Genetic diversity and phylogeography of cassava mosaic viruses in Kenya Free

Abstract

Cassava is a major factor in food security across sub-Saharan Africa. However, the crop is susceptible to losses due to biotic stresses, in particular to viruses of the genus (family ) that cause cassava mosaic disease (CMD). During the 1990s, an epidemic of CMD severely hindered cassava production across eastern and central Africa. A significant influence on the appearance of virus epidemics is virus diversity. Here, a survey of the genetic diversity of CMD-associated begomoviruses across the major cassava-growing areas of Kenya is described. Because an initial PCR-restriction fragment-length polymorphism analysis identified a much greater diversity of viruses than assumed previously, representative members of the population were characterized by sequence analysis. The full-length sequences of 109 components (68 DNA-A and 41 DNA-B) were determined, representing isolates of and , as well as a novel begomovirus species for which the name East African cassava mosaic Kenya virus is proposed. The DNA-B components were much less diverse than their corresponding DNA-A components, but nonetheless segregated into western and eastern (coastal) groups. All virus species and strains encountered showed distinct geographical distributions, highlighting the importance of preventing both the movement of viruses between these regions and the importation of the disease from adjacent countries and islands in the Indian Ocean that would undoubtedly encourage further diversification.

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2006-10-01
2024-03-28
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References

