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siRNA Deep Sequencing and Assembly: Piecing Together Viral Infections

Chapter
Part of the Plant Pathology in the 21st Century book series (ICPP, volume 5)

Abstract

RNA silencing constitutes a fundamental antiviral defense mechanism in plants in which host enzymes cut viral RNA into pieces of 20–24 nt. When isolated, sequenced en-mass and properly assembled or aligned these virus-derived small RNA (sRNA) sequences can reconstitute genomic sequence information of the viruses being targeted in the plant. This approach is independent of the ability to culture or purify the virus and does not require any specific amplification or enrichment of viral nucleic acids as it automatically enriches for small RNAs of viral origin by tapping into a natural antiviral defense mechanism. Using this technique known and novel DNA and RNA viruses as well as viroids have been identified at sensitivity levels comparable to PCR. This chapter will examine the strength and caveats of small RNA sequencing and assembly (sRSA), utilizing examples from literature as well as our own unpublished experiences and analysis of publically available plant sRNA sequence datasets.

Keywords

Diagnostics Small-RNA Sequencing Assembly Virus Viroid Detection Plants 

Notes

Acknowledgments

I acknowledge the contributions from the various present and previous members of my lab and colleagues at CIP, and Emanuele De Paoli and Manfred Ruddat for sharing information about the samples from their small RNA libraries. Sincere thanks also to Zhangjun Fei for critical reading and useful comments of this chapter. The work on sRSA in our lab has been funded by grants from the Howard Buffet Foundation (subgrant 20127-C), Bill and Melinda Gates Foundation through the SASHA project (Grant OPP53344), the National Science Foundation through its BREAD program (Award No. 1110080), ICGEB-TWAS-UNESCO/IBSP Joint Programme on Capacity Building in Basic Molecular Biology (Contract No.: CRP/101005) and EU FP7 through the QBOL project (Grant No. 226482).

