1932

Abstract

A fast, accurate, and full indexing of viruses and viroids in a sample for the inspection and quarantine services and disease management is desirable but was unrealistic until recently. This article reviews the rapid and exciting recent progress in the use of next-generation sequencing (NGS) technologies for the identification of viruses and viroids in plants. A total of four viroids/viroid-like RNAs and 49 new plant RNA and DNA viruses from 18 known or unassigned virus families have been identified from plants since 2009. A comparison of enrichment strategies reveals that full indexing of RNA and DNA viruses as well as viroids in a plant sample at single-nucleotide resolution is made possible by one NGS run of total small RNAs, followed by data mining with homology-dependent and homology-independent computational algorithms. Major challenges in the application of NGS technologies to pathogen discovery are discussed.

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2015-08-04
2024-04-17
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Literature Cited

  1. Adams IP, Glover RH, Monger WA, Mumford R, Jackeviciene E. 1.  et al. 2009. Next-generation sequencing and metagenomic analysis: a universal diagnostic tool in plant virology. Mol. Plant Pathol. 10:537–45 [Google Scholar]
  2. Adams IP, Miano DW, Kinyua ZM, Wangai A, Kimani E. 2.  et al. 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. 62:741–49 [Google Scholar]
  3. Al Rwahnih M, Daubert S, Golino D, Rowhani A. 3.  2009. Deep sequencing analysis of RNAs from a grapevine showing Syrah decline symptoms reveals a multiple virus infection that includes a novel virus. Virology 387:395–401 [Google Scholar]
  4. Al Rwahnih M, Daubert S, Urbez-Torres JR, Cordero F, Rowhani A. 4.  2011. Deep sequencing evidence from single grapevine plants reveals a virome dominated by mycoviruses. Arch. Virol. 156:397–403 [Google Scholar]
  5. Al Rwahnih M, Dave A, Anderson MM, Rowhani A, Uyemoto JK, Sudarshana MR. 5.  2013. Association of a DNA virus with grapevines affected by red blotch disease in California. Phytopathology 103:1069–76 [Google Scholar]
  6. Al Rwahnih M, Sudarshana MR, Uyemoto JK, Rowhani A. 6.  2012. Complete genome sequence of a novel vitivirus isolated from grapevine. J. Virol. 86:9545 [Google Scholar]
  7. Aliyari R, Wu Q, Li HW, Wang XH, Li F. 7.  et al. 2008. Mechanism of induction and suppression of antiviral immunity directed by virus-derived small RNAs in Drosophila. Cell Host Microbe 4:387–97 [Google Scholar]
  8. Ambros V, Lee RC. 8.  2004. Identification of microRNAs and other tiny noncoding RNAs by cDNA cloning. Methods Mol. Biol. 265:131–58 [Google Scholar]
  9. Barzon L, Lavezzo E, Militello V, Toppo S, Palu G. 9.  2011. Applications of next-generation sequencing technologies to diagnostic virology. Int. J. Mol. Sci. 12:7861–84 [Google Scholar]
  10. Bi YQ, Tugume AK, Valkonen JPT. 10.  2012. Small-RNA deep sequencing reveals Arctium tomentosum as a natural host of Alstroemeria virus X and a new putative Emaravirus. PLOS ONE 7:e427587 [Google Scholar]
  11. Bolduc F, Hoareau C, St-Pierre P, Perreault JP. 11.  2010. In-depth sequencing of the siRNAs associated with peach latent mosaic viroid infection. BMC Mol. Biol. 11:16 [Google Scholar]
  12. Candresse T, Filloux D, Muhire B, Julian C, Galzi S. 12.  et al. 2014. Appearances can be deceptive: revealing a hidden viral infection with deep sequencing in a plant quarantine context. PLOS ONE 9:e102945 [Google Scholar]
