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Characterization of siRNAs derived from rice stripe virus in infected rice plants by deep sequencing

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Abstract

RNA interference is a natural defense against viruses in plants. To date, the only viral siRNAs characterized have been those for positive-sense RNA viruses with one or two genome components. Here, we characterized siRNAs derived from rice stripe virus (RSV), a member of the genus Tenuivirus with four genomic RNAs and an ambisense coding strategy. Deep sequencing of small RNAs from infected rice leaves showed that siRNAs were derived almost equally from virion and complementary RNA strands and were mostly 20–22 nucleotides long. Most viral siRNAs were produced within the coding sequences and 5′ termini of the RSV genome. RSV siRNAs had a higher G and lower C content than the viral genome but a strong A/U bias at the first nucleotide and a U bias at the final one, suggesting preferential targeting of such sequences by rice Dicer-like proteins.

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Acknowledgments

This work was financially supported by the State Basic Research Program of China (2010CB126203), an International Science and Technology Cooperation Project of the Ministry of Science and Technology of China (2007DFB30350), the State High-Tech Research and Development Program of China (2007AA10Z414), the National Natural Science Foundation of China (30771402), and the Natural Science Foundation of Zhejiang Province (Z305165, Y307169, Y3080417). Rothamsted Research receives grant-aided support from the Biotechnology and Biological Sciences Research Council of the United Kingdom.

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Authors and Affiliations

  1. Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, People’s Republic of China

    Fei Yan, Hengmu Zhang, Jian Yang, Jiejun Peng & Jianping Chen

  2. Department of Plant Pathology and Microbiology, Rothamsted Research, Harpenden, Herts, AL5 2JQ, UK

    Michael J. Adams & John F. Antoniw

  3. Institution of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, People’s Republic of China

    Yijun Zhou

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  1. Fei Yan
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  2. Hengmu Zhang
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Correspondence to Jianping Chen.

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Yan, F., Zhang, H., Adams, M.J. et al. Characterization of siRNAs derived from rice stripe virus in infected rice plants by deep sequencing. Arch Virol 155, 935–940 (2010). https://doi.org/10.1007/s00705-010-0670-8

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  • DOI: https://doi.org/10.1007/s00705-010-0670-8

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