1887

Abstract

Sixteen viruses, belonging to 16 species of begomovirus, that infect crops and weeds in Vietnam were identified. Sequence analysis of the complete genomes showed that nine of the viruses (six monopartite and three bipartite) belong to novel species and five of them were identified in Vietnam for the first time. Additionally, eight DNA- and three nanovirus-like DNA-1 molecules were also found associated with some of the monopartite viruses. Five of the DNA- molecules were novel. Importantly, a second bipartite begomovirus, golden mosaic virus, shared several features with the previously characterized virus yellow vein virus and with other bipartite begomoviruses from the New World, supporting the hypothesis that New World-like viruses were present in the Old World. This, together with a high degree of virus diversity that included putative recombinant viruses, satellite molecules and viruses with previously undescribed variability in the putative stem–loop sequences, suggested that South-East Asia, and Vietnam in particular, is one of the origins of begomovirus diversity.

Loading

Article metrics loading...

/content/journal/jgv/10.1099/vir.0.83236-0
2008-01-01
2024-12-05
Loading full text...

Full text loading...

/deliver/fulltext/jgv/89/1/312.html?itemId=/content/journal/jgv/10.1099/vir.0.83236-0&mimeType=html&fmt=ahah

References

  1. Arguello-Astorga G. R., Ruiz-Medrano R. 2001; An iteron-related domain is associated to motif 1 in the replication proteins of geminiviruses: identification of potential interacting amino acid-base pairs by a comparative approach. Arch Virol 146:1465–1485 [CrossRef]
    [Google Scholar]
  2. Arguello-Astorga G. R., Guevara-Gonzalez R. G., Herrera-Estrella L. R., Rivera-Bustamante R. F. 1994; Geminivirus replication origins have a group-specific organization of iterative elements – a model for replication. Virology 203:90–100 [CrossRef]
    [Google Scholar]
  3. Briddon R. W., Stanley J. 2006; Subviral agents associated with plant single-stranded DNA viruses. Virology 344:198–210 [CrossRef]
    [Google Scholar]
  4. Briddon R. W., Bull S. E., Amin I., Mansoor S., Bedford I. D., Rishi N., Siwatch S. S., Zafar Y., Abdel-Salam A. M., Markham P. G. 2004; Diversity of DNA 1: a satellite-like molecule associated with monopartite begomovirus-DNA β complexes. Virology 324:462–474 [CrossRef]
    [Google Scholar]
  5. Briddon R. W., Bull S. E., Bedford I. D. 2006; Occurrence of Sweet potato leaf curl virus in Sicily. Plant Pathol 55:286
    [Google Scholar]
  6. Chakraborty S., Pandey P. K., Banerjee M. K., Kalloo G., Fauquet C. M. 2003; Tomato leaf curl Gujarat virus , a new begomovirus species causing a severe leaf curl disease of tomato in Varanasi, India. Phytopathology 93:1485–1495 [CrossRef]
    [Google Scholar]
  7. Fauquet C. 2002; Geminivirus species demarcation criteria study case. Webpage: Geminiviridae http://www.danforthcenter.org/iltab/geminiviridae/
    [Google Scholar]
  8. Fauquet C. M., Stanley J. 2003; Geminivirus classification and nomenclature: progress and problems. Ann Appl Biol 142:165–189 [CrossRef]
    [Google Scholar]
  9. Fauquet C. M., Stanley J. 2005; Revising the way we conceive and name viruses below the species level: a review of geminivirus taxonomy calls for new standardized isolate descriptors. Arch Virol 150:2151–2179 [CrossRef]
    [Google Scholar]
