Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A

BMC Genomics

Volumn 9, Issue , 2008, Pages

  Salzberg, Steven L ^a   Sommer, Daniel D ^a   Schatz, Michael C ^a   Phillippy, Adam M ^a   Rabinowicz, Pablo D ^b,c   Tsuge, Seiji ^d   Furutani, Ayako ^d,e   Ochiai, Hirokazu ^e   Delcher, Arthur L ^a   Kelley, David ^a   Madupu, Ramana ^b   Puiu, Daniela ^a   Radune, Diana ^b   Shumway, Martin ^b,f   Trapnell, Cole ^a   Aparna, Gudlur ^g   Jha, Gopaljee ^h   Pandey, Alok ^g   Patil, Prabhu B ^g   Ishihara, Hiromichi ⁱ   Meyer, Damien F ^j   Szurek, Boris ^k   Verdier, Valerie ^k   Koebnik, Ralf ^k   Maxwell, J Maxwell ^l   Ryan, Robert P ^l   Hirata, Hisae ^m   Tsuyumu, Shinji ^l   Won Lee, Sang ⁿ   Ronald, Pamela C ⁿ   Sonti, Ramesh V ^g   Van Sluys, Marie Anne ^h,o   Leach, Jan E ^h   White, Frank F ^p   Bogdanove, Adam J ^j   more..

^a Bldg 142   (United States)

^b J CRAIG VENTER INSTITUTE   (United States)

^c UNIVERSITY OF MARYLAND SCHOOL OF MEDICINE   (United States)

^d KYOTO PREFECTURAL UNIVERSITY   (Japan)

^e NATIONAL INSTITUTE OF AGROBIOLOGICAL SCIENCES   (Japan)

^f NATIONAL INSTITUTES OF HEALTH   (United States)

^g CENTRE FOR CELLULAR AND MOLECULAR BIOLOGY   (India)

^h CSIR INSTITUTE OF HIMALAYAN BIORESOURCE TECHNOLOGY   (India)

ⁱ Department of Environmental and Radiological Health Sciences   (United States)

^j IOWA STATE UNIVERSITY   (United States)

^k INSTITUT DE RECHERCHE POUR LE DÉVELOPPEMENT   (France)

^l UNIVERSITY COLLEGE CORK   (Ireland)

^m SHIZUOKA UNIVERSITY   (Japan)

ⁿ UNIVERSITY OF CALIFORNIA   (United States)

^o UNIVERSITY OF SÃO PAULO   (Brazil)

^p KANSAS STATE UNIVERSITY   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL BLIGHT; BACTERIAL GENE; BACTERIAL STRAIN; BACTERIAL VIRULENCE; CHROMOSOME REARRANGEMENT; CLUSTERED REGULARLY INTERSPERSED SHORT PALINDROMIC REPEAT; GENE INSERTION; GENETIC VARIABILITY; NONHUMAN; NUCLEOTIDE SEQUENCE; RICE; STRAIN DIFFERENCE; TANDEM REPEAT; XANTHOMONAS; XANTHOMONAS ORYZAE; BACTERIAL GENOME; GENE DUPLICATION; GENE REARRANGEMENT; GENETICS; GENOMICS; HORIZONTAL GENE TRANSFER; MICROBIOLOGY; MOLECULAR EVOLUTION; REPRODUCIBILITY; TIME; TRANSPOSON;

BACTERIA (MICROORGANISMS); ORYZA SATIVA; XANTHOMONAS ORYZAE PV. ORYZAE;

BACTERIAL PROTEIN; MICROSATELLITE DNA;

BACTERIAL PROTEINS; BASE SEQUENCE; DNA TRANSPOSABLE ELEMENTS; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENE REARRANGEMENT; GENE TRANSFER, HORIZONTAL; GENOME, BACTERIAL; GENOMICS; MICROSATELLITE REPEATS; ORYZA SATIVA; REPRODUCIBILITY OF RESULTS; TIME FACTORS; XANTHOMONAS;

EID: 46049099151     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-9-204     Document Type: Article

References (74)