  13. Candresse T, Marais A, Faure C, Gentit P. 13.  2013. Association of Little cherry virus 1 (LChV1) with the Shirofugen stunt disease and characterization of the genome of a divergent LChV1 isolate. Phytopathology 103:293–8 [Google Scholar]
  14. Carvajal-Yepes M, Olaya C, Lozano I, Cuervo M, Castano M, Cuellar WJ. 14.  2014. Unraveling complex viral infections in cassava (Manihot esculenta Crantz) from Colombia. Virus Res. 186:76–86 [Google Scholar]
  15. Coetzee B, Freeborough MJ, Maree HJ, Celton JM, Rees DJ, Burger JT. 15.  2010. Deep sequencing analysis of viruses infecting grapevines: virome of a vineyard. Virology 400:157–63 [Google Scholar]
  16. Cox-Foster DL, Conlan S, Holmes EC, Palacios G, Evans JD. 16.  et al. 2007. A metagenomic survey of microbes in honey bee colony collapse disorder. Science 318:283–87 [Google Scholar]
  17. Cuellar WJ, Cruzado RK, Fuentes S, Untiveros M, Soto M, Kreuze JF. 17.  2011. Sequence characterization of a Peruvian isolate of Sweet potato chlorotic stunt virus: further variability and a model for p22 acquisition. Virus Res. 157:111–15 [Google Scholar]
  18. de Andrade RRS, Vaslin MFS. 18.  2014. SearchSmallRNA: a graphical interface tool for the assemblage of viral genomes using small RNA libraries data. Virol. J. 11:45 [Google Scholar]
  19. De Souza J, Fuentes S, Savenkov EI, Cuellar W, Kreuze JF. 19.  2013. The complete nucleotide sequence of sweet potato C6 virus: a carlavirus lacking a cysteine-rich protein. Arch. Virol. 158:1393–96 [Google Scholar]
  20. Delwart EL. 20.  2007. Viral metagenomics. Rev. Med. Virol. 17:115–31 [Google Scholar]
  21. Di Serio F, Gisel A, Navarro B, Delgado S, Martinez de Alba AE. 21.  et al. 2009. Deep sequencing of the small RNAs derived from two symptomatic variants of a chloroplastic viroid: implications for their genesis and for pathogenesis. PLOS ONE 4e7539
  22. Ding S-W, Lu R. 22.  2011. Virus-derived siRNAs and piRNAs in immunity and pathogenesis. Curr. Opin. Virol. 1:533–44 [Google Scholar]
  23. Ding SW. 23.  2010. RNA-based antiviral immunity. Nat. Rev. Immunol. 10:632–44 [Google Scholar]
  24. Ding SW, Lu R. 24.  2011. Virus-derived siRNAs and piRNAs in immunity and pathogenesis. Curr. Opin. Virol. 1:533–44 [Google Scholar]
  25. Ding SW, Wang Y, Cao M, Ramachandran V, Du P, Wu Q. 25.  2012. Development of next-generation technologies for the diagnosis and identification of citrus viruses and viroids. Citrograph Nov./Dec.:32–35 [Google Scholar]
  26. Dodds JA, Morris TJ, Jordan RL. 26.  1984. Plant viral double-stranded RNA. Annu. Rev. Phytopathol. 22:151–68 [Google Scholar]
  27. Dombrovsky A, Glanz E, Lachman O, Sela N, Doron-Faigenboim A, Antignus Y. 27.  2013. The complete genomic sequence of Pepper yellow leaf curl virus (PYLCV) and its implications for our understanding of evolution dynamics in the genus Polerovirus. PLOS ONE 8:e70722 [Google Scholar]
  28. Dombrovsky A, Sapkota R, Lachman O, Antignus Y. 28.  2012. Eggplant mild leaf mottle virus (EMLMV), a new putative member of the genus Ipomovirus that harbors an HC-Pro gene. Virus Genes 44:329–37 [Google Scholar]
  29. Edgar RC. 29.  2010. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26:2460–61 [Google Scholar]
  30. Feng H, Shuda M, Chang Y, Moore PS. 30.  2008. Clonal integration of a polyomavirus in human Merkel cell carcinoma. Science 319:1096–100 [Google Scholar]
