Genomic diversity of sweet potato geminiviruses in a Brazilian germplasm bank

Virus Research

Volumn 149, Issue 2, 2010, Pages 224-233

  Paprotka, T ^a   Boiteux, L S ^b   Fonseca, M E N ^b   Resende, R O ^c   Jeske, H ^a   Faria, J C ^d   Ribeiro, S G ^e  

^a UNIVERSITY OF STUTTGART   (Germany)

^b EMBRAPA CERRADOS   (Brazil)

^c UNIVERSITY OF BRASILIA   (Brazil)

^d EMBRAPA ARROZ E FEIJÃO   (Brazil)

^e EMBRAPA RECURSOS GENÉTICOS E BIOTECNOLOGIA   (Brazil)

Author keywords

Begomovirus; Defective DNA; Diagnostics; Gene bank; Mitochondrial plasmid; RCA; Restriction fragment length polymorphism; RFLP; Rolling circle amplification; Secondary DNA structure

Indexed keywords

CIRCULAR DNA; DNA FRAGMENT; GENOMIC DNA; MITOCHONDRIAL DNA; PLASMID DNA; RESTRICTION ENDONUCLEASE; VIRUS DNA;

ARTICLE; BRAZIL; DNA SEQUENCE; GEMINIVIRUS; GENE AMPLIFICATION; GENE SEQUENCE; GENETIC ORGANIZATION; GENETIC RECOMBINATION; GENETIC VARIABILITY; GENOME ANALYSIS; GENOME SIZE; GERMPLASM; MOLECULAR CLONING; NEW SPECIES; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; ROLLING CIRCLE AMPLIFICATION; SWEET POTATO; VIRAL PLANT DISEASE; VIRUS GENOME; VIRUS STRAIN;

BEGOMOVIRUS; GEMINIVIRIDAE; IPOMOEA BATATAS;

EID: 77950626632     PISSN: 01681702     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.virusres.2010.02.003     Document Type: Article

References (73)