1. Ou SH Rice Diseases Kew, Surrey: Commonwealth Agricultural Bureau 2 1985.
2. Mew TW Current status and future prospects of research on bacterial blight of rice Annu Rev Phytopathol 1987, 25:359-382. 10.1146/ annurev.py.25.090187.002043
3. Nino-Liu DO Ronald PC Bogdanove AJ Xanthomonas oryzae pathovars: Model pathogens of a model crop Mol Plant Pathol 2006, 7(5):303-324. 10.1111/ j.1364-3703.2006.00344.x
4. Ronald P Leung H THE RICE GENOME: The most precious things are not jade and pearls... Science 2002, 296(5565):58-59. 10.1126/ science.1071337 11935008
5. Leach JE Leung H Nelson RJ Mew TW Population biology of Xanthomonas oryzae pv. oryzae and approaches to its control Curr Opin Biotechnol 1995, 6(3):298-304. 10.1016/0958-1669(95)80051-4
6. Khush GS Origin, dispersal, cultivation and variation of rice Plant Mol Biol 1997, 35(1-2):25-34. 10.1023/A:1005810616885 9291957
7. Zhang Q Genetics and improvement of resistance to bacterial blight in rice (in Chinese) Beijing: Science Press; 2007.
8. Hayward AC The hosts of Xanthomonas Xanthomonas London: Chapman and Hall Swings JG, Civerolo EL 1993:1-119.
9. Ochiai H Inoue Y Takeya M Sasaki A Kaku H Genome sequence of Xanthomonas oryzae pv. oryzae suggests contribution of large numbers of effector genes and insertion sequences to its race diversity Jpn Agric Res Q 2005, 39(4):275-287.
10. Lee BM Park YJ Park DS Kang HW Kim JG Song ES Park IC Yoon UH Hahn JH Koo BS The genome sequence of Xanthomonas oryzae pathovar oryzae KACC10331 the bacterial blight pathogen of rice Nucleic Acids Res 2005, 33(2):577-586. 548351 15673718 10.1093/nar/gki206
11. Rojas CM Ham JH Deng WL Doyle JJ Collmer A HecA, a member of a class of adhesins produced by diverse pathogenic bacteria, contributes to the attachment, aggregation, epidermal cell killing, and virulence phenotypes of Erwinia chrysanthemi EC16 on Nicotiana clevelandii seedlings Proc Natl Acad Sci USA 2002, 99(20):13142-13147. 130600 12271135 10.1073/pnas.202358699
12. Mew TW Vera Cruz CM Medalla ES Changes in race frequency of Xanthomonas oryzae pv. oryzae in response to rice cultivars planted in the Philippines Plant Dis 1992, 76:1029-1032.
13. Adhikari TB Cruz CMV Zhang Q Nelson RJ Skinner DZ Mew TW Leach JE Vera Cruz CM Genetic diversity of Xanthomonas oryzae pv. oryzae in Asia Appl Environ Microbiol 1995, 61(3):966-971. 1388379 16534980
14. Iyer AS McCouch SR The rice bacterial blight resistance gene xa5 encodes a novel form of disease resistance Mol Plant Microbe Interact 2004, 17(12):1348-1354. 10.1094/MPMI.2004.17.12.1348 15597740
15. Chu Z Yuan M Yao J Ge X Yuan B Xu C Li X Fu B Li Z Bennetzen JL Promoter mutations of an essential gene for pollen development result in disease resistance in rice Genes & development 2006, 20(10):1250-1255. 1472899 16648463 10.1101/gad.1416306
16. Gu K Yang B Tian D Wu L Wang D Sreekala C Yang F Chu Z Wang G-L White FF R gene expression induced by a type-III effector triggers disease resistance in rice Nature 2005, 435(7045):1122-1125. 10.1038/nature03630 15973413
17. Song WY Wang GL Chen LL Kim HS Pi LY Holsten T Gardner J Wang B Zhai WX Zhu LH A receptor kinase-like protein encoded by the rice disease resistance gene, Xa21 Science 1995, 270(5243):1804-1806. 10.1126/ science.270.5243.1804 8525370
18. Lobry JR Asymmetric substitution patterns in the two DNA strands of bacteria Mol Biol Evol 1996, 13(5):660-665. 8676740
19. Darling AC Mau B Blattner FR Perna NT Mauve: Multiple alignment of conserved genomic sequence with rearrangements Genome Res 2004, 14(7):1394-1403. 442156 15231754 10.1101/gr.2289704
20. Monteiro-Vitorello CB de Oliveira MC Zerillo MM Varani AM Civerolo E Van Sluys MA Xylella and Xanthomonas Mobil'omics Omics 2005, 9(2):146-159. 10.1089/omi.2005.9.146 15969647
