Browse > Article
http://dx.doi.org/10.5423/PPJ.2009.25.2.142

Complete Genome Sequence of the RNAs 3 and 4 Segments of Rice stripe virus Isolates in Korea and their Phylogenetic Relationships with Japan and China Isolates  

Jonson, Miranda Gilda (Department of Agricultural Biotechnology and Plant Genomics and Breeding Institute, Seoul National University)
Choi, Hong-Soo (Department of Agricultural Biology, National Academy of Agricultural Science, Rural Development Administration)
Kim, Jeong-Soo (Department of Agricultural Biology, National Academy of Agricultural Science, Rural Development Administration)
Choi, Il-Ryong (Plant Breeding, Genetic and Biotechnology Division, International Rice Research Institute)
Kim, Kook-Hyung (Department of Agricultural Biotechnology and Plant Genomics and Breeding Institute, Seoul National University)
Publication Information
The Plant Pathology Journal / v.25, no.2, 2009 , pp. 142-150 More about this Journal
Abstract
The complete genome sequences of RNA3 and RNA4 of the 13 different Rice stripe virus (RSV) isolates were determined and characterized in this study to address the possible causes of the recent re-emergence of RSV that affected many rice fields in Korea. The genome size of each RNA segment varied among isolates and significant differences were observed in the intergenic region. There was up to 4% average divergence in the RNA4 nucleotide sequence among 13 Korean isolates and only 1.4% in the RNA3. Phylogenetic relationships among different Korean isolates revealed that there were at least 2 types of RNA3 and 4 distinct types of RNA4 genomes present in Korea. However, Korean isolates with one type of RNA3 predominate over the other while the occurrences of the RSV Korean isolates with the 4 types of RNA4 genome were not correlated to specific geographical areas. Results further indicate that RNA4 had diverged more than RNA3 and these differences in accumulation of mutations in the individual RNA segments indicate that genetic reassortment were likely to contribute to the genetic divergence in the 13 Korean isolates. All of the Korean-RNA3 sequences except for one isolate grouped with Chinese isolates (JY and Z). In contrast, the RNA 4 sequences segregated together with either Chinese (JY and Z) and Japanese (M and T) isolates but genetic relationships of Korean isolates- RNAs 3 and 4 segments to Chinese-Y isolate were low. Altogether, these results suggest that the occurrence of mixtures of RNAs 3 and 4 genotypes in the natural population of RSV may have contributed to the sudden outbreak in Korea.
Keywords
phylogenetic relationship; rice; Rice stripe virus; Tenuivirus;
Citations & Related Records
Times Cited By KSCI : 1  (Citation Analysis)
Times Cited By Web Of Science : 1  (Related Records In Web of Science)
연도 인용수 순위
1 Falk, B. W., Tsai, J. H. and Lommel, S. A. 1987. Differences in levels of detection for the maize stripe virus capsid and major non-capsid proteins in plants and insect hosts. J. Gen. Virol. 68: 1801-1811   DOI
2 Felsenstein, J. 1993. PHYLIP (Phylogeny Interference Package) 3.5. Department of Genetics, University of Washington, Seattle, USA
3 Hamamatsu, C., Toriyama, S., Toyoda, T. and Ishihama, A. 1993. Ambisense coding strategy of the rice stripe virus genome: in vitro translation studies. J. Gen. Virol. 74:1125-1131   DOI   ScienceOn
4 Hemmes, H., Lakatos, L. Goldbach, R., Burgyan, J. and Prins, M. 2007. The NS3 protein of Rice hoja blanca tenuivirus suppresses RNA silencing in plant and insect hosts by efficiently binding both siRNAs and miRNAs. RNA 13: 1079-1089   DOI   ScienceOn
5 Kakutani, T., Hayano, Y., Hayashi, T. and Minobe, Y. 1990. Ambisense segment 4 of Rice stripe virus: Possible evolutionary relationship with phleboviruses and uukuviruses (Bunyaviridae). J. Gen. Virol. 71:1427-1432   DOI   ScienceOn
6 Lee, B. C., Hong, Y. K.. Kwak, D. Y., Park, S. T, Choi, J. I. and Lee, K. W. 2004. Cloning and sequencing of coat protein gene of the Korean isolate of Rice stripe virus. Plant Pathol. J. 20:313-315   DOI   ScienceOn
7 Miranda, G. J., Azzam, O. and Shirako, Y. 2000. Comparison of nucleotide sequences between northern and southern Philippine isolates of Rice grassy stunt virus indicates occurrence of natural genetic reassortment. Virology 266:26-32   DOI   ScienceOn