1. Abouzid A.M., Frischmuth T., Jeske H. A putative replicative form of the Abutilon mosaic virus (gemini group) in a chromatin-like structure. Mol. Gen. Genet. 1988, 212:252-258.
2. Alberter B., Rezaian A.M., Jeske H. Replicative intermediates of ToLCV and its satellite DNAs. Virology 2005, 331:441-448.
3. Backert S., Dorfel P., Borner T. Investigation of plant organellar DNAs by pulsed-field gel electrophoresis. Curr. Genet. 1995, 28:390-399.
4. Banks G.K., Bedford I.D., Beitia F.J., Rodriguez-Cerezo E., Markham P.G. A novel geminivirus of Ipomoea indica (Convolvulaceae) from southern Spain. Plant Dis. 1999, 83:486.
5. Benslimane A.A., Rode A., Quetier F., Hartmann C. Characterization of two minicircular plasmid-like DNAs isolated from date-palm mitochondria. Curr. Genet. 1994, 26:535-541.
6. Böttcher B., Unseld S., Ceulemans H., Russell R.B., Jeske H. Geminate structures of African cassava mosaic virus. J. Virol. 2004, 78:6758-6765.
7. Brewer B. When polymerases collide: replication and the transcriptional organization of the E. coli chromosome. Cell 1988, 53:679-686.
8. Briddon R., Bull S.E., Bedford I.D. Occurrence of sweet potato leaf curl virus in Sicily. Plant Pathol. 2006, 55:286.
9. Briddon R.W., Markham P.G. Universal primers for the PCR amplification of dicot-infecting geminiviruses. Mol. Biotechnol. 1994, 1:202-205.
10. Chen Y., Carlini D.B., Baines J.F., Parsch J., Braverman J.M., Tanda S., Stephan W. RNA secondary structure and compensatory evolution. Genes Genet. Syst. 1999, 74:271-286.
11. Clark C.A., Hoy M.W. Effects of common viruses on yield and quality of Beauregard sweet potato in Louisiana. Plant Dis. 2006, 90:83-88.
12. Cohen J., Milgram M., Antignus Y., Pearlsman M., Lachman O., Loebenstein G. Ipomoea crinkle leaf curl caused by a whitefly-transmitted gemini-like virus. Ann. Appl. Biol. 1997, 131:273-282.
13. Dellaporta S.L., Wood J., Hicks J.B. A plant DNA minipreparation: version II. Plant Mol. Biol. Rep. 1983, 1:19-21.
14. Duffy S., Holmes E.C. Phylogenetic evidence for rapid rates of molecular evolution in the single-stranded DNA begomovirus tomato yellow leaf curl virus. J. Virol. 2008, 82:957-965.
15. Erdmann J.B., Shepherd D.B., Martin D.P., Varsani A., Rybicki E.P., Jeske H. Replicative intermediates of Maize streak virus found during leaf development. J. Gen. Virol. 2010, 10.1099/vir.0.017574-0.
16. Fauquet C.M., Briddon R.W., Brown J.K., Moriones E., Stanley J., Zerbini M., Zhou X. Geminivirus strain demarcation and nomenclature. Arch. Virol. 2008, 153:783-821.
17. Fauquet C.M., Stanley J. Geminivirus classification and nomenclature: progress and problems. Ann. appl. Biol. 2003, 142:165-189.
18. Ferreira P.T., Lemos T.O., Nagata T., Inoue-Nagata A.K. One-step cloning approach for construction of agroinfectious begomovirus clones. J. Virol. Methods 2008, 147:351-354.
19. Frischmuth T., Engel M., Jeske H. Beet curly top virus DI DNA-mediated resistance is linked to its size. Mol. Breed. 1997, 3:213-217.
20. Frischmuth T., Ringel M., Kocher C. The size of encapsidated single-stranded DNA determines the multiplicity of African cassava mosaic virus particles. J. Gen. Virol. 2001, 82:673-676.
21. Frischmuth T., Stanley J. African cassava mosaic virus DI-DNA interferes with the replication of both genomic components. Virology 1991, 183:808-811.
22. Frischmuth T., Stanley J. Beet curly top virus symptom amelioration in Nicotiana benthamiana transformed with a naturally occurring viral subgenomic DNA. Virology 1994, 200:826-830.
23. Fuentes S., Salazar L.F. First report of sweet potato leaf curl virus in Peru. Plant Dis. 2003, 87:98.
24. Garcia-Andres S., Tomas D.M., Sanchez-Campos S., Navas-Castillo J., Moriones E. Frequent occurrence of recombinants in mixed infections of tomato yellow leaf curl disease-associated begomoviruses. Virology 2007, 365:210-219.
25. Haible D., Kober S., Jeske H. Rolling circle amplification revolutionizes diagnosis and genomics of geminiviruses. J. Virol. Methods 2006, 135:9-16.
26. Hall T.A. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 1999, 41:95-98. http://www.mbio.ncsu.edu/BioEdit/BioEdit.html.
27. Hanley-Bowdoin L., Settlage S.B., Orozco B.M., Nagar S., Robertson D. Geminiviruses: models for plant DNA replication, transcription, and cell cycle regulation. Crit. Rev. Plant Sci. 1999, 18:71-106.