21. Siguier P Perochon J Lestrade L Mahillon J Chandler M ISfinder: The reference centre for bacterial insertion sequences Nucleic Acids Res 2006, 34(Database):D32-36. 1347377 16381877 10.1093/nar/gkj014
22. Adhikari TB Mew TW Leach JE Genotypic and pathotypic diversity in Xanthomonas oryzae pv. oryzae in Nepal Phytopathology 1999, 89(8):687-694. 10.1094/PHYTO.1999.89.8.687
23. Schatz MC Phillippy AM Shneiderman B Salzberg SL Hawkeye: An interactive visual analytics tool for genome assemblies Genome Biol 2007, 8(3):R34. 1868940 17349036 10.1186/gb-2007-8-3-r34
24. Bonas U Stall RE Staskawicz B Genetic and structural characterization of the avirulence gene avrBs3 from Xanthomonas campestris pv. vesicatoria Mol Gen Genet 1989, 218(1):127-136. 10.1007/BF00330575 2550761
25. Swarup S De Feyter RD Brlansky R Gabriel DW A pathogenicity locus from Xanthomonas citri enables strains from several pathovars of X. campestris to elicit canker-like lesions on citrus Phytopathology 1991, 81:802-809. 10.1094/Phyto-81-802
26. Hopkins CM White FF Choi SH Guo A Leach JE Identification of a family of avirulence genes from Xanthomonas oryzae pv. oryzae Mol Plant Microbe Interact 1992, 5(6):451-459. 1335800
27. Schornack S Meyer A Romer P Jordan T Lahaye T Gene-for-gene-mediated recognition of nuclear-targeted AvrBs3-like bacterial effector proteins J Plant Physiol 2006, 163(3):256-272. 10.1016/j.jplph.2005.12.001 16403589
28. Kay S Boch J Bonas U Characterization of AvrBs3-like effectors from a Brassicaceae pathogen reveals virulence and avirulence activities and a protein with a novel repeat architecture Mol Plant Microbe Interact 2005, 18(8):838-848. 10.1094/MPMI-18-0838 16134896
29. Yang B Sugio A White FF Os8N3 is a host disease-susceptibility gene for bacterial blight of rice Proc Natl Acad Sci USA 2006, 103(27):10503-10508. 1502487 16798873 10.1073/pnas.0604088103
30. Yang B White FF Diverse members of the AvrBs3/PthA family of type III effectors are major virulence determinants in bacterial blight disease of rice Mol Plant Microbe Interact 2004, 17(11):1192-1200. 10.1094/ MPMI.2004.17.11.1192 15553245
31. Gu K Tian D Yang F Wu L Sreekala C Wang D Wang GL Yin Z High-resolution genetic mapping of Xa27(t), a new bacterial blight resistance gene in rice, Oryza sativa L Theor Appl Genet 2004, 108(5):800-807. 10.1007/ s00122-003-1491-x 15118822
32. Sugio A Yang B Zhu T White FF Two type III effector genes of Xanthomonas oryzae pv. oryzae control the induction of the host genes OsTFIIA gamma 1 and OsTFX1 during bacterial blight of rice sdfsdf Proc Natl Acad Sci USA 2007, 104(25):10720-10725. 1965579 17563377 10.1073/pnas.0701742104
33. Eisen JA Heidelberg JF White O Salzberg SL Evidence for symmetric chromosomal inversions around the replication origin in bacteria Genome Biol 2000, 1(6):rEsearch 11.01 09 10.1186/gb-2000-1-6-research0011
34. Haft DH Selengut J Mongodin EF Nelson KE A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes PLoS Comput Biol 2005, 1(6):e60. 1282333 16292354 10.1371/journal.pcbi.0010060
35. Bolotin A Quinquis B Sorokin A Ehrlich SD Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin Microbiology 2005, 151(Pt 8):2551-2561. 10.1099/ mic.0.28048-0 16079334
36. Barrangou R Fremaux C Deveau H Richards M Boyaval P Moineau S Romero DA Horvath P CRISPR provides acquired resistance against viruses in prokaryotes Science 2007, 315(5819):1709-1712. 10.1126/science.1138140 17379808
37. Heidelberg JF Eisen JA Nelson WC Clayton RA Gwinn ML Dodson RJ Haft DH Hickey EK Peterson JD Umayam L DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae Nature 2000, 406(6795):477-483. 10.1038/ 35020000 10952301