  31. Fuentes S, Heider B, Tasso RC, Romero E, Zum Felde T, Kreuze JF. 31.  2012. Complete genome sequence of a potyvirus infecting yam beans (Pachyrhizus spp.) in Peru. Arch. Virol. 157:773–76 [Google Scholar]
  32. Giampetruzzi A, Roumi V, Roberto R, Malossini U, Yoshikawa N. 32.  et al. 2012. A new grapevine virus discovered by deep sequencing of virus- and viroid-derived small RNAs in Cv Pinot gris. Virus Res. 163:262–8 [Google Scholar]
  33. Goodman RM. 33.  1977. Single-stranded DNA genome in a whitefly-transmitted plant virus. Virology 83:171–79 [Google Scholar]
  34. Gu YH, Tao X, Lai XJ, Wang HY, Zhang YZ. 34.  2014. Exploring the polyadenylated RNA virome of sweet potato through high-throughput sequencing. PLOS ONE 9:e98884 [Google Scholar]
  35. Hagen C, Frizzi A, Kao J, Jia L, Huang M. 35.  et al. 2011. Using small RNA sequences to diagnose, sequence, and investigate the infectivity characteristics of vegetable-infecting viruses. Arch. Virol. 156:1209–16 [Google Scholar]
  36. Hany U, Adams IP, Glover R, Bhat AI, Boonham N. 36.  2014. The complete genome sequence of Piper yellow mottle virus (PYMoV). Arch. Virol. 159:385–38 [Google Scholar]
  37. Harrison BD. 37.  1985. Advances in geminivirus research. Annu. Rev. Phytopathol. 23:55–82 [Google Scholar]
  38. Harrison BD, Barker H, Bock KR, Guthrie EJ, Meredith G, Atkinson M. 38.  1977. Plant viruses with circular single-stranded DNA. Nature 270:760–62 [Google Scholar]
  39. He Y, Yang Z, Hong N, Wang G, Ning G, Xu W. 39.  2015. Deep sequencing reveals a novel closterovirus associated with wild rose leaf rosette disease. Mol. Plant Pathol. 16:449–58 [Google Scholar]
  40. Ito T, Suzaki K, Nakano M. 40.  2013. Genetic characterization of novel putative rhabdovirus and dsRNA virus from Japanese persimmon. J. Gen. Virol. 94:1917–21 [Google Scholar]
  41. Ito T, Suzaki K, Nakano M, Sato A. 41.  2013. Characterization of a new apscaviroid from American persimmon. Arch. Virol. 158:2629–31 [Google Scholar]
  42. Jeck WR, Reinhardt JA, Baltrus DA, Hickenbotham MT, Magrini V. 42.  et al. 2007. Extending assembly of short DNA sequences to handle error. Bioinformatics 23:2942–44 [Google Scholar]
  43. Jiang HS, Lei R, Ding SW, Zhu SF. 43.  2014. Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads. BMC Bioinformatics 15:182 [Google Scholar]
  44. Kambara H, Takahashi S. 44.  1993. Multiple-sheathflow capillary array DNA analyser. Nature 361:565–66 [Google Scholar]
  45. Kashif M, Pietila S, Artola K, Jones RAC, Tugume AK. 45.  et al. 2012. Detection of viruses in sweetpotato from Honduras and Guatemala augmented by deep-sequencing of small-RNAs. Plant Dis. 96:1430–37 [Google Scholar]
  46. Kim MS, Whon TW, Bae JW. 46.  2013. Comparative viral metagenomics of environmental samples from Korea. Genomics Inform. 11:121–28 [Google Scholar]
  47. Kircher M, Kelso J. 47.  2010. High-throughput DNA sequencing—concepts and limitations. Bioessays 32:524–36 [Google Scholar]
  48. Kreuze J, Koenig R, De Souza J, Vetten HJ, Muller G. 48.  et al. 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. 173:431–35 [Google Scholar]
  49. Kreuze JF, Perez A, Untiveros M, Quispe D, Fuentes S. 49.  et al. 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 [Google Scholar]
  50. Kutnjak D, Silvestre R, Cuellar W, Perez W, Muller G. 50.  et al. 2014. Complete genome sequences of new divergent potato virus X isolates and discrimination between strains in a mixed infection using small RNAs sequencing approach. Virus Res. 191:45–50 [Google Scholar]
