1887

Abstract

Rice stripe virus (RSV) is one of the most economically important pathogens of rice and is repeatedly epidemic in China, Japan and Korea. The most recent outbreak of RSV in eastern China in 2000 caused significant losses and raised serious concerns. In this paper, we provide a genotyping profile of RSV field isolates and describe the population structure of RSV in China, based on the nucleotide sequences of isolates collected from different geographical regions during 1997–2004. RSV isolates could be divided into two or three subtypes, depending on which gene was analysed. The genetic distances between subtypes range from 0.050 to 0.067. The population from eastern China is composed only of subtype I/IB isolates. In contrast, the population from Yunnan province (southwest China) is composed mainly of subtype II isolates, but also contains a small proportion of subtype I/IB isolates and subtype IA isolates. However, subpopulations collected from different districts in eastern China or Yunnan province are not genetically differentiated and show frequent gene flow. RSV genes were found to be under strong negative selection. Our data suggest that the most recent outbreak of RSV in eastern China was not due to the invasion of new RSV subtype(s). The evolutionary processes contributing to the observed genetic diversity and population structure are discussed.

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2009-04-01
2019-11-22
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References

  1. Abubakar, Z., Ali, F., Pinel, A., Traore, O., N'Guessan, P., Notteghem, J. L., Kimmins, F., Konate, G. & Fargette, D. ( 2003; ). Phylogeography of rice yellow mottle virus in Africa. J Gen Virol 84, 733–743.[CrossRef]
    [Google Scholar]
  2. Arboleda, M. & Azzam, O. ( 2000; ). Inter- and intra-site genetic diversity of natural field populations of rice tungro bacilliform virus in the Philippines. Arch Virol 145, 275–289.[CrossRef]
    [Google Scholar]
  3. Azzam, O., Arboleda, M., Umadhay, K. M., de los Reyes, J. B., Cruz, F. S., Mackenzie, A. & McNally, K. L. ( 2000; ). Genetic composition and complexity of virus populations at tungro-endemic and outbreak rice sites. Arch Virol 145, 2643–2657.[CrossRef]
    [Google Scholar]
  4. Bedford, I. D., Briddon, R. W., Rosell, R. & Markham, P. G. ( 1994; ). Geminivirus transmission and biological characterization of Bemisia tabaci (Gennadius) biotypes from different geographic regions. Ann Appl Biol 125, 311–325.[CrossRef]
    [Google Scholar]
  5. Bucher, E., Sijen, T., De Haan, P., Goldbach, R. & Prins, M. ( 2003; ). Negative-strand tospoviruses and tenuiviruses carry a gene for a suppressor of gene silencing at analogous genomic positions. J Virol 77, 1329–1336.[CrossRef]
    [Google Scholar]
  6. Chare, E. R. & Holmes, E. C. ( 2004; ). Selection pressures in the capsid genes of plant RNA viruses reflect mode of transmission. J Gen Virol 85, 3149–3159.[CrossRef]
    [Google Scholar]
  7. Drake, J. W. & Holland, J. J. ( 1999; ). Mutation rates among RNA viruses. Proc Natl Acad Sci U S A 96, 13910–13913.[CrossRef]
    [Google Scholar]
  8. Falk, B. W. & Tsai, J. H. ( 1998; ). Biology and molecular biology of viruses in the genus tenuivirus. Annu Rev Phytopathol 36, 139–163.[CrossRef]
    [Google Scholar]
  9. Fargette, D., Konate, G., Fauquet, C., Muller, E., Peterschmitt, M. & Thresh, J. M. ( 2006; ). Molecular ecology and emergence of tropical plant viruses. Annu Rev Phytopathol 44, 235–260.[CrossRef]
    [Google Scholar]
  10. Fraile, A., Alonso-Prados, J. L., Aranda, M. A., Bernal, J. J., Malpica, J. M. & Garcia-Arenal, F. ( 1997; ). Genetic exchange by recombination or reassortment is infrequent in natural populations of a tripartite RNA plant virus. J Virol 71, 934–940.
    [Google Scholar]
  11. Garcia-Arenal, F., Fraile, A. & Malpica, J. M. ( 2001; ). Variability and genetic structure of plant virus populations. Annu Rev Phytopathol 39, 157–186.[CrossRef]
