMCID:
PMC2766432
Abstract Full Text PDF–679K
Host and Pathogen Factors Controlling the Rice-Xanthomonas oryzae Interaction
Frank F. White, Bing Yang
Plant Physiol. 2009 August; 150(4): 1677–1686. doi: 10.1104/pp.109.139360
PMCID:
PMC2719118
Full Text PDF–529K
Lifestyles of the Effector Rich: Genome-Enabled Characterization of Bacterial Plant Pathogens
Alan Collmer, David J. Schneider, Magdalen Lindeberg
Plant Physiol. 2009 August; 150(4): 1623–1630. doi: 10.1104/pp.109.140327
PMCID:
PMC2719148
Full Text PDF–120K
EDGAR: A software framework for the comparative analysis of prokaryotic genomes
Jochen Blom, Stefan P Albaum, Daniel Doppmeier, Alfred Pühler, Frank-Jörg Vorhölter, Martha Zakrzewski, Alexander Goesmann
BMC Bioinformatics. 2009; 10: 154. Published online 2009 May 20. doi: 10.1186/1471-2105-10-154
PMCID:
PMC2696450
Abstract Full Text PDF–482K
Acquisition and Evolution of Plant Pathogenesis–Associated Gene Clusters and Candidate Determinants of Tissue-Specificity in Xanthomonas
Hong Lu, Prabhu Patil, Marie-Anne Van Sluys, Frank F. White, Robert P. Ryan, J. Maxwell Dow, Pablo Rabinowicz, Steven L. Salzberg, Jan E. Leach, Ramesh Sonti, Volker Brendel, Adam J. Bogdanove
PLoS ONE. 2008; 3(11): e3828. Published online 2008 November 27. doi: 10.1371/journal.pone.0003828
PMCID:
PMC2585010
Abstract Full Text PDF–526K Supplementary Material
Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A
Steven L Salzberg, Daniel D Sommer, Michael C Schatz, Adam M Phillippy, Pablo D Rabinowicz, Seiji Tsuge, Ayako Furutani, Hirokazu Ochiai, Arthur L Delcher, David Kelley, Ramana Madupu, Daniela Puiu, Diana Radune, Martin Shumway, Cole Trapnell, Gudlur Aparna, Gopaljee Jha, Alok Pandey, Prabhu B Patil, Hiromichi Ishihara, Damien F Meyer, Boris Szurek, Valerie Verdier, Ralf Koebnik, J Maxwell Dow, Robert P Ryan, Hisae Hirata, Shinji Tsuyumu, Sang Won Lee, Young-Su Seo, Malinee Sriariyanum, Pamela C Ronald, Ramesh V Sonti, Marie-Anne Van Sluys, Jan E Leach, Frank F White, Adam J Bogdanove
BMC Genomics. 2008; 9: 534. Published online 2008 November 11. doi: 10.1186/1471-2164-9-534
Corrects:
BMC Genomics. 2008; 9: 204.
PMCID:
PMC2588604
Correction PDF–139K Original Article
New feel for new phyla
Michael Y Galperin
Environ Microbiol. 2008 August; 10(8): 1927–1933. doi: 10.1111/j.1462-2920.2008.01699.x
PMCID:
PMC2613244
Full Text PDF–93K
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