  51. Lee S, Hallam SJ. 51.  2009. Extraction of high molecular weight genomic DNA from soils and sediments. J. Vis. Exp. 33:1569 [Google Scholar]
  52. Li L, Victoria J, Kapoor A, Blinkova O, Wang C. 52.  et al. 2009. A novel picornavirus associated with gastroenteritis. J. Virol. 83:12002–6 [Google Scholar]
  53. Li R, Gao S, Fei Z, Ling KS. 53.  2013. Complete genome sequence of a new tobamovirus naturally infecting tomatoes in Mexico. Genome Announc. 1:e00794–13 [Google Scholar]
  54. Li R, Gao S, Hernandez AG, Wechter WP, Fei Z, Ling KS. 54.  2012. Deep sequencing of small RNAs in tomato for virus and viroid identification and strain differentiation. PLOS ONE 7:e37127 [Google Scholar]
  55. Li Y, Lu JF, Han YH, Fan XX, Ding SW. 55.  2013. RNA interference functions as an antiviral immunity mechanism in mammals. Science 342:231–34 [Google Scholar]
  56. Loconsole G, Onelge N, Potere O, Giampetruzzi A, Bozan O. 56.  et al. 2012. Identification and characterization of Citrus yellow vein clearing virus, a putative new member of the genus Mandarivirus. Phytopathology 102:1168–75 [Google Scholar]
  57. Loconsole G, Saldarelli P, Doddapaneni H, Savino V, Martelli GP, Saponari M. 57.  2012. Identification of a single-stranded DNA virus associated with citrus chlorotic dwarf disease, a new member in the family Geminiviridae. Virology 432:162–72 [Google Scholar]
  58. Maillard PV, Ciaudo C, Marchais A, Li Y, Jay F. 58.  et al. 2013. Antiviral RNA interference in mammalian cells. Science 342:235–38 [Google Scholar]
  59. Mardis ER. 59.  2008. Next-generation DNA sequencing methods. Annu. Rev. Genomics Hum. Genet. 9:387–402 [Google Scholar]
  60. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS. 60.  et al. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376–80 [Google Scholar]
  61. Massart S, Olmos A, Jijakli H, Candresse T. 61.  2014. Current impact and future directions of high throughput sequencing in plant virus diagnostics. Virus Res. 188:90–96 [Google Scholar]
  62. Mbanzibwa DR, Tugume AK, Chiunga E, Mark D, Tairo FD. 62.  2014. Small RNA deep sequencing-based detection and further evidence of DNA viruses infecting sweetpotato plants in Tanzania. Ann. Appl. Biol. 165:329–39 [Google Scholar]
  63. Metzker ML. 63.  2010. Sequencing technologies—the next generation. Nat. Rev. Genet. 11:31–46 [Google Scholar]
  64. Mokili JL, Rohwer F, Dutilh BE. 64.  2012. Metagenomics and future perspectives in virus discovery. Curr. Opin. Virol. 2:63–77 [Google Scholar]
  65. Molina LG, da Fonseca GC, de Morais GL, de Oliveira LFV, de Carvalho JB. 65.  et al. 2012. Metatranscriptomic analysis of small RNAs present in soybean deep sequencing libraries. Genet. Mol. Biol. 35:(Suppl. 1292–303 [Google Scholar]
  66. Monger WA, Adams IP, Glover RH, Barrett B. 66.  2010. The complete genome sequence of Canna yellow streak virus. Arch. Virol. 155:1515–18 [Google Scholar]
  67. Monger WA, Alicai T, Ndunguru J, Kinyua ZM, Potts M. 67.  et al. 2010. The complete genome sequence of the Tanzanian strain of Cassava brown streak virus and comparison with the Ugandan strain sequence. Arch. Virol. 155:429–33 [Google Scholar]
  68. Nakamura S, Yang CS, Sakon N, Ueda M, Tougan T. 68.  et al. 2009. Direct metagenomic detection of viral pathogens in nasal and fecal specimens using an unbiased high-throughput sequencing approach. PLOS ONE 4:e4219 [Google Scholar]