    [Google Scholar]
  12. Gessain, A., Gallo, R. C. & Franchini, G. ( 1992; ). Low degree of human T-cell lymphotropic virus type I genetic drift in vivo as a means of monitoring viral transmission and movement of ancient human populations. J Virol 66, 2288–2295.
    [Google Scholar]
  13. Giri, A., Slattery, J. P., Heneine, W., Gessain, A., Rivadeneira, E., Desrosiers, R. C., Rosen, L., Anthony, R., Pamungkas, J. & other authors ( 1997; ). The tax gene sequences form two divergent monophyletic lineages corresponding to types I and II of simian and human T-cell leukemia/lymphotropic viruses. Virology 231, 96–104.[CrossRef]
    [Google Scholar]
  14. Hibino, H. ( 1996; ). Biology and epidemiology of rice viruses. Annu Rev Phytopathol 34, 249–274.[CrossRef]
    [Google Scholar]
  15. Hoshizaki, S. ( 1997; ). Allozyme polymorphism and geographic variation in the small brown planthopper, Laodelphax striatellus (Homoptera: Delphacidae). Biochem Genet 35, 383–393.[CrossRef]
    [Google Scholar]
  16. Hudson, R. R. ( 2000; ). A new statistic for detecting genetic differentiation. Genetics 155, 2011–2014.
    [Google Scholar]
  17. Hudson, R. R., Boos, D. D. & Kaplan, N. L. ( 1992; ). A statistical test for detecting geographic subdivision. Mol Biol Evol 9, 138–151.
    [Google Scholar]
  18. Kakutani, T., Hayano, Y., Hayashi, T. & Minobe, Y. ( 1990; ). Ambisense segment 4 of rice stripe virus: possible evolutionary relationship with phleboviruses and uukuviruses (Bunyaviridae). J Gen Virol 71, 1427–1432.[CrossRef]
    [Google Scholar]
  19. Kakutani, T., Hayano, Y., Hayashi, T. & Minobe, Y. ( 1991; ). Ambisense segment 3 of rice stripe virus: the first instance of a virus containing two ambisense segments. J Gen Virol 72, 465–468.[CrossRef]
    [Google Scholar]
  20. Koralnik, I. J., Boeri, E., Saxinger, W. C., Monico, A. L., Fullen, J., Gessain, A., Guo, H. G., Gallo, R. C., Markham, P. & other authors ( 1994; ). Phylogenetic associations of human and simian T-cell leukemia/lymphotropic virus type I strains: evidence for interspecies transmission. J Virol 68, 2693–2707.
    [Google Scholar]
  21. Kumar, S., Tamura, K., Jakobsen, I. B. & Nei, M. ( 2001; ). mega2: molecular evolutionary genetics analysis software. Bioinformatics 17, 1244–1245.[CrossRef]
    [Google Scholar]
  22. Lin, Q. Y., Xie, L. H., Zhou, Z. J., Xie, L. Y. & Wu, Z. J. ( 1990; ). Studies on rice stripe I. Distribution of and losses caused by the disease. J Fujian Agric Coll 19, 421–425.
    [Google Scholar]
  23. Lin, H., Wei, T., Wu, Z., Lin, Q. & Xie, L. ( 1999; ). Molecular variability in coat protein and disease-specific protein genes among seven isolates of Rice stripe virus in China. In Abstracts of the XIth International Congress of Virology. Sydney, Australia, 9–13 August 1999, pp. 235–236. Utrecht, The Netherlands: International Union of Microbiological Societies.
  24. Lin, H., Wei, T., Wu, Z., Lin, Q. & Xie, L. ( 2001; ). Sequence analysis of RNA4 of a severe isolate of Rice stripe virus in China. Wei Sheng Wu Xue Bao 41, 25–30 (in Chinese).
    [Google Scholar]
  25. Lin, H., Wei, T., Wu, Z., Lin, Q. & Xie, L. ( 2002; ). Comparison of pathogenesis and biochemical properties of seven isolates of Rice stripe virus. J Fujian Agric Coll 31, 164–167.
    [Google Scholar]
  26. Lin, H. X., Rubio, L., Smythe, A. B. & Falk, B. W. ( 2004; ). Molecular population genetics of Cucumber mosaic virus in California: evidence for founder effects and reassortment. J Virol 78, 6666–6675.[CrossRef]
    [Google Scholar]
  27. McGrath, P. F. & Harrison, B. D. ( 1995; ). Transmission of tomato leaf curl geminiviruses by Bemisia tabaci: effects of virus isolate and vector biotype. Ann Appl Biol 126, 307–316.[CrossRef]
    [Google Scholar]
  28. Moya, A. & Garcia-Arenal, F. ( 1995; ). Population genetics of viruses. In Molecular Basis of Evolution, pp. 213–223. Edited by A. J. Gibbs, C. H. Calisher & F. Arenal-Garcia. Cambridge: Cambridge University Press.
