1887

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Volume 95, Issue 3

Unusual characteristics of dicistrovirus-derived small RNAs in the small brown planthopper, Free

Abstract

In this study, sequences of small RNA (sRNA) libraries derived from the insect vector were assembled into contigs and used as queries for database searches. A large number of contigs were highly homologous to the genome sequence of an insect dicistrovirus, himetobi P virus (HiPV). Interestingly, HiPV-derived sRNAs had a wide size distribution, and were relatively abundant throughout the 18–30 nt size range with only a slight peak at 22 nt. HiPV sRNAs had a strong bias towards the sense strand, whilst the antisense sRNAs were predominantly 21 and 22 nt. HiPV sRNAs do not have the typical features of PIWI-interacting RNAs, but their 3′ ends were preferentially cleaved at UA-rich sequences. Our data suggest that HiPV sRNAs may be derived both from activities of the RNA interference pathway and from cleavage of the viral genome by other host RNases.

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© 2014 SGM
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2014-03-01
2024-04-25
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References

  1. Aregger M., Borah B. K., Seguin J., Rajeswaran R., Gubaeva E. G., Zvereva A. S., Windels D., Vazquez F., Blevins T.other authors 2012; Primary and secondary siRNAs in geminivirus-induced gene silencing. PLoS Pathog 8:e1002941 [View Article][PubMed]
     [Google Scholar]
  2. Bi Y., Tugume A. K., Valkonen J. P. 2012; Small-RNA deep sequencing reveals Arctium tomentosum as a natural host of Alstroemeria virus X and a new putative Emaravirus. PLoS ONE 7:e42758 [View Article][PubMed]
     [Google Scholar]
  3. Crooks G. E., Hon G., Chandonia J. M., Brenner S. E. 2004; WebLogo: a sequence logo generator. Genome Res 14:1188–1190 [View Article][PubMed]
     [Google Scholar]
  4. Ding S. W., Lu R. 2011; Virus-derived siRNAs and piRNAs in immunity and pathogenesis. Curr Opin Virol 1:533–544 [View Article][PubMed]
     [Google Scholar]
  5. Ding S. W., Voinnet O. 2007; Antiviral immunity directed by small RNAs. Cell 130:413–426 [View Article][PubMed]
     [Google Scholar]
  6. Floyd-Smith G., Slattery E., Lengyel P. 1981; Interferon action: RNA cleavage pattern of a (2′-5′)oligoadenylate–dependent endonuclease. Science 212:1030–1032 [View Article][PubMed]
     [Google Scholar]
  7. Guy P. L., Toriyama S., Fuji S. 1992; Occurrence of a picorna-like virus in planthopper species and its transmission in Laodelphax striatellus. . J Invertebr Pathol 59:161–164 [View Article]
     [Google Scholar]
  8. Hogenhout S. A., Ammar E.-D., Whitfield A. E., Redinbaugh M. G. 2008; Insect vector interactions with persistently transmitted viruses. Annu Rev Phytopathol 46:327–359 [View Article][PubMed]
     [Google Scholar]
  9. Kreuze J. F., Perez A., Untiveros M., Quispe D., Fuentes S., Barker I., Simon R. 2009; Complete viral genome sequence and discovery of novel viruses by deep sequencing of small RNAs: a generic method for diagnosis, discovery and sequencing of viruses. Virology 388:1–7 [View Article][PubMed]
     [Google Scholar]
  10. Léger P., Lara E., Jagla B., Sismeiro O., Mansuroglu Z., Coppée J. Y., Bonnefoy E., Bouloy M. 2013; Dicer-2- and Piwi-mediated RNA interference in Rift Valley fever virus-infected mosquito cells. J Virol 87:1631–1648 [View Article][PubMed]
     [Google Scholar]
  11. Li J., Andika I. B., Shen J., Lv Y., Ji Y., Sun L., Chen J. 2013; Characterization of Rice black-streaked dwarf virus- and Rice stripe virus-derived siRNAs in singly and doubly infected insect vector Laodelphax striatellus . PLoS ONE 8:e66007 [View Article][PubMed]
     [Google Scholar]
  12. Liu S., Vijayendran D., Bonning B. C. 2011; Next generation sequencing technologies for insect virus discovery. Viruses 3:1849–1869 [View Article][PubMed]
     [Google Scholar]
  13. Ma M., Huang Y., Gong Z., Zhuang L., Li C., Yang H., Tong Y., Liu W., Cao W. 2011; Discovery of DNA viruses in wild-caught mosquitoes using small RNA high throughput sequencing. PLoS ONE 6:e24758 [View Article][PubMed]
     [Google Scholar]
  14. Morazzani E. M., Wiley M. R., Murreddu M. G., Adelman Z. N., Myles K. M. 2012; Production of virus-derived ping-pong-dependent piRNA-like small RNAs in the mosquito soma. PLoS Pathog 8:e1002470 [View Article][PubMed]
