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Complete genome of Hainan papaya ringspot virus using small RNA deep sequencing

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Abstract

Small RNA deep sequencing allows for virus identification, virus genome assembly, and strain differentiation. In this study, papaya plants with virus-like symptoms collected in Hainan province were used for deep sequencing and small RNA library construction. After in silicon subtraction of the papaya sRNAs, small RNA reads were used to in the viral genome assembly using a reference-guided, iterative assembly approach. A nearly complete genome was assembled for a Hainan isolate of papaya ringspot virus (PRSV-HN-2). The complete PRSV-HN-2 genome (accession no.: KF734962) was obtained after a 15-nucleotide gap was filled by direct sequencing of the amplified genomic region. Direct sequencing of several random genomic regions of the PRSV isolate did not find any sequence discrepancy with the sRNA-assembled genome. The newly sequenced PRSV-HN-2 genome shared a nucleotide identity of 96 and 94 % to that of the PRSV-HN (EF183499) and PRSV-HN-1 (HQ424465) isolates, and together with these two isolates formed a new PRSV clade. These data demonstrate that the small RNA deep sequencing technology provides a viable and rapid mean to assemble complete viral genomes in plants.

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Acknowledgments

The authors thank Professor J. S. Hu, Department of Plant and Environmental Protection Sciences, University of Hawaii, USA, Professor H. P. Li, South China Agricultural University, China and Dr. R. Z. Jia, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences for technical guide. This work was partially funded by National Natural Science Foundation of China (31201486) and Major Science and Technology Program of Hainan Province (ZDZX2013010-3 and ZDZX2013023-1).

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Authors and Affiliations

  1. Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China

    Yuliang Zhang, Naitong Yu, Qixing Huang, Anping Guo & Zhixin Liu

  2. College of Agriculture & Life Sciences, University of Arizona, Tucson, AZ, 85721, USA

    Guohua Yin

  3. BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA

    Xiangfeng Wang & Zhongguo Xiong

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  1. Yuliang Zhang
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  2. Naitong Yu
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  3. Qixing Huang
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  4. Guohua Yin
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  7. Zhongguo Xiong
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Correspondence to Zhixin Liu.

Additional information

Yuliang Zhang and Naitong Yu have contributed equally to this research.

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Zhang, Y., Yu, N., Huang, Q. et al. Complete genome of Hainan papaya ringspot virus using small RNA deep sequencing. Virus Genes 48, 502–508 (2014). https://doi.org/10.1007/s11262-014-1042-3

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  • DOI: https://doi.org/10.1007/s11262-014-1042-3

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