28. Hansen B.M., Marcker K.A. DNA sequence and transcription of a DNA minicircle isolated from male-fertile sugar beet mitochondria. Nucleic Acids Res. 1984, 12:4747-4756.
29. Homs M., Kober S., Kepp G., Jeske H. Mitochondrial plasmids of sugar beet amplified via rolling circle method detected during curtovirus screening. Virus Res. 2008, 136:124-129.
30. Husmeier D., McGuire G. Detecting recombination in 4-taxa DNA sequence alignments with Bayesian hidden Markov models and markov chain monte carlo. Mol. Biol. Evol. 2003, 20:315-337.
31. Inoue-Nagata A.K., Albuquerque L.C., Rocha W.B., Nagata T. A simple method for cloning the complete begomovirus genome using the bacteriophage phi29 DNA polymerase. J. Virol. Methods 2004, 116:209-211.
32. Jeske H. Geminiviruses. Torque Teno Virus: The Still Elusive Human Pathogens 2009, vol. 331:185-226. Springer, Berlin.
33. Jeske H., Gotthardt D., Kober S. In planta cloning of geminiviral DNA: The true Sida micrantha mosaic virus. J. Virol. Methods 2010, 163:301-308.
34. Jeske H., Lütgemeier M., Preiss W. Distinct DNA forms indicate rolling circle and recombination-dependent replication of Abutilon mosaic geminivirus. EMBO J. 2001, 20:6158-6167.
35. Jovel J., Preiß W., Jeske H. Characterization of DNA-intermediates of an arising geminivirus. Virus Res. 2007, 130:63-70.
36. Knierim D., Maiss E. Application of Phi29 DNA polymerase in identification and full-length clone inoculation of tomato yellow leaf curl Thailand virus and tobacco leaf curl Thailand virus. Arch. Virol. 2007, 152:941-954.
37. Kokkinos C.D., Clark C.A. Real-time PCR assays for detection and quantification of sweet potato viruses. Plant Dis. 2006, 90:783-788.
38. Larkin M.A., Blackshields G., Brown N.P., Chenna R., McGettigan P.A., McWilliam H., Valentin F., Wallace I.M., Wilm A., Lopez R., Thompson J.D., Gibson T.J., Higgins D.G. Clustal W and Clustal X version 2.0. Bioinformatics 2007, 23:2947-2948.
39. Lefeuvre P., Martin D.P., Hoareau M., Naze F., Delatte H., Thierry M., Varsani A., Becker N., Reynaud B., Lett J.M. Begomovirus 'melting pot' in the south-west Indian Ocean islands: molecular diversity and evolution through recombination. J. Gen. Virol. 2007, 88:3458-3468.
40. Li R.H., Salih S., Hurtt S. Detection of geminiviruses in sweetpotato by polymerase chain reaction. Plant Dis. 2004, 88:1347-1351.
41. Lotrakul P., Valverde R. Cloning of a DNA-A-like genomic component of sweet potato leaf curl virus: nucleotide sequence and phylogenetic relationships. Mol. Plant Pathol. 1999, Online. http://www.bspp.org.uk/mppol/1999/0422lotrakul/.
42. Lotrakul P., Valverde R.A., Clark C.A., Fauquet C.M. Properties of a begomovirus isolated from sweet potato [Ipomoea batatas (L.) Lam.] infected with sweet potato leaf curl virus. Rev. Mex. Fitopatol. 2003, 21:128-136.
43. Lotrakul P., Valverde R.A., Clark C.A., Hurtt S., Hoy M.W. Sweet potato leaf curl virus and related geminiviruses in sweet potato. Acta Hortic. 2002, 583:135-141.
44. Lotrakul P., Valverde R.A., Clark C.A., Sim J., De La Torre R. Detection of a geminivirus infecting sweet potato in the United States. Plant Dis. 1998, 82:1253-1257.
45. Lozano G., Trenado H.P., Valverde R.A., Navas-Castillo J. Novel begomovirus species of recombinant nature in sweet potato (Ipomoea batatas) and Ipomoea indica: taxonomic and phylogenetic implications. J. Gen. Virol. 2009, 90.
46. Luan Y.S., Zhang J., Liu D.M., Li W.L. Molecular characterization of sweet potato leaf curl virus isolate from China (SPLCV-CN) and its phylogenetic relationship with other members of the Geminiviridae. Virus Genes 2007, 35:379-385.
47. Martin D.P., Williamson C., Posada D. RDP2: recombination detection and analysis from sequence alignments. Bioinformatics 2005, 21:260-262.
48. Milne I., Wright F., Rowe G., Marshall D.F., Husmeier D., McGuire G. TOPALi: software for automatic identification of recombinant sequences within DNA multiple alignments. Bioinformatics 2004, 20:1806-1807.
49. Monci F., Sanchez-Campos S., Navas-Castillo J., Moriones E. A natural recombinant between the geminiviruses Tomato yellow leaf curl Sardinia virus and Tomato yellow leaf curl virus exhibits a novel pathogenic phenotype and is becoming prevalent in Spanish populations. Virology 2002, 303:317-326.