  69. Navarro B, Pantaleo V, Gisel A, Moxon S, Dalmay T. 69.  et al. 2009. Deep sequencing of viroid-derived small RNAs from grapevine provides new insights on the role of RNA silencing in plant-viroid interaction. PLOS ONE 4:e7686 [Google Scholar]
  70. Nicolaisen M. 70.  2011. An oligonucleotide-based microarray for detection of plant RNA viruses. J. Virol. Methods 173:137–43 [Google Scholar]
  71. Palacios G, Druce J, Du L, Tran T, Birch C. 71.  et al. 2008. A new arenavirus in a cluster of fatal transplant-associated diseases. N. Engl. J. Med. 358:991–98 [Google Scholar]
  72. Pallett DW, Ho T, Cooper I, Wang H. 72.  2010. Detection of Cereal yellow dwarf virus using small interfering RNAs and enhanced infection rate with Cocksfoot streak virus in wild cocksfoot grass (Dactylis glomerata). J. Virol. Methods 168:223–27 [Google Scholar]
  73. Pantaleo V, Saldarelli P, Miozzi L, Giampetruzzi A, Gisel A. 73.  et al. 2010. Deep sequencing analysis of viral short RNAs from an infected Pinot Noir grapevine. Virology 408:49–56 [Google Scholar]
  74. Petrosino JF, Highlander S, Luna RA, Gibbs RA, Versalovic J. 74.  2009. Metagenomic pyrosequencing and microbial identification. Clin. Chem. 55:856–66 [Google Scholar]
  75. Poojari S, Alabi OJ, Fofanov VY, Naidu RA. 75.  2013. A leafhopper-transmissible DNA virus with novel evolutionary lineage in the family Geminiviridae implicated in grapevine redleaf disease by next-generation sequencing. PLOS ONE 8:e64194 [Google Scholar]
  76. Quito-Avila DF, Jelkmann W, Tzanetakis IE, Keller K, Martin RR. 76.  2011. Complete sequence and genetic characterization of Raspberry latent virus, a novel member of the family Reoviridae. Virus Res. 155:397–405 [Google Scholar]
  77. Remmert M, Biegert A, Hauser A, Soding J. 77.  2012. HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nat. Methods 9:173–75 [Google Scholar]
  78. Reyes A, Haynes M, Hanson N, Angly FE, Heath AC. 78.  et al. 2010. Viruses in the faecal microbiota of monozygotic twins and their mothers. Nature 466:334–38 [Google Scholar]
  79. Richards RS, Adams IP, Kreuze JF, De Souza J, Cuellar W. 79.  et al. 2014. The complete genome sequences of two isolates of potato black ringspot virus and their relationship to other isolates and nepoviruses. Arch. Virol. 159:811–15 [Google Scholar]
  80. Rodamilans B, Leon DS, Muhlberger L, Candresse T, Neumuller M. 80.  et al. 2014. Transcriptomic analysis of Prunus domestica undergoing hypersensitive response to Plum pox virus infection. PLOS ONE 9:e100477 [Google Scholar]
  81. Rodriguez Pardina PE, Bejerman N, Luque AV, Di Feo L. 81.  2012. Complete nucleotide sequence of an Argentinean isolate of sweet potato virus G. Virus Genes 45:593–95 [Google Scholar]
  82. Romanovskaya A, Sarin LP, Bamford DH, Poranen MM. 82.  2013. High-throughput purification of double-stranded RNA molecules using convective interaction media monolithic anion exchange columns. J. Chromatogr. A 1278:54–60 [Google Scholar]
  83. Roossinck MJ. 83.  2011. The big unknown: plant virus biodiversity. Curr. Opin. Virol. 1:63–67 [Google Scholar]
  84. Roossinck MJ. 84.  2012. Plant virus metagenomics: biodiversity and ecology. Annu. Rev. Genet. 46:359–69 [Google Scholar]
  85. Roossinck MJ, Saha P, Wiley GB, Quan J, White JD. 85.  et al. 2010. Ecogenomics: using massively parallel pyrosequencing to understand virus ecology. Mol. Ecol. 19:Suppl. 181–88 [Google Scholar]