38. Holden MT Titball RW Peacock SJ Cerdeno-Tarraga AM Atkins T Crossman LC Pitt T Churcher C Mungall K Bentley SD Genomic plasticity of the causative agent of melioidosis, Burkholderia pseudomallei Proc Natl Acad Sci USA 2004, 101(39):14240-14245. 521101 15377794 10.1073/ pnas.0403302101
39. Kellis M Patterson N Endrizzi M Birren B Lander ES Sequencing and comparison of yeast species to identify genes and regulatory elements Nature 2003, 423(6937):241-254. 10.1038/nature01644 12748633
40. Noda T Horino O Ohuchi A Variability of pathogenicity in races of Xanthomonas campestris pv. oryzae in Japan Jpn Agric Res Q 1990, 23(3):182-189.
41. Pandey MP Singh H Singh RA Mani SC Das B Singh JP Breakdown of varietal resistance to bacterial blight (BB) at Pantnagar, India Int Rice Res Newsl 1987, 12(2):16-17.
42. Wu SZ Xu XM Liu JM Comparative studies on pathogenic reactions of isolates of Xanthomonas campestris pv. oryzae of Southeast Asia and South China on the Chinese differential hosts Acta Phytopathol Sin 1983, 13(4):21-26.
43. Henderson IR Navarro-Garcia F Desvaux M Fernandez RC Ala'Aldeen D Type V protein secretion pathway: The autotransporter story Microbiol Mol Biol Rev 2004, 68(4):692-744. 539010 15590781 10.1128/MMBR.68.4.692-744.2004
44. da Silva AC Ferro JA Reinach FC Farah CS Furlan LR Quaggio RB Monteiro-Vitorello CB Van Sluys MA Almeida NF Alves LM Comparison of the genomes of two Xanthomonas pathogens with differing host specificities Nature 2002, 417(6887):459-463. 10.1038/417459a 12024217
45. Qian W Jia Y Ren SX He YQ Feng JX Lu LF Sun Q Ying G Tang DJ Tang H Comparative and functional genomic analyses of the pathogenicity of phytopathogen Xanthomonas campestris pv. campestris Genome Res 2005, 15(6):757-767. 1142466 15899963 10.1101/gr.3378705
46. Thieme F Koebnik R Bekel T Berger C Boch J Buttner D Caldana C Gaigalat L Goesmann A Kay S Insights into genome plasticity and pathogenicity of the plant pathogenic bacterium Xanthomonas campestris pv. vesicatoria revealed by the complete genome sequence J Bacteriol 2005, 187(21):7254-7266. 1272972 16237009 10.1128/JB.187.21.7254-7266.2005
47. De Feyter RD Yang Y Gabriel DW Gene-for-genes interactions between cotton R genes and Xanthomonas campestris pv. malvacearum avr genes Mol Plant Microbe Interact 1993, 6(2):225-237. 8097122
48. Gagnevin L Leach JE Pruvost O Genomic variability of the Xanthomonas pathovar mangiferaeindicae, agent of mango bacterial black spot Appl Environ Microbiol 1997, 63(1):246-253. 1389104 16535490
49. Leach JE Rhoads ML Cruz CMV White FF Mew TW Leung H Vera Cruz CM Assessment of genetic diversity and population structure of Xanthomonas oryzae pv. oryzae with a repetitive DNA element Appl Environ Microbiol 1992, 58(7):2188-2195. 195754 1353345
50. Leach JE White FF Rhoads ML Leung H A repetitive DNA sequence differentiates Xanthomonas campestris pv. oryzae from other pathovars of X. campestris Mol Plant Microbe Interact 1990, 3(4):238-246.
51. Nelson RJ Baraoidan MR Cruz CM Yap IV Leach JE Mew TW Leung H Relationship between phylogeny and pathotype for the bacterial blight pathogen of rice Appl Environ Microbiol 1994, 60(9):3275-3283. 201799 16349380
52. Ryba-White M Notteghem JL Leach JE Comparison of Xanthomonas oryzae pv. orzyae strains from Africa, North America, and Asia by restriction fragment length polymorphism analysis Int Rice Res Notes 1995, 20:25-26.
53. Ryba-White M Sakthivel N Yun C White F Leach JE Identification and characterization of IS1112 and IS1113 insertion element sequences in Xanthomonas oryzae pv. oryzae DNA Seq 2005, 16(1):75-79. 16040351
54. Choi S Cruz CMV Leach JE Choi SH Distribution of Xanthomonas oryzae pv. oryzae DNA modification systems in Asia Appl Environ Microbiol 1998, 64(5):1663-1668. 106212 9572933