References

  1. Adams IP, Glover RH, Monger WA, Mumford R, Jackeviciene E, Navalinskiene M, Samuitiene M, Boonham N (2009) Next-generation sequencing and metagenomic analysis: a universal diagnostic tool in plant virology. Mol Plant Pathol 10(4):537–545. doi: 10.1111/j.1364-3703.2009.00545.x PubMedCrossRefGoogle Scholar
  2. Adams IP, Miano DW, Kinyua ZM, Wangai A, Kimani E, Phiri N, Reeder R, Harju V, Glover R, Hany U, Souza-Richards R, Nath PD, Nixon T, Fox A, Barnes A, Smith J, Skelton A, Thwaites R, Mumford R, Boonham N (2013) Use of next-generation sequencing for the identification and characterization of maize chlorotic mottle virus and sugarcane mosaic virus causing maize lethal necrosis in Kenya. Plant Pathol 62(4):741–749. doi: 10.1111/j.1365-3059.2012.02690.x CrossRefGoogle Scholar
  3. Al Rwahnih M, Daubert S, Golino D, Rowhani A (2009) Deep sequencing analysis of RNAs from a grapevine showing Syrah decline symptoms reveals a multiple virus infection that includes a novel virus. Virology 387(2):395–401. doi: 10.1016/j.virol.2009.02.028 PubMedCrossRefGoogle Scholar
  4. Al Rwahnih M, Daubert S, Urbez-Torres JR, Cordero F, Rowhani A (2011) Deep sequencing evidence from single grapevine plants reveals a virome dominated by mycoviruses. Arch Virol 156(3):397–403. doi: 10.1007/s00705-010-0869-8 PubMedCrossRefPubMedCentralGoogle Scholar
  5. Bi Y, Tugume AK, Valkonen JP (2012) Small-RNA deep sequencing reveals Arctium tomentosum as a natural host of Alstroemeria virus X and a new putative Emaravirus. PLoS One 7(8):e42758. doi: 10.1371/journal.pone.0042758 PubMedCrossRefPubMedCentralGoogle Scholar
  6. Candresse T, Marais A, Faure C, Gentit P (2013) Association of little cherry virus 1 (LChV1) with the Shirofugen stunt disease and characterization of the genome of a divergent LChV1 isolate. Phytopathology 103(3):293–298. doi: 10.1094/phyto-10-12-0275-r PubMedCrossRefGoogle Scholar
  7. Chen Y-R, Zheng Y, Liu B, Zhong S, Giovannoni J, Fei Z (2012) A cost-effective method for Illumina small RNA-Seq library preparation using T4 RNA ligase 1 adenylated adapters. Plant Methods 8:4CrossRefGoogle Scholar
  8. Coetzee B, Freeborough MJ, Maree HJ, Celton JM, Rees DJ, Burger JT (2010) Deep sequencing analysis of viruses infecting grapevines: virome of a vineyard. Virology 400(2):157–163. doi: 10.1016/j.virol.2010.01.023 PubMedCrossRefGoogle Scholar
  9. Cuellar WJ, Cruzado RK, Fuentes S, Untiveros M, Soto M, Kreuze JF (2011) Sequence characterization of a Peruvian isolate of sweet potato chlorotic stunt virus: further variability and a model for p22 acquisition. Virus Res 157(1):111–115. doi: 10.1016/j.virusres.2011.01.010 PubMedCrossRefPubMedCentralGoogle Scholar
  10. De Souza J, Fuentes S, Savenkov S, Cuellar W, Kreuze J (2013) The complete nucleotide sequence of sweet potato C6 virus: a carlavirus lacking a cysteine-rich protein. Arch Virol 158(6):1393–1396. doi: 10.1007/s00705-013-1614-x PubMedCrossRefGoogle Scholar
  11. Fuentes S, Heider B, Tasso RC, Romero E, Zum Felde T, Kreuze JF (2012) Complete genome sequence of a potyvirus infecting yam beans (Pachyrhizus spp.) in Peru. Arch Virol 157(4):773–776. doi: 10.1007/s00705-011-1214-6 PubMedCrossRefGoogle Scholar
  12. Geering AD, Olszewski NE, Harper G, Lockhart BE, Hull R, Thomas JE (2005) Banana contains a diverse array of endogenous badnaviruses. J Gen Virol 86(Pt 2):511–520. doi: 10.1099/vir.0.80261-0 PubMedCrossRefGoogle Scholar
  13. Gregor W, Mette MF, Staginnus C, Matzke MA, Matzke AJM (2004) A distinct endogenous pararetrovirus family in Nicotiana tomentosiformis, a diploid progenitor of polyploid tobacco. Plant Physiol 134(3):1191–1199. doi: 10.1104/pp. 103.031112 PubMedCrossRefPubMedCentralGoogle Scholar
  14. Haasnoot J, Westerhout EM, Berkhout B (2007) RNA interference against viruses: strike and counterstrike. Nat Biotechnol 12:1435–1443CrossRefGoogle Scholar
  15. Hagen C, Frizzi A, Gabriels S, Huang M, Salati R, Gabor B, Huang S (2012) Accurate and sensitive diagnosis of geminiviruses through enrichment, high-throughput sequencing and automated sequence identification. Arch Virol 157(5):907–915. doi: 10.1007/s00705-012-1253-7 PubMedCrossRefGoogle Scholar
