JZUS - Journal of Zhejiang University SCIENCE

Journal of Zhejiang University SCIENCE B 2013 Vol.14 No.10 P.875-885

Genetic variability and evolution of rice stripe virus

Author(s): Ling-zhe Huang, Li-xia Rao, Xue-ping Zhou, Jian-xiang Wu
Affiliation(s): State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
Corresponding email(s): wujx@zju.edu.cn
Key Words: Rice stripe virus, Genetic variability, Genetic evolution

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Abstract: rice stripe virus (RSV) is the type member of the genus Tenuivirus. RSV is known to have four segmented, single-stranded RNA molecules and causes rice stripe disease in the rice fields of China, Japan, and Korea. Based on the complete genomic sequences of the determined 6 RSV isolates (from Yunnan, Jiangsu, Zhejiang, and Liaoning Provinces, China) and 27 other RSV isolates (from Yunnan, Jiangsu, Anhui, Henan, and Shandong Provinces of China, also Japan and Korea) downloaded from GenBank, we provided a genotyping profile of RSV field isolates and described the population structure of RSV. All RSV isolates, except isolate CX, could be divided into two subtypes, one including 6 isolates from Yunnan Province, and the other including 26 isolates from different parts of China, Japan, and Korea, which were referred to as subtype II and subtype I, respectively. The amino acid distances between subtypes range from 0.053 to 0.085. RSV isolates in Yunnan Province were genetically differentiated from other parts of China, Japan, and Korea and showed infrequent gene flow. The RSV populations collected from other parts of China, Japan, and Korea were only composed of subtype I and showed very low genetic diversity. We speculated that isolate CX may be the result of recombination of isolates from two subtypes. Two potential recombination events were detected in RNA4 of isolate CX.

Reference

[1]Domingo, E., Holland, J.J., 1997. RNA virus mutations and fitness for survival. Annu. Rev. Microbiol., 51(1):151-178.

[2]Elena, S.F., Sanjuán, R., 2007. Virus evolution: insights from an experimental approach. Annu. Rev. Ecol. Evol. Syst., 38(1):27-52.

[3]Falk, B.W., Tsai, J.H., 1998. Biology and molecular biology of viruses in the genus Tenuivirus. Annu. Rev. Phytopathol., 36(1):139-163.

[4]Felsenstein, J., 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution, 39(4):783-791.

[5]Hudson, R.R., 2000. A new statistic for detecting genetic differentiation. Genetics, 155(4):2011-2014.

[6]Hudson, R.R., Boos, D.D., Kaplan, N.L., 1992. A statistical test for detecting geographic subdivision. Mol. Biol. Evol., 9(1):138-151.

[7]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(2):465-468.

[8]Koganezawa, H., 1975. Purification of rice stripe virus. Annu. Phytopathol. Soc. Jpn., 41:148-154 (in Japanese).

[9]Lauring, A.S., Andino, R., 2010. Quasispecies theory and the behavior of RNA viruses. PLoS Pathog., 6(7):e1001005.

[10]Librado, P., Rozas, J., 2009. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25(11):1451-1452.

[11]Martin, D.P., Lemey, P., Lott, M., Moulton, V., Posada, D., Lefeuvre, P., 2010. RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics, 26(19):2462-2463.

[12]Nei, M., Gojobori, T., 1986. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol., 3(5):418-426.

[13]Ramirez, B.C., Haenni, A.L., 1994. Molecular biology of tenuiviruses, a remarkable group of plant viruses. J. Gen. Virol., 75(3):467-475.

[14]Roossinck, M.J., 1997. Mechanisms of plant virus evolution. Annu. Rev. Phytopathol., 35(1):191-209.

[15]Saitou, N., Nei, M., 1987. The Neighbor-Joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol., 4(4):406-425.

[16]Sanjuán, R., Nebot, M.R., Chirico, N., Mansky, L.M., Belshaw, R., 2010. Viral mutation rates. J. Virol., 84(19):9733-9747.

[17]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(4):769-773.

[18]Tamura, K., Nei, M., Kumar, S., 2004. Prospects for inferring very large phylogenies by using the Neighbor-Joining method. PNAS, 101(30):11030-11035.

[19]Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., Kumar, S., 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol., 28(10):2731-2739.

[20]Toriyama, S., 1986. Rice stripe virus: prototype of a new group of viruses that replicate in plants and insects. Microbiol. Sci., 3:347-351.

[21]Toriyama, S., Takahashi, M., Sano, Y., Shimizu, T., Ishihama, A., 1994. Nucleotide sequence of RNA1, the largest genomic segment of rice stripe virus, the prototype of the tenuiviruses. J. Gen. Virol., 75(12):3569-3579.

[22]Wang, G., Zhou, Y., Chen, Z., Zhou, X., 2004. Production of monoclonal antibodies to rice stripe virus and application in virus detection. Acta Phytopathol. Sin., 34:302-306 (in Chinese).

[23]Wei, T.Y., Yang, J.G., Liao, F.L., Gao, F.L., Lu, L.M., Zhang, X.T., Li, F., Wu, Z.J., Lin, Q.Y., Xie, L.H., et al., 2009. Genetic diversity and population structure of rice stripe virus in China. J. Gen. Virol., 90(4):1025-1034.

[24]Xiong, R., Wu, J., Zhou, Y., Zhou, X., 2008. Identification of a movement protein of the tenuivirus rice stripe virus. J. Virol., 82(24):12304-12311.

[25]Xiong, R., Wu, J., Zhou, Y., Zhou, X., 2009. Characterization and subcellular localization of an RNA silencing suppressor encoded by rice stripe tenuivirus. Virology, 387(1):29-40.

[26]Zhu, Y., Hayakawa, T., Toriyama, S., Takahashi, M., 1991. Complete nucleotide sequence of RNA3 of rice stripe virus: an ambisense coding strategy. J. Gen. Virol., 72(4):763-767.

[27]Zhu, Y., Hayakawa, T., 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(5):1309-1312.

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