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Profile of siRNAs derived from green fluorescent protein (GFP)-tagged Papaya leaf distortion mosaic virus in infected papaya plants

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Abstract

We used green fluorescent protein (GFP)-tagged Papaya leaf distortion mosaic virus (PLDMV-GFP) to track PLDMV infection by fluorescence. The virus-derived small interfering RNAs (vsiRNAs) of PLDMV-GFP were characterized from papaya plants by next-generation sequencing. The foreign GFP gene inserted into the PLDMV genome was also processed as a viral gene into siRNAs by components involved in RNA silencing. The siRNAs derived from PLDMV-GFP accumulated preferentially as 21- and 22-nucleotide (nt) lengths, and most of the 5′-terminal ends were biased towards uridine (U) and adenosine (A). The single-nucleotide resolution map revealed that vsiRNAs were heterogeneously distributed throughout the PLDMV-GFP genome, and vsiRNAs derived from the sense strand were more abundant than those from the antisense strand. The hotspots were mainly distributed in the P1 and GFP coding region of the antisense strand. In addition, 979 papaya genes targeted by the most abundant 1000 PLDMV-GFP vsiRNAs were predicted and annotated using GO and KEGG classification. Results suggest that vsiRNAs play key roles in PLDMV–papaya interactions. These data on the characterization of PLDMV-GFP vsiRNAs will help to provide insight into the function of vsiRNAs and their host target regulation patterns.

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Acknowledgements

This work was supported by Innovative Research Team of the Natural Science Foundation of Hainan Province, China (Grant No. 2018CXTD343) and the National Nonprofit Institute Research Grant (1630052016005).

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Authors and Affiliations

  1. Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China

    Guangyuan Zhao, Peng Zhou & Wentao Shen

  2. 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, China

    Guangyuan Zhao, Decai Tuo, Pu Yan, Xiaoying Li, Peng Zhou & Wentao Shen

Authors
  1. Guangyuan Zhao
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  2. Decai Tuo
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  3. Pu Yan
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  4. Xiaoying Li
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  5. Peng Zhou
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  6. Wentao Shen
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Contributions

Conceived and designed the experiments: GZ, WS, and PZ; performed the experiments: GZ, WS, PY, and DT; analyzed the data: GZ, WS, and PY; contributed reagents/materials/analysis tools: PY, GZ, and XL; wrote the paper: WS, GZ, and PZ.

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Correspondence to Peng Zhou or Wentao Shen.

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The authors declare that they have no conflicts of interest.

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This research had no human or animal subjects.

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Edited by Karel Petrzik.

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Zhao, G., Tuo, D., Yan, P. et al. Profile of siRNAs derived from green fluorescent protein (GFP)-tagged Papaya leaf distortion mosaic virus in infected papaya plants. Virus Genes 54, 833–839 (2018). https://doi.org/10.1007/s11262-018-1601-0

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  • DOI: https://doi.org/10.1007/s11262-018-1601-0

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