  16. Hansen CN, Harper G, Heslop-Harrison JS (2005) Characterisation of pararetrovirus-like sequences in the genome of potato (Solanum tuberosum). Cytogenet Genome Res 110(1–4):559–565. doi: 10.1159/000084989 PubMedCrossRefGoogle Scholar
  17. Huang Y, Mi ZQ, Zhuang L, Ma MJ, An XP, Liu W, Cao WC, Tong YG (2013) Presence of entomobirnaviruses in Chinese mosquitoes in the absence of Dengue virus co-infection. J Gen Virol 94:663–667. doi: 10.1099/vir.0.048231-0 PubMedCrossRefGoogle Scholar
  18. Hwang YT, Kalischuk M, Fusaro AF, Waterhouse PM, Kawchuk L (2013) Small RNA sequencing of potato leafroll virus-infected plants reveals an additional subgenomic RNA encoding a sequence-specific RNA-binding protein. Virology 438(2):61–69. doi: 10.1016/j.virol.2012.12.012 PubMedCrossRefGoogle Scholar
  19. Isakov O, Modai S, Shomron N (2011) Pathogen detection using short-RNA deep sequencing subtraction and assembly. Bioinformatics 27(15):2027–2030. doi: 10.1093/bioinformatics/btr349 PubMedCrossRefPubMedCentralGoogle Scholar
  20. Jakowitsch J, Mette MF, van der Winden J, Matzke MA, Matzke AJM (1999) Integrated pararetroviral sequences define a unique class of dispersed repetitive DNA in plants. Proc Natl Acad Sci U S A 96(23):13241–13246. doi: 10.1073/pnas.96.23.13241 PubMedCrossRefPubMedCentralGoogle Scholar
  21. Kashif M, Pietilä S, Artola K, Jones RAC, Tugume AK, Mäkinen V, Valkonen JPT (2012) Detection of viruses in sweetpotato from Honduras and Guatemala augmented by deep-sequencing of small-RNAs. Plant Dis 96(10):1430–1437. doi: 10.1094/pdis-03-12-0268-re CrossRefGoogle Scholar
  22. Kircher M, Sawyer S, Meyer M (2012) Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform. Nucleic Acids Res 40(1):e3. doi: 10.1093/nar/gkr771 PubMedCrossRefPubMedCentralGoogle Scholar
  23. Kreuze JF, Pérez 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):1–7. doi: 10.1016/j.virol.2009.03.024 PubMedCrossRefGoogle Scholar
  24. Kreuze J, Koenig R, De Souza J, Vetten HJ, Muller G, Flores B, Ziebell H, Cuellar W (2013) The complete genome sequences of a Peruvian and a Colombian isolate of Andean potato latent virus and partial sequences of further isolates suggest the existence of two distinct potato-infecting tymovirus species. Virus Res 173(2):431–435PubMedCrossRefGoogle Scholar
  25. Kunii M, Kanda M, Nagano H, Uyeda I, Kishima Y, Sano Y (2004) Reconstruction of putative DNA virus from endogenous rice tungro bacilliform virus-like sequences in the rice genome: implications for integration and evolution. BMC Genomics 5(10):80. doi: 10.1186/1471-2164-5-80 PubMedCrossRefPubMedCentralGoogle Scholar
  26. Li R, Gao S, Hernandez AG, Wechter WP, Fei Z, Ling KS (2012) Deep sequencing of small RNAs in tomato for virus and viroid identification and strain differentiation. PLoS One 7(5):e37127. doi: 10.1371/journal.pone.0037127 PubMedCrossRefPubMedCentralGoogle Scholar
  27. Linsen SE, de Wit E, Janssens G, Heater S, Chapman L, Parkin RK, Fritz B, Wyman SK, de Bruijn E, Voest EE, Kuersten S, Tewari M, Cuppen E (2009) Limitations and possibilities of small RNA digital gene expression profiling. Nat Methods 6(7):474–476. doi: 10.1038/nmeth0709-474 PubMedCrossRefGoogle Scholar
  28. Lockhart BE, Menke J, Dahal G, Olszewski NE (2000) Characterization and genomic analysis of tobacco vein clearing virus, a plant pararetrovirus that is transmitted vertically and related to sequences integrated in the host genome. J Gen Virol 81:1579–1585PubMedGoogle Scholar
  29. Loconsole G, Onelge N, Potere O, Giampetruzzi A, Bozan O, Satar S, De Stradis A, Savino V, Yokomi RK, Saponari M (2012a) Identification and characterization of citrus yellow vein clearing virus, a putative new member of the genus Mandarivirus. Phytopathology 102(12):1168–1175. doi: 10.1094/PHYTO-06-12-0140-R PubMedCrossRefGoogle Scholar
  30. Loconsole G, Saldarelli P, Doddapaneni H, Savino V, Martelli GP, Saponari M (2012b) Identification of a single-stranded DNA virus associated with citrus chlorotic dwarf disease, a new member in the family Geminiviridae. Virology 432(1):162–172. doi: 10.1016/j.virol.2012.06.005 PubMedCrossRefGoogle Scholar
  31. 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(9):e24758. doi: 10.1371/journal.pone.0024758.t001 PubMedCrossRefPubMedCentralGoogle Scholar