  1. Briddon R. W., Markham P. G. 1994; Universal primers for the PCR amplification of dicot-infecting geminiviruses. Mol Biotechnol 1:202–205 [CrossRef]
    [Google Scholar]
  2. Briddon R. W., Robertson I., Markham P. G., Stanley J. 2004; Occurrence of South African cassava mosaic virus (SACMV) in Zimbabwe. Plant Pathol 53:233 [CrossRef]
    [Google Scholar]
  3. Brown J. K., Idris A. M., Torres-Jerez I., Banks G. K., Wyatt S. D. 2001; The core region of the coat protein gene is highly useful for establishing the provisional identification and classification of begomoviruses. Arch Virol 146:1581–1598 [CrossRef]
    [Google Scholar]
  4. Bull S. E., Karakacha H. W., Briddon R. W., Nzioki S., Maruthi M. N., Stanley J., Winter S. 2003; Occurrence of East African cassava mosaic Zanzibar virus (EACMZV) in coastal Kenya. Plant Pathol 52:791 [CrossRef]
    [Google Scholar]
  5. Chellappan P., Vanitharani R., Fauquet C. M. 2004; Short interfering RNA accumulation correlates with host recovery in DNA virus-infected hosts, and gene silencing targets specific viral sequences. J Virol 78:7465–7477 [CrossRef]
    [Google Scholar]
  6. Devereux J., Haeberli P., Smithies O. 1984; A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res 12:387–395 [CrossRef]
    [Google Scholar]
  7. Dutt N., Briddon R. W., Dasgupta I. 2005; Identification of a second begomovirus, Sri Lankan cassava mosaic virus, causing cassava mosaic disease in India. Arch Virol 150:2101–2108 [CrossRef]
    [Google Scholar]
  8. 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]
  9. Gibson R. W., Otim-Nape G. W. 1997; Factors determining recovery and reversion in mosaic-affected African cassava mosaic virus resistant cassava. Ann Appl Biol 131:259–271 [CrossRef]
    [Google Scholar]
  10. Gorbalenya A. E., Koonin E. V., Wolf Y. I. 1990; A new superfamily of putative NTP-binding domains encoded by genomes of small DNA and RNA viruses. FEBS Lett 262:145–148 [CrossRef]
    [Google Scholar]
  11. Hanley-Bowdoin L., Settlage S. B., Orozco B. M., Nagar S., Robertson D. 1999; Geminiviruses: models for plant DNA replication, transcription, and cell cycle regulation. Crit Rev Plant Sci 18:71–106 [CrossRef]
    [Google Scholar]
  12. Hanley-Bowdoin L., Settlage S. B., Robertson D. 2004; Reprogramming plant gene expression: a prerequisite to geminivirus DNA replication. Mol Plant Pathol 5:149–156 [CrossRef]
    [Google Scholar]
  13. Hong Y. G., Harrison B. D. 1995; Nucleotide sequences from tomato leaf curl viruses from different countries: evidence for three geographically separate branches in evolution of the coat protein of whitefly-transmitted geminiviruses. J Gen Virol 76:2043–2049 [CrossRef]
    [Google Scholar]
  14. Hong Y. G., Robinson D. J., Harrison B. D. 1993; Nucleotide sequence evidence for the occurrence of three distinct whitefly-transmitted geminiviruses in cassava. J Gen Virol 74:2437–2443 [CrossRef]
    [Google Scholar]
  15. Legg J. P., Fauquet C. M. 2004; Cassava mosaic geminiviruses in Africa. Plant Mol Biol 56:585–599 [CrossRef]
    [Google Scholar]
  16. Martin D., Rybicki E. 2000; rdp: detection of recombination amongst aligned sequences. Bioinformatics 16:562–563 [CrossRef]
    [Google Scholar]
  17. Maruthi M. N., Seal S., Colvin J., Briddon R. W., Bull S. E. 2004; East African cassava mosaic Zanzibar virus – a recombinant begomovirus species with a mild phenotype. Arch Virol 149:2365–2377 [CrossRef]
    [Google Scholar]
  18. Ndunguru J., Legg J. P., Aveling T. A. S., Thompson G., Fauquet C. M. 2005; Molecular biodiversity of cassava begomoviruses in Tanzania: evolution of cassava geminiviruses in Africa and evidence for East Africa being a center of diversity of cassava geminiviruses. Virol J 2:21 [CrossRef]
    [Google Scholar]
  19. Okao-Okuja G., Legg J. P., Traore L., Jorge M. A. 2004; Viruses associated with cassava mosaic disease in Senegal and Guinea Conakry. J Phytopathol 152:69–76 [CrossRef]
    [Google Scholar]
  20. Page R. D. M. 1996; TreeView: an application to display phylogenetic trees on personal computers. Comput Appl Biosci 12:357–358
    [Google Scholar]
  21. Pita J. S., Fondong V. N., Sangaré A., Otim-Nape G. W., Ogwal S., Fauquet C. M. 2001; Recombination, pseudorecombination and synergism of geminiviruses are determinant keys to the epidemic of severe cassava mosaic disease in Uganda. J Gen Virol 82:655–665
    [Google Scholar]
  22. Ranomenjanahary S., Rabindran R., Robinson D. J. 2002; Occurrence of three distinct begomoviruses in cassava in Madagascar. Ann Appl Biol 140:315–318 [CrossRef]
    [Google Scholar]
  23. Saunders K., Salim N., Mali V. R., Malathi V. G., Briddon R. W., 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]
  24. Sseruwagi P., Sserubombwe W. S., Legg J. P., Ndunguru J., Thresh J. M. 2004; Methods of surveying the incidence and severity of cassava mosaic disease and whitefly vector populations on cassava in Africa: a review. Virus Res 100:129–142 [CrossRef]
    [Google Scholar]
  25. Stanley J., Gay M. R. 1983; Nucleotide sequence of cassava latent virus DNA. Nature 301:260–262 [CrossRef]
    [Google Scholar]
  26. 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  301–326 Edited by Fauquet C. M., Mayo M. A., Maniloff J., Desselberger U., Ball L. A. London: Elsevier/Academic Press;
    [Google Scholar]
  27. 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]
  28. Vanitharani R., Chellappan P., Pita J. S., Fauquet C. M. 2004; Differential roles of AC2 and AC4 of cassava geminiviruses in mediating synergism and suppression of posttranscriptional gene silencing. J Virol 78:9487–9498 [CrossRef]
    [Google Scholar]
  29. Vanitharani R., Chellappan P., Fauquet C. M. 2005; Geminiviruses and RNA silencing. Trends Plant Sci 10:144–151 [CrossRef]
    [Google Scholar]
  30. Voinnet O., Pinto Y. M., Baulcombe D. C. 1999; Suppression of gene silencing: a general strategy used by diverse DNA and RNA viruses of plants. Proc Natl Acad Sci U S A 23:14147–14152
    [Google Scholar]
  31. Walker J. E., Saraste M., Runswick M. J., Gay N. J. 1982; Distantly related sequences in the α - and β -subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold. EMBO J 1:945–951
    [Google Scholar]
  32. Were H. K., Winter S., Maiss E. 2004a; Occurrence and distribution of cassava begomoviruses in Kenya. Ann Appl Biol 145:175–184 [CrossRef]
    [Google Scholar]
  33. Were H. K., Winter S., Maiss E. 2004b; Viruses infecting cassava in Kenya. Plant Dis 88:17–22 [CrossRef]
    [Google Scholar]
  34. Zhou X., Liu Y., Calvert L., Munoz C., Otim-Nape G. W., Robinson D. J., Harrison B. D. 1997; Evidence that DNA-A of a geminivirus associated with severe cassava mosaic disease in Uganda has arisen by interspecific recombination. J Gen Virol 78:2101–2111
    [Google Scholar]
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