     [Google Scholar]
  15. Nakashima N., Sasaki J., Toriyama S. 1999; Determining the nucleotide sequence and capsid-coding region of Himetobi P virus: a member of a novel group of RNA viruses that infect insects. Arch Virol 144:2051–2058 [View Article][PubMed]
     [Google Scholar]
  16. Nakashima N., Kawahara N., Omura T., Noda H. 2006; Characterization of a novel satellite virus and a strain of Himetobi P virus (Dicistroviridae) from the brown planthopper, Nilaparvata lugens . J Invertebr Pathol 91:53–56 [View Article][PubMed]
     [Google Scholar]
  17. Nandety R. S., Fofanov V. Y., Koshinsky H., Stenger D. C., Falk B. W. 2013; Small RNA populations for two unrelated viruses exhibit different biases in strand polarity and proximity to terminal sequences in the insect host Homalodisca vitripennis . Virology 442:12–19 [View Article][PubMed]
     [Google Scholar]
  18. Player M. R., Torrence P. F. 1998; The 2-5A system: modulation of viral and cellular processes through acceleration of RNA degradation. Pharmacol Ther 78:55–113 [View Article][PubMed]
     [Google Scholar]
  19. Sabin L. R., Hanna S. L., Cherry S. 2010; Innate antiviral immunity in Drosophila . Curr Opin Immunol 22:4–9 [View Article][PubMed]
     [Google Scholar]
  20. Sela N., Luria N., Dombrovsky A. 2012; Genome assembly of bell pepper endornavirus from small RNA. J Virol 86:7721 [View Article][PubMed]
     [Google Scholar]
  21. Shinkai A. 1962; Studies on insect transmission of rice virus diseases in Japan. Bull Natl Inst Agric Sci C 14:1–112
     [Google Scholar]
  22. Singh K., Kaur R., Qiu W. 2012; New virus discovery by deep sequencing of small RNAs. In RNA Abundance Analysis pp. 177–191Edited by Jin H., Gassmann W. New York: Springer; [View Article]
     [Google Scholar]
  23. Siomi M. C., Sato K., Pezic D., Aravin A. A. 2011; PIWI-interacting small RNAs: the vanguard of genome defence. Nat Rev Mol Cell Biol 12:246–258 [View Article][PubMed]
     [Google Scholar]
  24. Siu R. W., Fragkoudis R., Simmonds P., Donald C. L., Chase-Topping M. E., Barry G., Attarzadeh-Yazdi G., Rodriguez-Andres J., Nash A. A.other authors 2011; Antiviral RNA interference responses induced by Semliki Forest virus infection of mosquito cells: characterization, origin, and frequency-dependent functions of virus-derived small interfering RNAs. J Virol 85:2907–2917 [View Article][PubMed]
     [Google Scholar]
  25. Toriyama S. 1986; Rice stripe virus: prototype of a new group of viruses that replicate in plants and insects. Microbiol Sci 3:347–351[PubMed]
     [Google Scholar]
  26. Toriyama S., Guy P. L., Fuji S., Takahashi M. 1992; Characterization of a new picorna-like virus, himetobi P virus, in planthoppers. J Gen Virol 73:1021–1023 [View Article][PubMed]
     [Google Scholar]
  27. Vodovar N., Bronkhorst A. W., van Cleef K. W., Miesen P., Blanc H., van Rij R. P., Saleh M. C. 2012; Arbovirus-derived piRNAs exhibit a ping-pong signature in mosquito cells. PLoS ONE 7:e30861 [View Article][PubMed]
     [Google Scholar]
  28. Wreschner D. H., McCauley J. W., Skehel J. J., Kerr I. M. 1981; Interferon action – sequence specificity of the ppp(A2′p)nA-dependent ribonuclease. Nature 289:414–417 [View Article][PubMed]
     [Google Scholar]
  29. Wu Q., Luo Y., Lu R., Lau N., Lai E. C., Li W. X., Ding S. W. 2010; Virus discovery by deep sequencing and assembly of virus-derived small silencing RNAs. Proc Natl Acad Sci U S A 107:1606–1611 [View Article][PubMed]
     [Google Scholar]
  30. Xu Y., Huang L., Fu S., Wu J., Zhou X. 2012; Population diversity of rice stripe virus-derived siRNAs in three different hosts and RNAi-based antiviral immunity in Laodelphgax striatellus . PLoS ONE 7:e46238 [View Article][PubMed]
     [Google Scholar]
  31. Zerbino D. R., Birney E. 2008; Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821–829 [View Article][PubMed]
     [Google Scholar]
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Unusual characteristics of dicistrovirus-derived small RNAs in the small brown planthopper, Laodelphax striatellus
J. Gen. Virol. 95, 712 (2014); https://doi.org/10.1099/vir.0.059626-0
/content/journal/jgv/10.1099/vir.0.059626-0
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