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Diagnosis of Plant Viruses Using Next-Generation Sequencing and Metagenomic Analysis

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Current Research Topics in Plant Virology

Abstract

Next generation sequencing (NGS) is revolutionising the diagnosis of plant viral disease. This chapter describes the sequencing platforms (Illumina, 454, Pacific Biosciences, IonTorrent, Nanopore) and techniques used to produce and analyse NGS virus data. At present NGS has been used for plant viral disease diagnosis in a number of exemplar cases but, as yet, it has still to be routinely adopted for frontline diagnostic applications. The barriers to this uptake including access, cost, analysis, validation and interpretation are discussed.

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References

  • 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

    Article  CAS  PubMed  Google Scholar 

  • Adams IP, Glover R, Souza-Richards R, Bennett S, Hany U, Boonham N (2013a) Complete genome sequence of arracacha virus B: a novel cheravirus. Arch Virol 158(4):909–913. doi:10.1007/s00705-012-1546-x

    Article  CAS  PubMed  Google Scholar 

  • Adams IP, Miano DW, Kinyua ZM, Wangai A, Kimani E, Phiri N, Reeder R, Harju V, Glover R, Hany U, Souza-Richards R, Deb Nath P, Nixon T, Fox A, Barnes A, Smith J, Skelton A, Thwaites R, Mumford R, Boonham N (2013b) 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

    Article  CAS  Google Scholar 

  • Adams IP, Harju VA, Hodges T, Hany U, Skelton A, Rai S, Deka M, Smith J, Fox A, Uzayisenga B, Ngaboyisonga C, Uwumukiza B, Rutikanga A, Rutherford M, Ricthis B, Phiri N, Boonham N (2014a) First report of maize lethal necrosis disease in Rwanda. New Dis Rep 29(22)

    Google Scholar 

  • Adams IP, Skelton A, Macarthur R, Hodges T, Hinds H, Flint L, Nath PD, Boonham N, Fox A (2014b) Carrot yellow leaf virus is associated with carrot internal necrosis. PLoS One 9(11):e109125. doi:10.1371/journal.pone.0109125

    Article  PubMed  PubMed Central  Google Scholar 

  • Akin A, Wu CC, Lin TL (1998) A comparison of two RNA isolation methods for double-stranded RNA of infectious bursal disease virus. J Virol Methods 74(2):179–184

    Article  CAS  PubMed  Google Scholar 

  • Al Rwahnih M, Daubert S, Golino D, Islas C, Rowhani A (2015) Comparison of next-generation sequencing versus biological indexing for the optimal detection of viral pathogens in Grapevine. Phytopathology 105(6):758–763. doi:10.1094/phyto-06-14-0165-r

    Article  PubMed  Google Scholar 

  • Ames SK, Hysom DA, Gardner SN, Lloyd GS, Gokhale MB, Allen JE (2013) Scalable metagenomic taxonomy classification using a reference genome database. Bioinformatics 29(18):2253–2260. doi:10.1093/bioinformatics/btt389

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • AWS (2015) Amazon web services. http://aws.amazon.com/. Accessed 27 July 2015

  • Barba M, Czosnek H, Hadidi A (2014) Historical perspective, development and applications of next-generation sequencing in plant virology. Viruses 6(1):106–136. doi:10.3390/v6010106

    Article  PubMed  PubMed Central  Google Scholar 

  • Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2010) GenBank. Nucleic Acids Res 39:D32–D37. doi:10.1093/nar/gkq1079

    Article  PubMed  PubMed Central  Google Scholar 

  • Boonham N, Tomlinson J, Mumford R (2007) Microarrays for rapid identification of plant viruses. Annu Rev Phytopathol 45:307–328

    Article  CAS  PubMed  Google Scholar 

  • Boonham N, Kreuze J, Winter S, van der Vlugt R, Bergervoet J, Tomlinson J, Mumford R (2014) Methods in virus diagnostics: From ELISA to next generation sequencing. Virus Research 186 (0):20–31. doi:http://dx.doi.org/10.1016/j.virusres.2013.12.007

  • Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL (2009) BLAST+: architecture and applications. BMC Bioinform 10:421. doi:10.1186/1471-2105-10-421

