Comparative genome analysis of wheat blue dwarf phytoplasma, an obligate pathogen that causes wheat blue dwarf disease in China

PLoS ONE

Volumn 9, Issue 5, 2014, Pages

  Chen, Wang ^a   Li, Yan ^a   Wang, Qiang ^a   Wang, Nan ^a   Wu, Yunfeng ^a  

^a NORTHWEST A F UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

COBALT; DIPEPTIDE; MANGANESE; OLIGOPEPTIDE; PROTEIN SAP11; PROTEIN SAP54; PROTEIN TENGU; PUTRESCINE; RIBOSOME RNA; SPERMIDINE; TRANSFER RNA; UNCLASSIFIED DRUG; VIRULENCE FACTOR; ZINC;

ARTICLE; BACTERIAL CHROMOSOME; BACTERIAL GENOME; BACTERIAL PLANT DISEASE; BACTERIAL VIRULENCE; CENTRIFUGATION; CHINA; CONTIG MAPPING; CONTROLLED STUDY; GENE AMPLIFICATION; GENETIC PROCEDURES; GENOME ANALYSIS; GENOME SIZE; NONHUMAN; OPERON; PHYTOPLASMA; PLASMID; PROTEIN SECRETION; PULSED FIELD GEL ELECTROPHORESIS; RRNA GENE; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SHOTGUN SEQUENCING; SIGNAL TRANSDUCTION; TRANSPORT KINETICS; TRNA GENE; WHEAT BLUE DWARF DISEASE; WHEAT BLUE DWARF PHYTOPLASMA; AMINO ACID SEQUENCE; CHEMISTRY; GENETICS; MICROBIOLOGY; MOLECULAR GENETICS; PLANT DISEASE; SEQUENCE ALIGNMENT; WHEAT;

AMINO ACID SEQUENCE; CHINA; GENOME, BACTERIAL; MOLECULAR SEQUENCE ANNOTATION; PHYTOPLASMA; PLANT DISEASES; SEQUENCE ALIGNMENT; TRITICUM; VIRULENCE FACTORS;

EID: 84900462820     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0096436     Document Type: Article

References (42)

