Virus Genes

, Volume 54, Issue 6, pp 833–839 | Cite as

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

  • Guangyuan Zhao
  • Decai Tuo
  • Pu Yan
  • Xiaoying Li
  • Peng ZhouEmail author
  • Wentao ShenEmail author


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.


PLDMV vsiRNA Next-generation sequencing Target gene Carica papaya 



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).

Author 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.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflicts of interest.

Research involving human participants and/or animals

This research had no human or animal subjects.

Supplementary material

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Supplementary material 1 (XLSX 3150 KB)
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Supplementary material 2 (XLS 725 KB)
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Supplementary material 3 (XLS 822 KB)


  1. 1.
    Zhu H, Guo H (2012) The role of virus-derived small interfering RNAs in RNA silencing in plants. Sci China Life Sci 55:119–125CrossRefGoogle Scholar
  2. 2.
    Llave C (2010) Virus-derived small interfering RNAs at the core of plant-virus interactions. Trends Plant Sci 15:701–707CrossRefGoogle Scholar
  3. 3.
    Zhang C, Wu Z, Li Y, Wu J (2015) Biogenesis, function, and applications of virus-derived small RNAs in plants. Front Microbiol 6:1237PubMedPubMedCentralGoogle Scholar
  4. 4.
    Fukudome A, Fukuhara T (2017) Plant dicer-like proteins: double-stranded RNA-cleaving enzymes for small RNA biogenesis. J Plant Res 130:33–44CrossRefGoogle Scholar
  5. 5.
    Qin C, Li B, Fan Y, Zhang X, Yu Z, Ryabov E, Zhao M, Wang H, Shi N, Zhang P, Jackson S, Tör M, Cheng Q, Liu Y, Gallusci P, Hong Y (2017) Roles of Dicer-Like Proteins 2 and 4 in intra- and intercellular antiviral silencing. Plant Physiol 174:1067–1081CrossRefGoogle Scholar
  6. 6.
    Wang XB, Jovel J, Udomporn P, Wang Y, Wu Q, Li WX, Gasciolli V, Vaucheret H, Ding SW (2011) The 21-nucleotide, but not 22-nucleotide, viral secondary small interfering RNAs direct potent antiviral defence by two cooperative argonautes in Arabidopsis thaliana. Plant Cell 23:1625–1638CrossRefGoogle Scholar
  7. 7.
    Carbonell A (2017) Plant argonautes: features, functions, and unknowns. Methods Mol Biol 1640:1–21CrossRefGoogle Scholar
  8. 8.
    Carbonell A, Carrington JC (2015) Antiviral roles of plant ARGONAUTES. Curr Opin Plant Biol 27:111–117CrossRefGoogle Scholar
  9. 9.
    Wang XB, Wu Q, Ito T, Cillo F, Li WX, Chen X, Yu JL, Ding SW (2010) RNAi-mediated viral immunity requires amplification of virus-derived siRNAs in Arabidopsis thaliana. Proc Natl Acad Sci USA 107:484–489CrossRefGoogle Scholar
  10. 10.
    Shimura H, Pantaleo V, Ishihara T, Myojo N, Inaba J, Sueda K, Burgyán J, Masuta C (2011) A viral satellite RNA induces yellow symptoms on tobacco by targeting a gene involved in chlorophyll biosynthesis using the RNA silencing machinery. PLoS Pathog 7:e1002021CrossRefGoogle Scholar
  11. 11.
    Smith NA, Eamens AL, Wang MB (2011) Viral small interfering RNAs target host genes to mediate disease symptoms in plants. PLoS Pathog 7:e1002022CrossRefGoogle Scholar
  12. 12.
    Shi B, Lin L, Wang S, Guo Q, Zhou H, Rong L, Li J, Peng J, Lu Y, Zheng H, Yang Y, Chen Z, Zhao J, Jiang T, Song B, Chen J, Yan F (2016) Identification and regulation of host genes related to Rice stripe virus symptom production. New Phytol 209:1106–1119CrossRefGoogle Scholar
  13. 13.
    Navarro B, Gisel A, .Rodio ME, Delgado S, Flores R, Di Serio F (2012) Small RNAs containing the pathogenic determinant of a chloroplast-replicating viroid guide the degradation of a host mRNA as predicted by RNA silencing. Plant J 70:991–1003CrossRefGoogle Scholar
  14. 14.
    Hadidi A, Flores R, Candresse T, Barba M (2016) Next-generation sequencing and genome editing in plant virology. Front Microbiol 7:1325CrossRefGoogle Scholar
  15. 15.
    Mitter N, Koundal V, Williams S, Pappu H (2013) Differential expression of tomato spotted wilt virus-derived viral small RNAs in infected commercial and experimental host plants. PLoS ONE 8:e76276CrossRefGoogle Scholar
  16. 16.
    Xia Z, Peng J, Li Y, Chen L, Li S, Zhou T, Fan Z (2014) Characterization of small interfering RNAs derived from Sugarcane mosaic virus in infected maize plants by deep sequencing. PLoS ONE 9:e97013CrossRefGoogle Scholar
  17. 17.
    Visser M, Maree HJ, Rees DJ, Burger JT (2014) High-throughput sequencing reveals small RNAs involved in ASGV infection. BMC Genomics 15:568CrossRefGoogle Scholar
  18. 18.