50. Morilla G., Krenz B., Jeske H., Bejarano E.R., Wege C. Tête à tête of Tomato yellow leaf curl virus (TYLCV) and Tomato yellow leaf curl Sardinia virus (TYLCSV) in single nuclei. J. Virol. 2004, 78:10715-10723.
51. Olavarrieta L., Martinez-Robles M.L., Sogo J.M., Stasiak A., Hernandez P., Krimer D.B., Schvartzman J.B. Supercoiling, knotting and replication fork reversal in partially replicated plasmids. Nucleic Acids Res. 2002, 30:656-666.
52. Onuki M., Hanada K. PCR amplification and partial nucleotide sequences of three dicot-infecting geminiviruses occurring in Japan. Ann. Phytopathol. Soc. Jpn. 1998, 64:116-120.
53. Onuki M., Honda Y., Hanada K. Geminate particle morphology of sweet potato leaf curl virus in partially purified preparation and its serological relationship to two begomoviruses by western blotting. J. Gen. Plant Pathol. 2000, 66:182-184.
54. Owor B.E., Martin D.P., Shepherd D.N., Edema R., Monjane A.L., Rybicki E.P., Thomson J.A., Varsani A. Genetic analysis of maize streak virus isolates from Uganda reveals widespread distribution of a recombinant variant. J. Gen. Virol. 2007, 88:3154-3165.
55. Owor B.E., Shepherd D.N., Taylor N.J., Edema R., Monjane A.L., Thomson J.A., Martin D.P., Varsani A. Successful application of FTA classic card technology and use of bacteriophage phi29 DNA polymerase for large-scale field sampling and cloning of complete maize streak virus genomes. J. Virol. Methods 2007, 140:100-105.
56. Padidam M., Sawyer S., Fauquet C.M. Possible emergence of new geminiviruses by frequent recombination. Virology 1999, 285:218-225.
57. Patil B.L., Dasgupta I. Defective interfering DNAs of plant viruses. Crit. Rev. Plant Sci. 2006, 24:1-18.
58. Pilartz M., Jeske H. Abutilon mosaic geminivirus double-stranded DNA is packed into minichromosomes. Virology 1992, 189:800-802.
59. Pilartz M., Jeske H. Mapping of Abutilon mosaic geminivirus minichromosomes. J. Virol. 2003, 77:10808-10818.
60. Preiss W., Jeske H. Multitasking in replication is common among geminiviruses. J. Virol. 2003, 77:2972-2980.
61. Ribeiro S.G., Martin D.P., Lacorte C., Simoes I.C., Orlandini D.R.S., Inoue-Nagata A.K. Molecular and biological characterization of tomato chlorotic mottle virus suggests that recombination underlies the evolution and diversity of Brazilian tomato begomoviruses. Phytopathology 2007, 97:702-711.
62. Sambrook J., Russell D.W. Molecular Cloning: A Laboratory Manual 2001, Cold Spring Harbor Press, Cold Spring Harbor, NY. 3rd ed.
63. Schubert J., Habekuß A., Kazmaier K., Jeske H. Surveying cereal-infecting geminiviruses in Germany-diagnostics and direct sequencing using rolling circle amplification. Virus Res. 2007, 127:61-70.
64. Schvartzman J.B., Stasiak A. A topological view of the replicon. EMBO Rep. 2004, 5:256-261.
65. Shung C.Y., Sunter J., Sirasanagandla S.S., Sunter G. Distinct viral sequence elements are necessary for expression of Tomato golden mosaic virus complementary sense transcripts that direct AL2 and AL3 gene expression. Mol. Plant Microbe Interact. 2006, 19:1394-13405.
66. Stanley J., Frischmuth T., Ellwood S. Defective viral DNA ameliorates symptoms of geminivirus infection in transgenic plants. Proc. Natl. Acad. Sci. U.S.A. 1990, 87:6291-6295.
67. Stocsits R.R., Hofacker I.L., Fried C., Stadler P.F. Multiple sequence alignments of partially coding nucleic acid sequences. BMC Bioinform. 2005, 6:160.
68. Tu J., Sunter G. A conserved binding site within the Tomato golden mosaic virus AL-1629 promoter is necessary for expression of viral genes important for pathogenesis. Virology 2007, 367:117-125.
69. Valverde R.A., Clark C.A., Valkonen J.P. Virus and virus disease complexes of sweetpotato. Plant Viruses 2007, 1:116-126.
70. Valverde R.A., Sim J., Lotrakul P. Whitefly transmission of sweet potato viruses. Virus Res. 2004, 100:123-128.
71. Wu C.Y., Lai Y.C., Lin N.S., Hsu Y.H., Tsai H.T., Liao J.Y., Hu C.C. A simplified method of constructing infectious clones of begomovirus employing limited restriction enzyme digestion of products of rolling circle amplification. J. Virol. Methods 2008, 147:355-359.
72. Zhang W., Olson N.H., Baker T.S., Faulkner L., Agbandje-McKenna M., Boulton M., Davies J.W., McKenna R. Structure of the maize streak virus geminate particle. Virology 2001, 279:471-477.
73. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003, 31:3406-3415.