    Article  Google Scholar 

  • Clark MF, Adams AN (1977) Characteristics of the microplate method of enzyme-linked immunosorbent assay for the detection of plant viruses. J Gen Virol 34(3):475–483. doi:10.1099/0022-1317-34-3-475

    Article  CAS  PubMed  Google Scholar 

  • Cox MP, Peterson DA, Biggs PJ (2010) SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data. BMC Bioinform 11:485. doi:10.1186/1471-2105-11-485

    Article  Google Scholar 

  • Dodds JA, Morris TJ, Jordan RL (1984) Plant viral double-stranded RNA. Annual Rev Phytopathol 22(1):151–168. doi:10.1146/annurev.py.22.090184.001055

    Google Scholar 

  • EPPO (2014) PM 7/98 (2): specific requirements for laboratories preparing accreditation for a plant pest diagnostic activity. EPPO Bull 44(1):30. doi:10.1111/j.1365-2338.2009.02347.x

    Google Scholar 

  • Ewing B, Green P (1998) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8(3):186–194

    Article  CAS  PubMed  Google Scholar 

  • Fox A, Adams IP, Hany U, Hodges T, Forde S, Jackson L, Skelton A, Barton V (2015) The application of Next-Generation Sequencing for screening seeds for viruses and viroids. Seeds Science and Technology 43:531–535

    Google Scholar 

  • Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotech 29(7):644–652. doi:http://www.nature.com/nbt/journal/v29/n7/abs/nbt.1883.html#supplementary-information

  • Hall RJ, Draper JL, Nielsen FGG, Dutilh BE (2015) Beyond research: a primer for considerations on using viral metagenomics in the field and clinic. Front Microbiol 6:8. doi:10.3389/fmicb.2015.00224

    Google Scholar 

  • Hamilton AJ, Baulcombe DC (1999) A species of small antisense RNA in posttranscriptional gene silencing in plants. Science 286(5441):950–952. doi:10.1126/science.286.5441.950

    Article  CAS  PubMed  Google Scholar 

  • Huson DH, Mitra S, Ruscheweyh HJ, Weber N, Schuster SC (2011) Integrative analysis of environmental sequences using MEGAN4. Genome Res 21(9):1552–1560. doi:10.1101/gr.120618.111

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kreuze JF, 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):1–7

    Article  CAS  PubMed  Google Scholar 

  • Kutnjak D, Rupar M, Gutierrez-Aguirre I, Curk T, Kreuze JF, Ravnikar M (2015) Deep sequencing of virus-derived small interfering RNAs and RNA from viral particles shows highly similar mutational landscapes of a plant virus population. J Virol 89(9):4760–4769. doi:10.1128/jvi.03685-14

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Laver T, Harrison J, O’Neill PA, Moore K, Farbos A, Paszkiewicz K, Studholme DJ (2015) Assessing the performance of the Oxford Nanopore Technologies MinION. Biomol Detect Quantif 3:1–8. doi:http://dx.doi.org/10.1016/j.bdq.2015.02.001

    Google Scholar 

  • Magoc T, Salzberg SL (2011) FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27(21):2957–2963. doi:10.1093/bioinformatics/btr507

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mahuku G, Wangai AW, Sadessa K, Teklewold A, Wegary D, Adams I, Smith J, Braidwood L, Feyissa B, Regassa B, Wanjala B, Kimunye JN, Mugambi C, Bottomley E, Bryce S, Ayalneh D, Prasanna BM (2015) First report of Maize chlorotic mottle virus and Maize lethal necrosis on maize in Ethiopia. Plant Dis. doi:10.1094/PDIS-04-15-0373-PDN

    Google Scholar 

  • Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer ML, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg JM (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437(7057):376–380

    CAS  PubMed  PubMed Central  Google Scholar 

  • Mumford RA, Walsh K, Barker I, Boonham N (2000) Detection of potato mop top virus and tobacco rattle virus using a multiplex real-time fluorescent reverse-transcription polymerase chain reaction assay. Phytopathology 90(5):448–453. doi:10.1094/phyto.2000.90.5.448