  10. Fauquet C. M., Bisaro D. M., Briddon R. W., Brown J. K., Harrison B. D., Rybicki E. P., Stenger D. C., Stanley J. 2003; Revision of taxonomic criteria for species demarcation in the family Geminiviridae , and an updated list of begomovirus species. Arch Virol 148:405–421 [CrossRef]
    [Google Scholar]
  11. Fontes E. P., Eagle P. A., Sipe P. S., Luckow V. A., Hanley-Bowdoin L. 1994a; Interaction between a geminivirus replication protein and origin DNA is essential for viral replication. J Biol Chem 269:8459–8465
    [Google Scholar]
  12. Fontes E. P., Gladfelter H. J., Schaffer R. L., Petty I. T., Hanley-Bowdoin L. 1994b; Geminivirus replication origins have a modular organization. Plant Cell 6:405–416 [CrossRef]
    [Google Scholar]
  13. Gibbs M. J., Armstrong J. S., Gibbs A. J. 2000; Sister-Scanning: a Monte Carlo procedure for assessing signals in recombinant sequences. Bioinformatics 16:573–582 [CrossRef]
    [Google Scholar]
  14. Gilbertson R. L., Hidayat S. H., Paplomatas E. J., Rojas M. R., Hou Y. M., Maxwell D. P. 1993; Pseudorecombination between infectious cloned DNA-components of tomato mottle and bean dwarf mosaic geminiviruses. J Gen Virol 74:23–31 [CrossRef]
    [Google Scholar]
  15. Green S. K., Tsai W. S., Shih S. L., Black L. L., Rezaian A., Rashid M. H., Roff M. M. N., Myint Y. Y., Hong L. T. A. 2001; Molecular characterization of begomoviruses associated with leafcurl diseases of tomato in Bangladesh, Laos, Malaysia, Myanmar, and Vietnam. Plant Dis 85, 1286
    [Google Scholar]
  16. Guerra-Peraza O., Kirk D., Seltzer V., Veluthambi K., Schmit A. C., Hohn T., Herzog E. 2005; Coat proteins of Rice tungro bacilliform virus and Mungbean yellow mosaic virus contain multiple nuclear-localization signals and interact with importin α . J Gen Virol 86:1815–1826 [CrossRef]
    [Google Scholar]
  17. Guo X., Zhou X. 2005; Molecular characterization of Alternanthera yellow vein virus: a new begomovirus species infecting Alternanthera philoxeroides . J Phytopathol 153:694–696 [CrossRef]
    [Google Scholar]
  18. Guo X. J., Zhou X. P. 2006; Molecular characterization of a new begomovirus infecting Sida cordifolia and its associated satellite DNA molecules. Virus Genes 33:279–285
    [Google Scholar]
  19. Ha C., Coombs S., Revill P., Harding R., Vu M., Dale J. 2006; Corchorus yellow vein virus , a New World geminivirus from the Old World. J Gen Virol 87:997–1003 [CrossRef]
    [Google Scholar]
  20. Hanley-Bowdoin L., Settlage S. B., Orozco B. M., Nagar S., Robertson D. 2000; Geminiviruses: models for plant DNA replication, transcription, and cell cycle regulation. Crit Rev Biochem Mol Biol 35:105–140
    [Google Scholar]
  21. Harrison B. D., Swanson M. M., Fargette D. 2002; Begomovirus coat protein: serology, variation and functions. Physiol Mol Plant Pathol 60:257–271 [CrossRef]
    [Google Scholar]
  22. Hattermann K., Schmitt C., Soike D., Mankertz A. 2003; Cloning and sequencing of Duck circovirus (DuCV). Arch Virol 148:2471–2480 [CrossRef]
    [Google Scholar]
  23. Hill J. E., Strandberg J. O., Hiebert E., Lazarowitz S. G. 1998; Asymmetric infectivity of pseudorecombinants of Cabbage leaf curl virus and Squash leaf curl virus : implications for bipartite geminivirus evolution and movement. Virology 250:283–292 [CrossRef]
    [Google Scholar]
  24. Idris A. M., Brown J. K. 2004; Cotton leaf crumple virus is a distinct Western Hemisphere begomovirus species with complex evolutionary relationships indicative of recombination and reassortment. Phytopathology 94:1068–1074 [CrossRef]