8 Rodriguez, L. L., Owens, J. H., Peters, C. J. and Nichol, S. T. 1998. Genetic reassortant among viruses causing hantavirus pulmonary syndrome. Virology 242:99-106   DOI   ScienceOn
9 Saitou, N. and Nei, M. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425   PUBMED   ScienceOn
10 Thompson, J. D., Higgins, D. G. and 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   DOI   ScienceOn
11 Toriyama, S. 2000. Rice stripe virus. CMI/AAB Description of Plant Viruses. No. 375
12 Zhu, Y., Hayakawa, T. and Toriyama, S. 1992. Complete nucleotide sequence of RNA4 of Rice stripe virus isolate T, and comparison with another isolate and with maize stripe virus. J. Gen. Virol. 73:1309-1312   DOI   ScienceOn
13 Jeger, M. J., Seal, S. E. and van den Bosch, F. 2006. Evolutionary epidemiology of plant virus disease. Adv. Virus Res. 67:163-203   DOI   ScienceOn
14 Kakutani, T, Hayano, Y., Hayashi, T and 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   DOI   ScienceOn
15 de Miranda, J., Ramirez, B. C., Munoz, M., Lozano, I., Wu, R., Haenni, A L., Espinosa, A M. and Calvert, L. A. 1997. Comparison of Colombian and Costa Rican strains of Rice hoja blanca tenuivirus. Virus Genes 15: 191-193   DOI   ScienceOn
16 Xiong, R., Wu, J., Zhou, Y. and Zhou, X. 2008. Identification of movement protein of Rice stripe Tenuivirus. J. Virol. 82:12304-12311   DOI   ScienceOn
17 Hall, T. A. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl. Acids. Symp. Ser. 41 :95-98
18 Henderson, W. W., Monroe, M. C., St. Jeor, S. C., Thayer, W. P., Rowe, J. E., Peters, C. J. and Nichol, S. T 1995. Naturally occurring Sin nombre virus genetic reassortants. Virology 214:602-610   DOI   ScienceOn
19 Qu, Z., Liang, D., Harper, G. and 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   DOI   ScienceOn
20 Gu, H., Zhang, C. and Ghabrial, S. A. 2007. Novel naturally occurring Bean pod mottle virus reassortants with mixed heterologous RNA Igenomes. Phytopathology 97:79-86   DOI   ScienceOn
21 Zhang, H.-M., Yang. J., Sun, H.-R., Xin, X., Wang, H.-D., Chen J.-P. and Adams M. J. 2007. Genomic analysis of Rice stripe virus Zhejiang isolate shows the presence of an OTU-like domain in the RNA 1 protein and a novel sequence motif conserved within the intergenic regions of ambisense segments of tenuiviruses. Arch. Virol. 152:1917-1923   DOI   ScienceOn
22 Hibino, H. 1996. Biology and epidemiology of rice viruses. Annu. Rev. Phytopathol. 34:249-274   DOI   PUBMED   ScienceOn
23 Zhu, Y., Hayakawa, T., Toriyama, S. and Takahashi, M. 1991. Complete nucleotide sequence of RNA3 of Rice stripe virus: An ambisense coding strategy. J. Gen. Virol. 72:763-767   DOI   ScienceOn
24 Haenni A-L., de Miranda J. R., FaIk B. W., Goldbach R., Mayo M. A., Shirako Y. and Toriyama S. 2005. Tenuivirus. In: Virus taxonomy. Eighth report of the International Committee on taxonomy of viruses, ed. by C. M. Fauquet, M. A. Mayo, J. Maniloff, U. Desselberger and L. A. Ball, pp.717-723. Elsevier Academic Press, San Diego
25 Lijun, C., Xizhi, M., Lin, K., Kejing, D., Shouyuan, Z. and Changben, L. 2003. Detecting Rice stripe virus (RSV) in the small brown planthopper (Laodelphax striatellus) with high specificity by RT-PCR. J. Virol. Methods 112: 115-120   DOI   PUBMED   ScienceOn
26 Falk, B. W. and Tsai, J. H. 1998. Biology and molecular biology of viruses in the genus tenuiviruses. Annu. Rev. Phytopathol. 36:139-163   DOI   ScienceOn
27 Toriyama, S., Takahashi, M., Sano, Y., Shimizu, T. and Ishihama, A. 1994. Nucleotide sequence of RNA 1, the largest genomic segment of Rice stripe virus, the prototype of the tenuivirus. J. Gen. Virol. 75:3569-3579   DOI   ScienceOn
28 Liang, D., Qu, Z., Ma, X. and Hull, R. 2005. Detection and localization of Rice stripe virus gene products in vivo. Virus Genes 31 :211-221   DOI
29 Wang, H.-D., Chen, J.-P., Zhang, H.-M., Sun, X.-L., Zhu, J.-L., Wang, A.-G, Sheng, W.-X. and Adams, M. J. 2008. Recent Rice stripe virus epidemics in Zhejiang province, China, and experiments on sowing date, disease-yield loss relationships, and seedling susceptibility. Plant Dis. 92: 1190-1196   DOI   ScienceOn