  86. Roy A, Choudhary N, Guillermo LM, Shao J, Govindarajulu A. 86.  et al. 2013. A novel virus of the genus Cilevirus causing symptoms similar to citrus leprosis. Phytopathology 103:488–500 [Google Scholar]
  87. Saqib M, Wylie SJ, Jones MGK. 87.  2014. Serendipitous identification of a new Iflavirus-like virus infecting tomato and its subsequent characterization. Plant Pathol. 64:519–24 [Google Scholar]
  88. Schadt EE, Turner S, Kasarskis A. 88.  2010. A window into third-generation sequencing. Hum. Mol. Genet. 19:R227–40 [Google Scholar]
  89. Schowalter RM, Pastrana DV, Pumphrey KA, Moyer AL, Buck CB. 89.  2010. Merkel cell polyomavirus and two previously unknown polyomaviruses are chronically shed from human skin. Cell Host Microbe 7:509–15 [Google Scholar]
  90. Schulz MH, Zerbino DR, Vingron M, Birney E. 90.  2012. Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics 28:1086–92 [Google Scholar]
  91. Seguin J, Rajeswaran R, Malpica-Lopez N, Martin RR, Kasschau K. 91.  et al. 2014. De novo reconstruction of consensus master genomes of plant RNA and DNA viruses from siRNAs. PLOS ONE 9:e88513 [Google Scholar]
  92. Shendure J, Porreca GJ, Reppas NB, Lin X, McCutcheon JP. 92.  et al. 2005. Accurate multiplex polony sequencing of an evolved bacterial genome. Science 309:1728–32 [Google Scholar]
  93. Sheveleva A, Kudryavtseva A, Speranskaya A, Belenikin M, Melnikova N, Chirkov S. 93.  2013. Complete genome sequence of a novel Plum pox virus strain W isolate determined by 454 pyrosequencing. Virus Genes 47:385–8 [Google Scholar]
  94. van der Meijden E, Janssens RW, Lauber C, Bouwes Bavinck JN, Gorbalenya AE, Feltkamp MC. 94.  2010. Discovery of a new human polyomavirus associated with Trichodysplasia spinulosa in an immunocompromized patient. PLOS Pathog. 6:e1001024 [Google Scholar]
  95. Verbeek M, Dullemans AM, van Raaij HMG, Verhoeven JTJ, van der Vlugt RAA. 95.  2014. Lettuce necrotic leaf curl virus, a new plant virus infecting lettuce and a proposed member of the genus Torradovirus. Arch. Virol. 159:801–5 [Google Scholar]
  96. Victoria JG, Kapoor A, Li L, Blinkova O, Slikas B. 96.  et al. 2009. Metagenomic analyses of viruses in stool samples from children with acute flaccid paralysis. J. Virol. 83:4642–51 [Google Scholar]
  97. Vives MC, Velazquez K, Pina JA, Moreno P, Guerri J, Navarro L. 97.  2013. Identification of a new Enamovirus associated with citrus vein enation disease by deep sequencing of small RNAs. Phytopathology 103:1077–86 [Google Scholar]
  98. Wang YL, Cheng XF, Wu XX, Wang AM, Wu XY. 98.  2014. Characterization of complete genome and small RNA profile of pagoda yellow mosaic associated virus, a novel badnavirus in China. Virus Res. 188:103–8 [Google Scholar]
  99. Widana Gamage S, Persley DM, Higgins CM, Dietzgen RG. 99.  2015. First complete genome sequence of a capsicum chlorosis tospovirus isolate from Australia with an unusually large S RNA intergenic region. Arch. Virol. 160:869–72 [Google Scholar]
  100. Willner D, Furlan M, Schmieder R, Grasis JA, Pride DT. 100.  et al. 2011. Metagenomic detection of phage-encoded platelet-binding factors in the human oral cavity. Proc. Natl. Acad. Sci. USA 108:Suppl. 14547–53 [Google Scholar]
  101. Wu Q, Luo Y, Lu R, Lau N, Lai EC. 101.  et al. 2010. Virus discovery by deep sequencing and assembly of virus-derived small silencing RNAs. Proc. Natl. Acad. Sci. USA 107:1606–11 [Google Scholar]