55. Hu J Zhang Y Qian W He C Avirulence gene and insertion element-based RFLP as well as RAPD markers reveal high levels of genomic polymorphism in the rice pathogen Xanthomonas oryzae pv. oryzae Syst Appl Microbiol 2007, 30(8):587-600. 10.1016/j.syapm.2007.08.003 17959329
56. Zhang Q Leach JE Nelson RJ Wang CL Mew TW Preliminary analysis of the population structure of Xanthomonas oryzae pv. oryzae in China Chin J Rice Sci 1995, 9(1):7-14.
57. Ardales EY Leung H Vera-Cruz CM Mew TW Leach JE Nelson RJ Hierarchical analysis of spatial variation of the rice bacterial blight pathogen across diverse agroecosystems in the Philippines Phytopathology 1996, 86(3):241-252. 10.1094/Phyto-86-241
58. Kaku H Hirayae K Ochiai H Kanematsu S Noda T Tsuchiya K Hibi T Comparative RFLP profiles among representative strains of Japanese races of Xanthomonas oryzae pv. oryzae using the repetitive DNA probe pJEL101 Ann Phytopathol Soc Jpn 1996, 62(1):53-56.
59. Vera Cruz CM Ardales EY Skinner DZ Talag J Nelson RJ Louws FJ Leung H Mew TW Leach JE Measurement of haplotypic variation in Xanthomonas oryzae pv. oryzae within a single field by rep-PCR and RFLP analyses Phytopathology 1996, 86(12):1352-1359.
60. Gonzalez C Szurek B Manceau C Mathieu T Sere Y Verdier V Molecular and pathotypic characterization of new Xanthomonas oryzae strains from West Africa Mol Plant Microbe Interact 2007, 20(5):534-546. 10.1094/ MPMI-20-5-0534 17506331
61. Sambrook J Fritsch EF Maniatis T Molecular cloning: A laboratory manual Cold Spring Harbor, NY: Cold Spring Laboratory Press 2; 1989.
62. Sanger F Nicklen S Coulson AR DNA sequencing with chain-terminating inhibitors Proc Natl Acad Sci USA 1977, 74(12):5463-5467. 431765 271968 10.1073/pnas.74.12.5463
63. Myers EW Sutton GG Delcher AL Dew IM Fasulo DP Flanigan MJ Kravitz SA Mobarry CM Reinert KH Remington KA A whole-genome assembly of Drosophila Science 2000, 287(5461):2196-2204. 10.1126/science.287.5461.2196 10731133
64. Delcher AL Bratke KA Powers EC Salzberg SL Identifying bacterial genes and endosymbiont DNA with Glimmer Bioinformatics 2007, 23(6):673-679. 2387122 17237039 10.1093/bioinformatics/btm009
65. Delcher AL Harmon D Kasif S White O Salzberg SL Improved microbial gene identification with GLIMMER Nucleic Acids Res 1999, 27(23):4636-4641. 148753 10556321 10.1093/nar/27.23.4636
66. Kingsford CL Ayanbule K Salzberg SL Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake Genome Biol 2007, 8(2):R22. 1852404 17313685 10.1186/gb-2007-8-2-r22
67. Lowe TM Eddy SR tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence Nucleic Acids Res 1997, 25(5):955-964. 146525 9023104 10.1093/nar/25.5.955
68. Altschul SF Gish W Miller W Myers EW Lipman DJ Basic local alignment search tool J Mol Biol 1990, 215:403-410. 2231712
69. Ward N Larsen E Sakwa J Bruseth L Khouri H Durkin AS Dimitrov G Jiang L Scanlan D Kang KH Genomic Insights into Methanotrophy: The Complete Genome Sequence of Methylococcus capsulatus (Bath) PLoS Biol 2004, 2(10):E303. 517821 15383840 10.1371/journal.pbio.0020303
70. Manatee Manatee http://manatee.sourceforge.net
71. Salzberg SL Salzberg AJ Kerlavage AR Tomb JF Skewed oligomers and origins of replication Gene 1998, 217(1-2):57-67. 10.1016/ S0378-1119(98)00374-6 9795135
72. Kurtz S Phillippy A Delcher AL Smoot M Shumway M Antonescu C Salzberg SL Versatile and open software for comparing large genomes Genome Biol 2004, 5(2):R12. 395750 14759262 10.1186/gb-2004-5-2-r12
73. The NCBI Trace Archive The NCBI Trace Archive http://www.ncbi.nih.gov/ Traces
74. Salzberg SL Church D DiCuccio M Yaschenko E Ostell J The genome Assembly Archive: A new public resource PLoS Biol 2004, 2(9):E285. 516794 15367931 10.1371/journal.pbio.0020285