  32. Mlotshwa S, Pruss GJ, Vance V (2008) Small RNAs in viral infection and host defense. Trends Plant Sci 13(7):375–382PubMedCrossRefGoogle Scholar
  33. Ng TFF, Duffy S, Polston JE, Bixby E, Vallad GE, Breitbart M (2011) Exploring the diversity of plant DNA viruses and their satellites using vector-enabled metagenomics on whiteflies. PLoS One 6(4):e19050. doi: 10.1371/journal.pone.0019050 PubMedCrossRefPubMedCentralGoogle Scholar
  34. Richert-Poggeler KR, Noreen F, Schwarzacher T, Harper G, Hohn T (2003) Induction of infectious petunia vein clearing (pararetro) virus from endogenous provirus in petunia. EMBO J 22(18):4836–4845. doi: 10.1093/emboj/cdg443 PubMedCrossRefPubMedCentralGoogle Scholar
  35. Roossinck MJ, Saha P, Wiley GB, Quan J, White JD, Lai H, Chavarría F, Shen G, Roe BA (2010) Ecogenomics: using massively parallel pyrosequencing to understand virus ecology. Mol Ecol 19(1):81–88PubMedCrossRefGoogle Scholar
  36. Roy A, Choudhary N, Guillermo LM, Shao J, Govindarajulu A, Achor D, Wei G, Picton DD, Levy L, Nakhla MK, Hartung JS, Brlansky RH (2013) A novel virus of the genus Cilevirus causing symptoms similar to Citrus leprosis. Phytopathology 103(5):488–500. doi: 10.1094/phyto-07-12-0177-r PubMedCrossRefGoogle Scholar
  37. Sela N, Luria N, Dombrovsky A (2012) Genome assembly of bell pepper endornavirus from small RNA. J Virol 86(14):7721–7721. doi: 10.1128/jvi.00983-12 PubMedCrossRefPubMedCentralGoogle Scholar
  38. Staginnus C, Gregor W, Mette MF, Teo CH, Borroto-Fernandez EG, Machado ML, Matzke M, Schwarzacher T (2007) Endogenous pararetroviral sequences in tomato (Solanum lycopersicum) and related species. BMC Plant Biol 7:24. doi: 10.1186/1471-2229-7-24 PubMedCrossRefPubMedCentralGoogle Scholar
  39. Untiveros M, Quispe D, Kreuze J (2010) Analysis of complete genomic sequences of isolates of the Sweet potato feathery mottle virus strains C and EA: molecular evidence for two distinct potyvirus species and two P1 protein domains. Arch Virol 155(12):2059–2063. doi: 10.1007/s00705-010-0805-y PubMedCrossRefGoogle Scholar
  40. Vodovar N, Goic B, Blanc H, Saleh MC (2011) In silico reconstruction of viral genomes from small RNAs improves virus-derived small interfering RNA profiling. J Virol 85(21):11016–11021. doi: 10.1128/JVI.05647-11 PubMedCrossRefPubMedCentralGoogle Scholar
  41. Wu Q, Luo Y, Lu R, Lau N, Lai EC, 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(4):1606–1611. doi: 10.1073/pnas.0911353107 PubMedCrossRefPubMedCentralGoogle Scholar
  42. Wu Q, Wang Y, Cao M, Pantaleo V, Burgyan J, Li W-X, Ding S-W (2012) Homology-independent discovery of replicating pathogenic circular RNAs by deep sequencing and a new computational algorithm. Proc Natl Acad Sci U S A 109(10):3938–3943. doi: 10.1073/pnas.1117815109 PubMedCrossRefPubMedCentralGoogle Scholar
  43. Wylie SJ, Jones MGK (2011) The complete genome sequence of a Passion fruit woodiness virus isolate from Australia determined using deep sequencing, and its relationship to other potyviruses. Arch Virol 156(3):479–482. doi: 10.1007/s00705-010-0845-3 PubMedCrossRefGoogle Scholar
  44. Wylie SJ, Luo H, Li H, Jones MGK (2012a) Multiple polyadenylated RNA viruses detected in pooled cultivated and wild plant samples. Arch Virol 157(2):271–284. doi: 10.1007/s00705-011-1166-x PubMedCrossRefGoogle Scholar
  45. Wylie SJ, Tan AJY, Li H, Dixon KW, Jones MGK (2012b) Caladenia virus A, an unusual new member of the family Potyviridae from terrestrial orchids in Western Australia. Arch Virol 157(12):2447–2452. doi: 10.1007/s00705-012-1452-2 PubMedCrossRefGoogle Scholar
  46. Wylie SJ, Li H, Dixon KW, Richards H, Jones MGK (2013) Exotic and indigenous viruses infect wild populations and captive collections of temperate terrestrial orchids (Diuris species) in Australia. Virus Res 171(1):22–32. doi: 10.1016/j.virusres.2012.10.003 PubMedCrossRefGoogle Scholar
  47. Zhang Y, Singh K, Kaur R, Qiu W (2011) Association of a novel DNA virus with the grapevine vein-clearing and vine decline syndrome. Phytopathology 101(9):1081–1090. doi: 10.1094/PHYTO-02-11-0034 PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  1. 1.Laboratory of VirologyPeru International Potato Center (CIP)La MolinaPeru

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