  102. Wu Q, Wang Y, Cao M, Pantaleo V, Burgyan J. 102.  et al. 2012. Homology-independent discovery of replicating pathogenic circular RNAs by deep sequencing and a new computational algorithm. Proc. Natl. Acad. Sci. USA 109:3938–43 [Google Scholar]
  103. Wylie S, Jones M. 103.  2011. Hardenbergia virus A, a novel member of the family Betaflexiviridae from a wild legume in Southwest Australia. Arch. Virol. 156:1245–50 [Google Scholar]
  104. Wylie SJ, Jones MGK. 104.  2011. Characterisation and quantitation of mutant and wild-type genomes of Hardenbergia mosaic virus isolates co-infecting a wild plant of Hardenbergia comptoniana. Arch. Virol. 156:1251–55 [Google Scholar]
  105. Wylie SJ, Jones MGK. 105.  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. 156:479–82 [Google Scholar]
  106. Wylie SJ, Jones MGK. 106.  2012. Complete genome sequences of seven carlavirus and potyvirus isolates from Narcissus and Hippeastrum plants in Australia, and proposals to clarify their naming. Arch. Virol. 157:1471–80 [Google Scholar]
  107. Wylie SJ, Li H, Dixon KW, Richards H, Jones MGK. 107.  2013. Exotic and indigenous viruses infect wild populations and captive collections of temperate terrestrial orchids (Diuris species) in Australia. Virus Res. 171:22–32 [Google Scholar]
  108. Wylie SJ, Li H, Liu J, Jones MGK. 108.  2014. First report of Narcissus mosaic virus from Australia and from Iris. Australas. Plant Dis. Notes 9:1–2 [Google Scholar]
  109. Wylie SJ, Li H, Jones MGK. 109.  2012. First report of an isolate of Japanese iris necrotic ring virus from Australia. Australas. Plant Dis. Notes 7:107–10 [Google Scholar]
  110. Wylie SJ, Li H, Jones MGK. 110.  2013. Donkey orchid symptomless virus: a viral ‘platypus’ from Australian terrestrial orchids. PLOS ONE 8:e79587 [Google Scholar]
  111. Wylie SJ, Li H, Jones MGK. 111.  2014. Yellow tailflower mild mottle virus: a new tobamovirus described from Anthocercis littorea (Solanaceae) in Western Australia. Arch. Virol. 159:791–95 [Google Scholar]
  112. Wylie SJ, Li H, Saqib M, Jones MGK. 112.  2014. The global trade in fresh produce and the vagility of plant viruses: a case study in garlic. PLOS ONE 9:e105044 [Google Scholar]
  113. Wylie SJ, Tan AJ, Li H, Dixon KW, Jones MGK. 113.  2012. Caladenia virus A, an unusual new member of the family Potyviridae from terrestrial orchids in Western Australia. Arch. Virol. 157:2447–52 [Google Scholar]
  114. Xie G, Yu J, Duan Z. 114.  2013. New strategy for virus discovery: viruses identified in human feces in the last decade. Sci. China Life Sci. 56:688–96 [Google Scholar]
  115. Zablocki O, Pietersen G. 115.  2014. Characterization of a novel citrus tristeza virus genotype within three cross-protecting source GFMS12 sub-isolates in South Africa by means of Illumina sequencing. Arch. Virol. 159:2133–39 [Google Scholar]
  116. Zerbino DR, Birney E. 116.  2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18:821–29 [Google Scholar]
  117. Zhang Y, Singh K, Kaur R, Qiu W. 117.  2011. Association of a novel DNA virus with the grapevine vein-clearing and vine decline syndrome. Phytopathology 101:1081–90 [Google Scholar]
  118. Zhang YL, Yu NT, Huang QX, Yin GH, Guo AP. 118.  et al. 2014. Complete genome of Hainan papaya ringspot virus using small RNA deep sequencing. Virus Genes 48:502–8 [Google Scholar]
  119. Zhang ZX, Qi SS, Tang N, Zhang XX, Chen SS. 119.  et al. 2014. Discovery of replicating circular RNAs by RNA-Seq and computational algorithms. PLOS Pathog. 10:e1004553 [Google Scholar]
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