    [Google Scholar]
  25. Jeske H., Lutgemeier M., Preiss W. 2001; DNA forms indicate rolling circle and recombination-dependent replication of Abutilon mosaic virus . EMBO J 20:6158–6167 [CrossRef]
    [Google Scholar]
  26. Jupin I., Hericourt F., Benz B., Gronenborn B. 1995; DNA replication specificity of TYLCV geminivirus is mediated by the amino-terminal 116 amino acids of the Rep protein. FEBS Lett 362:116–120 [CrossRef]
    [Google Scholar]
  27. Kunik T., Palanichelvam K., Czosnek H., Citovsky V., Gafni Y. 1998; Nuclear import of the capsid protein of Tomato yellow leaf curl virus (TYLCV) in plant and insect cells. Plant J 13:393–399 [CrossRef]
    [Google Scholar]
  28. Lazarowitz S. G. 1992; Geminiviruses: genome structure and gene function. Crit Rev Plant Sci 11:327–349 [CrossRef]
    [Google Scholar]
  29. Lotrakul P., Valverde R. A. 1999; Cloning of a DNA-A-like genomic component of sweet potato leaf curl virus: nucleotide sequence and phylogenetic relationships. Mol Plant Pathol On-Line http://www.bspp.org.uk/mppol/1999/0422lotrakul/index.htm
    [Google Scholar]
  30. Lotrakul P., Valverde R. A., Clark C. A., Sim J., De La Torre R. 1998; Detection of a geminivirus infecting sweet potato in the United States. Plant Dis 82:1253–1257 [CrossRef]
    [Google Scholar]
  31. Martin D., Rybicki E. 2000; rdp: detection of recombination amongst aligned sequences. Bioinformatics 16:562–563 [CrossRef]
    [Google Scholar]
  32. Martin D. P., Williamson C., Posada D. 2005; rdp2: recombination detection and analysis from sequence alignments. Bioinformatics 21:260–262 [CrossRef]
    [Google Scholar]
  33. Orozco B. M., Hanley-Bowdoin L. 1996; A DNA structure is required for geminivirus replication origin function. J Virol 70:148–158
    [Google Scholar]
  34. Padidam M., Beachy R. N., Fauquet C. M. 1996; The role of AV2 (“precoat”) and coat protein in viral replication and movement in tomato leaf curl geminivirus. Virology 224:390–404 [CrossRef]
    [Google Scholar]
  35. Padidam M., Sawyer S., Fauquet C. M. 1999; Possible emergence of new geminiviruses by frequent recombination. Virology 265:218–225 [CrossRef]
    [Google Scholar]
  36. Page R. D. M. 1996; TreeView: an application to display phylogenetic trees on personal computers. Comput Appl Biosci 12:357–358
    [Google Scholar]
  37. Paximadis M., Idris A. M., Torres-Jerez I., Villarreal A., Rey M. E. C., Brown J. K. 1999; Characterization of tobacco geminiviruses in the Old and New World. Arch Virol 144:703–717 [CrossRef]
    [Google Scholar]
  38. Posada D., Crandall K. A. 2001; Evaluation of methods for detecting recombination from DNA sequences: computer simulations. Proc Natl Acad Sci U S A 98:13757–13762 [CrossRef]
    [Google Scholar]
  39. Revill P. A., Ha C. V., Porchun S. C., Vu M. T., Dale J. L. 2003; The complete nucleotide sequence of two distinct geminiviruses infecting cucurbits in Vietnam. Arch Virol 148:1523–1541 [CrossRef]
    [Google Scholar]
  40. Revill P. A., Ha C. V., Lines R. E., Bell K. E., Vu M. T., Dale J. L. 2004; PCR and ELISA-based virus surveys of banana, papaya and cucurbit crops in Vietnam. Asia Pac J Mol Biol Biotechnol 12:27–32
    [Google Scholar]
  41. Rigden J. E., Dry I. B., Mullineaux P. M., Rezaian M. A. 1993; Mutagenesis of the virion-sense open reading frames of tomato leaf curl geminivirus. Virology 193:1001–1005 [CrossRef]