1. Lee IM, Davis RE, Gundersen-Rindal DE (2000) Phytoplasma: phytopathogenic mollicutes. Annu Rev Microbiol 54: 221-255.
2. Weintraub PG, Beanland L (2006) Insect vectors of phytoplasmas. Annu Rev Entomol 51: 91-111. (Pubitemid 43107816)
3. Oshima K, Kakizawa S, Nishigawa H, Jung HY, Wei W, et al. (2004) Reductive evolution suggested from the complete genome sequence of a plant-pathogenic phytoplasma. Nat Genet 36: 27-29. (Pubitemid 38056204)
4. Bai X, Zhang J, Ewing A, Miller SA, Jancso Radek A, et al. (2006) Living with genome instability: the adaptation of phytoplasmas to diverse environments of their insect and plant hosts. J Bacteriol 188: 3682-3696. (Pubitemid 43726231)
5. Tran-Nguyen LT, Kube M, Schneider B, Reinhardt R, Gibb KS (2008) Comparative genome analysis of "Candidatus Phytoplasma australiense" (subgroup tuf-Australia I; rp-A) and "Ca. Phytoplasma asteris" Strains OY-M and AY-WB. J Bacteriol 190: 3979-3991. (Pubitemid 351732878)
6. Andersen MT, Liefting LW, Havukkala I, Beever RE (2013) Comparison of the complete genome sequence of two closely related isolates of 'Candidatus Phytoplasma australiense' reveals genome plasticity. BMC Genomics 14: 529.
7. Kube M, Schneider B, Kuhl H, Dandekar T, Heitmann K, et al. (2008) The linear chromosome of the plant-pathogenic mycoplasma 'Candidatus Phytoplasma mali'. BMC Genomics 9: 306.
8. Saccardo F, Martini M, Palmano S, Ermacora P, Scortichini M, et al. (2012) Genome drafts of four phytoplasma strains of the ribosomal group 16SrIII. Microbiology 158: 2805-2814.
9. Chung WC, Chen LL, Lo WS, Lin CP, Kuo CH (2013) Comparative analysis of the peanut witches'-broom phytoplasma genome reveals horizontal transfer of potential mobile units and effectors. PLoS One 8: e62770.
10. Zhang QF, Xiang JY, Yang Y, zhang Q (1996) The primary infection of wheat mycoplasmalike organism blue dwarf disease (WMBD). Acta Phytopathologica sinica 11: 107-110.
11. Wu YF, Hao XG, Li ZN, Gu PW, An FQ, et al. (2010) Identification of the Phytoplasma Associated with Wheat Blue Dwarf Disease in China. Plant Disease 94: 977-985.
12. Zhang CP (2010) Research on Pathogens Diversity of Wheat Blue Dwarf Disease. Master's thesis, Yangling, Shaanxi, China: Northwest A&F University. 51 p
13. Coskun S, Alsmadi O (2007) Whole genome amplification from a single cell: a new era for preimplantation genetic diagnosis. Prenat Diagn 27: 297-302. (Pubitemid 46597905)
14. Zhang K, Martiny AC, Reppas NB, Barry KW, Malek J, et al. (2006) Sequencing genomes from single cells by polymerase cloning. Nat Biotechnol 24: 680-686. (Pubitemid 43882119)
15. Chen W, Li Y, Wu YF (2013) Isolation of chromosome DNA of wheat blue dwarf phytoplasma. Microbiology China 40: 5.
16. Boetzer M, Henkel CV, Jansen HJ, Butler D, Pirovano W (2011) Scaffolding pre-assembled contigs using SSPACE. Bioinformatics 27: 578-579.
17. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, et al. (2009) BLAST+: architecture and applications. BMC Bioinformatics 10: 421.
18. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, et al. (2010) Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11: 119.
19. Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25: 955-964. (Pubitemid 27298263)
20. Lagesen K, Hallin P, Rodland EA, Staerfeldt HH, Rognes T, et al. (2007) RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35: 3100-3108. (Pubitemid 47073647)
21. Li L, Stoeckert CJ Jr, Roos DS (2003) OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 13: 2178-2189. (Pubitemid 37161775)
22. Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M (2007) KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res 35: W182-185.
23. Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, et al. (2003) The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4: 41.
24. Bai X, Correa VR, Toruno TY, Ammar el D, Kamoun S, et al. (2009) AY-WB phytoplasma secretes a protein that targets plant cell nuclei. Mol Plant Microbe Interact 22: 18-30.
25. Bendtsen JD, Nielsen H, von Heijne G, Brunak S (2004) Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 340: 783-795. (Pubitemid 38829638)
26. Krogh A, Larsson B, von Heijne G, Sonnhammer EL (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 305: 567-580. (Pubitemid 33032862)
27. Nakai K, Horton P (1999) PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization. Trends Biochem Sci 24: 34-36.
28. Husemann P, Stoye J (2010) r2cat: synteny plots and comparative assembly. Bioinformatics 26: 570-571.
29. Chitsaz H, Yee-Greenbaum JL, Tesler G, Lombardo MJ, Dupont CL, et al. (2011) Efficient de novo assembly of single-cell bacterial genomes from short-read data sets. Nat Biotechnol 29: 915-921.
30. Duan Y, Zhou L, Hall DG, Li W, Doddapaneni H, et al. (2009) Complete genome sequence of citrus huanglongbing bacterium, 'Candidatus Liberibacter asiaticus' obtained through metagenomics. Mol Plant Microbe Interact 22: 1011-1020.
31. Chen W, Li Y, Wu YF (2014) Molecular characterization and tissue specific copy number of three plasmids from wheat blue dwarf phytoplasma. Journal of Plant Pathology 96: in press.
32. Frank AC, Lobry JR (2000) Oriloc: prediction of replication boundaries in unannotated bacterial chromosomes. Bioinformatics 16: 560-561.
33. Silva Z, Sampaio MM, Henne A, Bohm A, Gutzat R, et al. (2005) The high-affinity maltose/trehalose ABC transporter in the extremely thermophilic bacterium Thermus thermophilus HB27 also recognizes sucrose and palatinose. J Bacteriol 187: 1210-1218. (Pubitemid 40299445)
34. Mori H, Ito K (2001) The Sec protein-translocation pathway. Trends Microbiol 9: 494-500. (Pubitemid 32939357)
35. Hoshi A, Oshima K, Kakizawa S, Ishii Y, Ozeki J, et al. (2009) A unique virulence factor for proliferation and dwarfism in plants identified from a phytopathogenic bacterium. Proc Natl Acad Sci U S A 106: 6416-6421.
36. Sugio A, Kingdom HN, MacLean AM, Grieve VM, Hogenhout SA (2011) Phytoplasma protein effector SAP11 enhances insect vector reproduction by manipulating plant development and defense hormone biosynthesis. Proc Natl Acad Sci U S A 108: E1254-1263.
37. MacLean AM, Sugio A, Makarova OV, Findlay KC, Grieve VM, et al. (2011) Phytoplasma effector SAP54 induces indeterminate leaf-like flower development in Arabidopsis plants. Plant Physiol 157: 831-841.
38. Takaya A, Tomoyasu T, Matsui H, Yamamoto T (2004) The DnaK/DnaJ chaperone machinery of Salmonella enterica serovar Typhimurium is essential for invasion of epithelial cells and survival within macrophages, leading to systemic infection. Infect Immun 72: 1364-1373. (Pubitemid 38263757)
39. Chanda PK, Mondal R, Sau K, Sau S (2009) Antibiotics, arsenate and H2O2 induce the promoter of Staphylococcus aureus cspC gene more strongly than cold. J Basic Microbiol 49: 205-211.
40. Ventura M, Canchaya C, Zhang Z, Fitzgerald GF, van Sinderen D (2007) Molecular characterization of hsp20, encoding a small heat shock protein of bifidobacterium breve UCC2003. Appl Environ Microbiol 73: 4695-4703. (Pubitemid 47122618)
41. Kloda A, Martinac B (2002) Common evolutionary origins of mechanosensitive ion channels in Archaea, Bacteria and cell-walled Eukarya. Archaea 1: 35-44. (Pubitemid 38871629)
42. Miura C, Sugawara K, Neriya Y, Minato N, Keima T, et al. (2012) Functional characterization and gene expression profiling of superoxide dismutase from plant pathogenic phytoplasma. Gene 510: 107-112.