Abstract
Rice grassy stunt virus (RGSV, Tenuivirus) recently emerged on rice in Vietnam, causing high yield losses during 2006–2009. The genetic diversity of RGSV is poorly documented. In this study, the two genes encoded by each ambisense segment RNA3 and RNA5 of RGSV isolates from six provinces of South Vietnam were sequenced. P3 and Pc3 (RNA3) have unknown function, P5 (RNA5) encodes the putative silencing suppressor, and Pc5 (RNA5) encodes the nucleocapsid protein (N). The sequences of 17 Vietnamese isolates were compared with reference isolates from North and South Philippines. The average nucleotide diversity among the isolates was low. We confirmed a higher variability of RNA3 than RNA5 and Pc3 than P3. No relationships between the genetic diversity and the geographic distribution of RGSV isolates could be ascertained, likely because of the long-distance migration of the insect vector. This data will contribute to a better understanding on the RGSV epidemiology in South Vietnam, a prerequisite for further management of the disease and rice breeding for resistance.
This is a preview of subscription content, log in via an institution to check access.
References
T.H. Anh, N.V. Vien, N.T. Anh, T.T.T. Huyen, N.V. Chung, N.D. Phuong, One-step RT-PCR for detection of rice grassy stunt and rice ragged stunt viruses. J. Plant Protect. (in Vietnamese) 5, 21–26 (2009)
J.R. de Miranda, B.C. Ramirez, M. Munoz, I. Lozano, R. Wu, A.L. Haenni, A.M. Espinoza, L.A. Calvert, Comparison of Colombian and Costa Rican strains of rice hoja blanca tenuivirus. Virus Genes 15, 191–193 (1997)
M.G. Jonson, H.S. Choi, J.S. Kim, I.R. Choi, K.H. Kim, 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. Plant Pathol. J. 25, 142–150 (2009)
M.G. Jonson, H.S. Choi, J.S. Kim, I.R. Choi, K.H. Kim, Sequence and phylogenetic analysis of the RNA1 and RNA2 segments of Korean Rice stripe virus isolates and comparison with those of China and Japan. Arch. Virol. 154, 1705–1708 (2009)
D. Liang, Z. Qu, X. Ma, R. Hull, Detection and localization of Rice stripe virus gene products in vivo. Virus Genes 31, 211–221 (2005)
P. Librado, J. Rozas, DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25, 1451–1452 (2009)
A. Mahmoud, M. Royer, M. Granier, E.D. Ammar, M. Peterschmitt, High genetic identity between RNA 3 segments of an Old World isolate and a New World isolate of Maize stripe virus. Arch. Virol. 152, 1583–1586 (2007)
G.J. Miranda, O. Azzam, Y. Shirako, 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 (2000)
A. Otuka, Migration of rice planthoppers and simulation techniques, in Planthoppers: new threats to the sustainability of intensive rice production systems in Asia, ed. by K.L. Heong, B. Hardy (International Rice Research Institute, Los Banos, 2009), pp. 343–356
Y. Shirako, B.W. Falk, A.L. Haenni, Genus Tenuivirus, in Virus taxonomy: classification and nomenclature of viruses: Ninth Report of the International Committee on Taxonomy of Viruses, ed. by A.M.Q. King, E.J. Lefkowitz, M.J. Adams, E.B. Carstens (Elsevier Academic Press, San Diego, 2011), pp. 771–776
K. Tamura, D. Peterson, N. Peterson, G. Stecher, M. Nei, S. Kumar, MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28, 2731–2739 (2011)
J.D. Thompson, D.G. Higgins, T.J. Gibson, 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 (1994)
S. Toriyama, T. Kimishima, M. Takahashi, The proteins encoded by rice grassy stunt virus RNA5 and RNA6 are only distantly related to the corresponding proteins of other members of the genus Tenuivirus. J. Gen. Virol. 78(Pt 9), 2355–2363 (1997)
Vien, N. V., Lam, N. V., Thanh, T. T., Thanh, D. V., Cuong, N. N. & Ta-Hoang, A. (2007). Study on Rice grassy stunt virus and Rice ragged stunt virus and their management, in Annual Report of PPRI (in Vietnamese)
T.Y. Wei, J.G. Yang, F.R. Liao, F.L. Gao, L.M. Lu, X.T. Zhang, F. Li, Z.J. Wu, Q.Y. Lin, L.H. Xie, H.X. Lin, Genetic diversity and population structure of rice stripe virus in China. J. Gen. Virol. 90, 1025–1034 (2009)
F. Zhang, H. Guo, H. Zheng, T. Zhou, Y. Zhou, S. Wang, R. Fang, W. Qian, X. Chen, Massively parallel pyrosequencing-based transcriptome analyses of small brown planthopper (Laodelphax striatellus), a vector insect transmitting rice stripe virus (RSV). BMC Genomics 11, 303 (2010)
Acknowledgments
This work was supported by a BEST grant from Département de Soutien et Formation (DSF IRD), a bilateral project funded by Ministry of Science and Technology of Vietnam and Ministère des Affaires Etrangères de la France (PHC Hoa Sen Lotus 23968UL) and a Project from Groupement de Recherche International (GDRI BMI CNRS/IRD).
Author information
Authors and Affiliations
Corresponding author
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Ta, HA., Nguyen, DP., Causse, S. et al. Molecular diversity of Rice grassy stunt virus in Vietnam. Virus Genes 46, 383–386 (2013). https://doi.org/10.1007/s11262-012-0845-3
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11262-012-0845-3