    [Google Scholar]
  42. Rochester D. E., Kositratana W., Beachy R. N. 1990; Systemic movement and symptom production following agroinoculation with a single DNA of tomato yellow leaf curl geminivirus (Thailand). Virology 178:520–526 [CrossRef]
    [Google Scholar]
  43. Rojas M. R., Hagen C., Lucas W. J., Gilbertson R. L. 2005; Exploiting chinks in the plant's armor: evolution and emergence of geminiviruses. Annu Rev Phytopathol 43:361–394 [CrossRef]
    [Google Scholar]
  44. Rybicki E. P. 1994; A phylogenetic and evolutionary justification for 3 genera of Geminiviridae . Arch Virol 139:49–77 [CrossRef]
    [Google Scholar]
  45. Salminen M. O., Carr J. K., Burke D. S., McCutchan F. E. 1995; Identification of breakpoints in intergenotypic recombinants of HIV type-1 by bootscanning. AIDS Res Hum Retroviruses 11:1423–1425 [CrossRef]
    [Google Scholar]
  46. Saunders K., Salim N., Mali V. R., Malathi V. G., Briddon R., Markham P. G., Stanley J. 2002; Characterisation of Sri Lankan cassava mosaic virus and Indian cassava mosaic virus : evidence for acquisition of a DNA B component by a monopartite begomovirus. Virology 293:63–74 [CrossRef]
    [Google Scholar]
  47. Seal S. E., vandenBosch F., Jeger M. J. 2006; Factors influencing begomovirus evolution and their increasing global significance: implications for sustainable control. Crit Rev Plant Sci 25:23–46 [CrossRef]
    [Google Scholar]
  48. Sharma P., Rishi N., Malathi V. G. 2005; Molecular cloning of coat protein gene of an Indian cotton leaf curl virus (CLCuV-HS2) isolate and its phylogenetic relationship with others members of Geminiviridae . Virus Genes 30:85–91 [CrossRef]
    [Google Scholar]
  49. Smith J. M. 1992; Analyzing the mosaic structure of genes. J Mol Evol 34:126–129
    [Google Scholar]
  50. Stanley J., Bisaro D. M., Briddon R. W., Brown J. K., Fauquet C. M., Harrison B. D., Rybicki E. P., Stenger D. C. 2005; Family Geminiviridae . In Virus Taxonomy: Eighth Report of the International Committee on Taxonomy of Viruses pp 301–326Edited by Fauquet C. M., Mayo M. A., Maniloff J., Desselberger U., Ball L. A. London: Elsevier Academic Press;
    [Google Scholar]
  51. Stonor J., Hart P., Gunther M., DeBarro P., Rezaian M. A. 2003; Tomato leaf curl geminivirus in Australia: occurrence, detection, sequence diversity and host range. Plant Pathol 52:379–388 [CrossRef]
    [Google Scholar]
  52. Thompson J. D., Gibson T. J., Plewniak F., Jeanmougin F., Higgins D. G. 1997; The clustal_x windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882 [CrossRef]
    [Google Scholar]
  53. Unseld S., Hohnle M., Ringel M., Frischmuth T. 2001; Subcellular targeting of the coat protein of African cassava mosaic geminivirus. Virology 286:373–383 [CrossRef]
    [Google Scholar]
  54. Wang X.-Y., Xie Y., Zhou X.-P. 2004; Molecular characterization of two distinct begomoviruses from papaya in China. Virus Genes 29:303–309 [CrossRef]
    [Google Scholar]
  55. Zhou X.-P., Xie Y., Tao X.-R., Zhang Z.-K., Li Z.-H., Fauquet C. M. 2003; Characterization of DNA beta associated with begomoviruses in China and evidence for co-evolution with their cognate viral DNA-A. J Gen Virol 84:237–247 [CrossRef]
    [Google Scholar]
/content/journal/jgv/10.1099/vir.0.83236-0
Loading
/content/journal/jgv/10.1099/vir.0.83236-0
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error