    Yang J, Zheng SL, Zhang HM, Liu XY, Li J, Chen JP (2014) Analysis of small RNAs derived from Chinese wheat mosaic virus. Arch Virol 159:3077–3082CrossRefGoogle Scholar
  19. 19.
    Liu J, Zhang X, Yang Y, Hong N, Wang G, Wang A, Wang L (2016) Characterization of virus-derived small interfering RNAs in apple stem grooving virus-infected in vitro-cultured Pyrus pyrifolia shoot tips in response to high temperature treatment. Virol J 13:166CrossRefGoogle Scholar
  20. 20.
    Li Y, Deng C, Shang Q, Zhao X, Liu X, Zhou Q (2016) Characterization of siRNAs derived from cucumber green mottle mosaic virus in infected cucumber plants. Arch Virol 161:455–458CrossRefGoogle Scholar
  21. 21.
    Ogwok E, Ilyas M, Alicai T, Rey ME, Taylor NJ (2016) Comparative analysis of virus-derived small RNAs within cassava (Manihot esculenta Crantz) infected with cassava brown streak viruses. Virus Res 215:1–11CrossRefGoogle Scholar
  22. 22.
    Wang J, Tang Y, Yang Y, Ma N, Ling X, Kan J, He Z, Zhang B (2016) Cotton leaf curl Multan virus-derived viral small RNAs can target cotton genes to promote viral infection. Front Plant Sci 7:1162PubMedPubMedCentralGoogle Scholar
  23. 23.
    Xu D, Zhou G (2017) Characteristics of siRNAs derived from Southern rice black-streaked dwarf virus in infected rice and their potential role in host gene regulation. Virol J 14:27CrossRefGoogle Scholar
  24. 24.
    Li L, Andika IB, Xu Y, Zhang Y, Xin X, Hu L, Sun Z, Hong G, Chen Y, Yan F, Yang J, Li J, Chen J (2017) Differential characteristics of viral siRNAs between leaves and roots of wheat plants naturally infected with wheat yellow mosaic virus, a soil-borne virus. Front Microbiol 8:1802CrossRefGoogle Scholar
  25. 25.
    Zhou CJ, Zhang XY, Liu SY, Wang Y, Li DW, Yu JL, Han CG (2017) Synergistic infection of BrYV and PEMV 2 increases the accumulations of both BrYV and BrYV-derived siRNAs in Nicotiana benthamiana. Sci Rep 7:45132CrossRefGoogle Scholar
  26. 26.
    Qiu Y, Zhang Y, Hu F, Zhu S (2017) Characterization of siRNAs derived from Cucumber mosaic virus in infected tobacco plants. Arch Virol 162:2077–2082CrossRefGoogle Scholar
  27. 27.
    Lan Y, Li Y, E Z, Sun F, Du L, Xu Q, Zhou T, Zhou Y, Fan Y (2018) Identification of virus-derived siRNAs and their targets in RBSDV-infected rice by deep sequencing. J Basic Microbiol 58:227–237CrossRefGoogle Scholar
  28. 28.
    Tuo D, Shen W, Yan P, Li C, Gao L, Li X, Li H, Zhou P (2013) Complete genome sequence of an isolate of papaya leaf distortion mosaic virus from commercialized PRSV-resistant transgenic papaya in China. Acta Virol 57:452–455CrossRefGoogle Scholar
  29. 29.
    Tuo D, Fu L, Shen W, Li X, Zhou P, Yan P (2017) Generation of stable infectious clones of plant viruses by using Rhizobium radiobacter for both cloning and inoculation. Virology 510:99–103CrossRefGoogle Scholar
  30. 30.
    Tuo D, Yan P, Zhao GY, Li XY, Zhou P, Shen WT (2018) Two agroinfection-compatible fluorescent protein-tagged infectious cDNA clones of papaya leaf distortion mosaic virus facilitate the tracking of virus infection. Acta Virol 62:202–207CrossRefGoogle Scholar
  31. 31.
    Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359CrossRefGoogle Scholar
  32. 32.
    Chen W, Zhang X, Fan Y, Li B, Ryabov E, Shi N, Zhao M, Yu Z, Qin C, Zheng Q, Zhang P, Wang H, Jackson S, Cheng Q, Liu Y, Gallusci P, Hong Y (2018) Genetic network for systemic RNA silencing in plants. Plant Physiol 176:2700–2719CrossRefGoogle Scholar
  33. 33.
    Sharma VK, Kushwaha N, Basu S, Singh AK, Chakraborty S (2015) Identification of siRNA generating hot spots in multiple viral suppressors to generate broad-spectrum antiviral resistance in plants. Physiol Mol Biol Plants 21:9–18CrossRefGoogle Scholar
  34. 34.
    Yan T, Yoo D, Berardini TZ, Mueller LA, Weems DC, Weng S, Cherry JM, Rhee SY (2005) PatMatch: a program for finding patterns in peptide and nucleotide sequences. Nucleic Acids Res 33(Web Server issue):W262–W266CrossRefGoogle Scholar
  35. 35.
    The Gene Ontology Consortium (2017) Expansion of the gene ontology knowledgebase and resources. Nucleic Acids Res 45:D331–D338CrossRefGoogle Scholar
  36. 36.
    Kanehisa M, Goto S, Kawashima S, Nakaya A (2002) The KEGG databases at GenomeNet. Nucleic Acids Res 30:42–46CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Institute of Tropical Agriculture and ForestryHainan UniversityHaikouChina
  2. 2.Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture & Institute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesHaikouChina

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