    Article  CAS  PubMed  Google Scholar 

  • Najoshi (2011) Sickle – a windowed adaptive trimming tool for FASTQ files using quality. https://github.com/najoshi/sickle

  • Richards RS, Adams IP, Kreuze JF, De Souza J, Cuellar W, Dullemans AM, Van Der Vlugt RA, Glover R, Hany U, Dickinson M, Boonham N (2014) The complete genome sequences of two isolates of potato black ringspot virus and their relationship to other isolates and nepoviruses. Arch Virol 159(4):811–815. doi:10.1007/s00705-013-1871-8

    Article  PubMed  Google Scholar 

  • Roossinck MJ, Martin DP, Roumagnac P (2015) Plant virus metagenomics: advances in virus discovery. Phytopathology 105(6):716–727. doi:10.1094/phyto-12-14-0356-rvw

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  PubMed  Google Scholar 

  • Soueidan H, Schmitt LA, Candresse T, Nikolski M (2014) Finding and identifying the viral needle in the metagenomic haystack: trends and challenges. Front Microbiol 5:739. doi:10.3389/fmicb.2014.00739

    PubMed  Google Scholar 

  • Stobbe AH, Daniels J, Espindola AS, Verma R, Melcher U, Ochoa-Corona F, Garzon C, Fletcher J, Schneider W (2013) E-probe Diagnostic Nucleic acid Analysis (EDNA): a theoretical approach for handling of next generation sequencing data for diagnostics. J Microbiol Methods 94(3):356–366. doi:10.1016/j.mimet.2013.07.002

    Article  CAS  PubMed  Google Scholar 

  • Thapa V, Melcher U, Wiley GB, Doust A, Palmer MW, Roewe K, Roe BA, Shen G, Roossinck MJ, Wang YM, Kamath N (2012) Detection of members of the Secoviridae in the Tallgrass Prairie Preserve, Osage County, Oklahoma, USA. Virus Res 167(1):34–42. doi:10.1016/j.virusres.2012.03.016

    Article  CAS  PubMed  Google Scholar 

  • Tomlinson JA, Ostoja-Starzewska S, Adams IP, Miano DW, Abidrabo P, Kinyua Z, Alicai T, Dickinson MJ, Peters D, Boonham N, Smith J (2013) Loop-mediated isothermal amplification for rapid detection of the causal agents of cassava brown streak disease. J Virol Methods 191(2):148–154. doi:10.1016/j.jviromet.2012.07.015

    Article  CAS  PubMed  Google Scholar 

  • van Brunschot SL, Bergervoet JH, Pagendam DE, de Weerdt M, Geering AD, Drenth A, van der Vlugt RA (2014) Development of a multiplexed bead-based suspension array for the detection and discrimination of pospiviroid plant pathogens. PLoS One 9(1):e84743. doi:10.1371/journal.pone.0084743

    Article  PubMed  PubMed Central  Google Scholar 

  • Wang J, Moore NE, Deng Y-M, Eccles DA, Hall RJ (2015) MinION nanopore sequencing of an influenza genome. Front Microbiol 6:766. doi:10.3389/fmicb.2015.00766

    PubMed  PubMed Central  Google Scholar 

  • Wetterstrand KA (2015) DNA sequencing costs: data from the NHGRI Genome Sequencing Program (GSP). http://www.genome.gov/sequencingcosts/. Accessed 27 July 2015

  • Wood DE, Salzberg SL (2014) Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol 15(3):R46. doi:10.1186/gb-2014-15-3-r46

    Article  PubMed  PubMed Central  Google Scholar 

  • Wu Q, Ding SW, Zhang Y, Zhu S (2015) Identification of viruses and Viroids by next-generation sequencing and homology-dependent and homology-independent algorithms. Annu Rev Phytopathol 53:425–444. doi:10.1146/annurev-phyto-080614-120030

    Google Scholar 

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Adams, I., Fox, A. (2016). Diagnosis of Plant Viruses Using Next-Generation Sequencing and Metagenomic Analysis. In: Wang, A., Zhou, X. (eds) Current Research Topics in Plant Virology. Springer, Cham. https://doi.org/10.1007/978-3-319-32919-2_14

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