  29. Palukaitis, P., Roossinck, M. J., Dietzgen, R. G. & Francki, F. I. B. ( 1992; ). Cucumber mosaic virus. Adv Virus Res 41, 281–348.
    [Google Scholar]
  30. Power, A. G. ( 2000; ). Insect transmision of plant viruses: a constraint on virus variability. Curr Opin Plant Biol 3, 336–340.[CrossRef]
    [Google Scholar]
  31. Qu, Z., Liang, D., Harper, G. & Hull, R. ( 1997; ). Comparison of sequences of RNAs 3 and 4 of rice stripe virus from China with those of Japanese isolates. Virus Genes 15, 99–103.[CrossRef]
    [Google Scholar]
  32. Rozas, J., Sanchez-DelBarrio, J. C., Messeguer, X. & Rozas, R. ( 2003; ). DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19, 2496–2497.[CrossRef]
    [Google Scholar]
  33. Schneider, W. L. & Roossinck, M. J. ( 2000; ). Evolutionarily related Sindbis-like plant viruses maintain different levels of population diversity in a common host. J Virol 74, 3130–3134.[CrossRef]
    [Google Scholar]
  34. Schneider, W. L. & Roossinck, M. J. ( 2001; ). Genetic diversity in RNA virus quasispecies is controlled by host–virus interactions. J Virol 75, 6566–6571.[CrossRef]
    [Google Scholar]
  35. Swofford, D. L. ( 2002; ). paup*: Phylogenetic analysis using parsimony (*and other methods), version 4. Sunderland, MA: Sinauer Associates.
  36. Takahashi, M., Toriyama, S., Hamamatsu, C. & Ishihama, A. ( 1993; ). Nucleotide sequence and possible ambisense coding strategy of rice stripe virus RNA segment 2. J Gen Virol 74, 769–773.[CrossRef]
    [Google Scholar]
  37. Thompson, J. D., Higgins, D. G. & Gibson, T. J. ( 1994; ). clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22, 4673–4680.[CrossRef]
    [Google Scholar]
  38. Toriyama, S. ( 1986; ). Rice stripe virus: prototype of a new group of viruses that replicate in plants and insects. Microbiol Sci 3, 347–351.
    [Google Scholar]
  39. Toriyama, S., Takahashi, M., Sano, Y., Shimizu, T. & Ishihama, A. ( 1994; ). Nucleotide sequence of RNA 1, the largest genomic segment of rice stripe virus, the prototype of the tenuiviruses. J Gen Virol 75, 3569–3579.[CrossRef]
    [Google Scholar]
  40. Wang, Z. F., Qiu, B. S. & Tien, P. ( 1992; ). Molecular biology of rice stripe virus III. Sequence analysis of coat protein gene. Virol Sin 7, 463–466.
    [Google Scholar]
  41. Wei, T., Lin, H., Wu, Z., Lin, Q. & Xie, L. ( 2003a; ). Sequence analysis of intergenic region of rice stripe virus RNA4: evidence for mixed infection and genetic variation. Wei Sheng Wu Xue Bao 43, 577–585 (in Chinese).
    [Google Scholar]
  42. Wei, T. Y., Wang, H., Lin, H. X., Wu, Z. J., Lin, Q. Y. & Xie, L. H. ( 2003b; ). Sequence analysis of RNA3 of rice stripe virus isolates found in China: evidence for reassortment in Tenuivirus. Sheng Wu Hua Xue Yu Sheng Wu Wu Li Xue Bao (Shanghai) 35, 97–103 (in Chinese).
    [Google Scholar]
  43. Xie, L. H., Wei, T. Y., Lin, H. X., Wu, Z. J. & Lin, Q. Y. ( 2001; ). The molecular biology of Rice stripe virus. J Fujian Agric Coll 30, 269–279.
    [Google Scholar]
  44. Xiong, R., Wu, J., Zhou, Y. & Zhou, X. ( 2008; ). Identification of a movement protein of rice stripe tenuivirus. J Virol 82, 12304–12311.[CrossRef]
    [Google Scholar]
  45. Zhu, Y., Hayakawa, T., Toriyama, S. & Takahashi, M. ( 1991; ). Complete nucleotide sequence of RNA 3 of rice stripe virus: an ambisense coding strategy. J Gen Virol 72, 763–767.[CrossRef]
    [Google Scholar]
  46. Zhu, Y., Hayakawa, T. & Toriyama, S. ( 1992; ). Complete nucleotide sequence of RNA 4 of rice stripe virus isolate T, and comparison with another isolate and with maize stripe virus. J Gen Virol 73, 1309–1312.[CrossRef]
    [Google Scholar]
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vol. , part 4, pp. 1025 – 1034

Geographical location, collection year, GenBank accession numbers and rice variety of RSV isolates, and associated references [ PDF] (152 KB)



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