Skip to main content

Advertisement

SpringerLink
Log in

Accurate and sensitive diagnosis of geminiviruses through enrichment, high-throughput sequencing and automated sequence identification

  • Original Article
  • Published:
Archives of Virology Aims and scope Submit manuscript

Abstract

Existing diagnostic techniques used to identify plant-infecting DNA viruses and their associated molecules are often limited in their specificity and can be challenged by samples containing multiple viruses. We adapted a simple method of amplifying circular viral DNA and, in combination with high-throughput sequencing and bioinformatic analysis, used it as a virus diagnostic method. We validated this diagnostic method with a plant sample infected with a tomato yellow leaf curl geminivirus infectious clone and also compared PCR- and high-throughput-sequencing diagnostics on a geminivirus-infected field sample, showing that both methods gave similar results. Finally, we analyzed infected field samples of pepper from Mexico and tomato from India using this approach, demonstrating that it is both sensitive and capable of simultaneously identifying multiple discrete DNA viruses and subviral DNA elements in densely infected samples.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

  1. Bock KR (1982) Geminivirus diseases of tropical crops. Plant Dis 66(3):266–270

    Article  Google Scholar 

  2. Saunders K, Bedford ID, Yahara T, Stanley J (2003) Aetiology: the earliest recorded plant virus disease. Nature 422(6934):831

    Article  PubMed  CAS  Google Scholar 

  3. Storey HH, Nichols RW (1938) Studies of the mosaic diseases of cassava. Ann Appl Biol 25:790–806

    Article  Google Scholar 

  4. Legg JP, Fauquet CM (2004) Cassava mosaic geminiviruses in africa. Plant Mol Biol 56(4):585–599

    Article  PubMed  CAS  Google Scholar 

  5. Salati R, Nahkla MK, Rojas MR, Guzman P, Jaquez J, Maxwell DP, Gilbertson RL (2002) Tomato yellow leaf curl virus in the dominican republic: characterization of an infectious clone, virus monitoring in whiteflies, and identification of reservoir hosts. Phytopathology 92(5):487–496

    Article  PubMed  Google Scholar 

  6. Ji Y, Schuster DJ, Scott JW (2007) Ty-3, a begomovirus resistance locus near the tomato yellow leaf curl virus resistance locus ty-1 on chromosome 6 of tomato. Mol Breeding 20(3):271–284

    Article  CAS  Google Scholar 

  7. Bian XY, Thomas MR, Rasheed MS, Saeed M, Hanson P, De Barro PJ, Rezaian MA (2007) A recessive allele (tgr-1) conditioning tomato resistance to geminivirus infection is associated with impaired viral movement. Phytopathology 97(8):930–937

    Article  PubMed  CAS  Google Scholar 

  8. Gilbertson RL, Ullman DE, Salati R, Maxwell DE, Grafton-Cardwell EE, Polek M (1998) Insect-transmitted viruses threaten agricuture. Calif Agric 52:23–28

    Article  Google Scholar 

  9. Csizinszky AA, Schuster DJ, Kring JB (1995) Color mulches influence yield and insect pest populations in tomatoes. J Am Soc Hortic Sci 120(5):778–784

    Google Scholar 

  10. Velasco L, Simon B, Janssen D, Cenis JL (2008) Incidences and progression of tomato chlorosis virus disease and tomato yellow leaf curl virus disease in tomato under different greenhouse covers in southeast Spain. Ann Appl Biol 153(3):335–344

    Article  Google Scholar 

  11. Rojas MR, Gilbertson RL, Russell DR, Maxwell DP (1993) Use of degenerate primers in the polymerase chain reaction to detect whitefly-transmitted geminiviruses. Plant Dis 77(4):340–347

    Article  CAS  Google Scholar 

  12. Wyatt SD, Brown JK (1996) Detection of subgroup iii geminivirus isolates in leaf extracts by degenerate primers and polymerase chain reaction. Phytopathology 86(12):1288–1293

    Article  Google Scholar 

  13. Dry IB, Krake LR, Rigden JE, Rezaian MA (1997) A novel subviral agent associated with a geminivirus: the first report of a DNA satellite. Proc Natl Acad Sci USA 94(13):7088–7093

    Article  PubMed  CAS  Google Scholar 

  14. Mansoor S, Briddon RW, Zafar Y, Stanley J (2003) Geminivirus disease complexes: an emerging threat. Trends Plant Sci 8(3):128–134

    Article  PubMed  CAS  Google Scholar 

  15. Maniatis T, Fritsch EF, Sambrook J (1982) Molecular cloning, a laboratory manual, vol 1. Cold Spring Harbor Laboratory, New York

    Google Scholar 

  16. Gilbertson RL, Hidayat SH, Martinez RT, Leong SA, Faria JC, Morales F, Maxwell DP (1991) Differentiation of bean-infecting geminiviruses by nucleic-acid hybridization probes and aspects of bean golden mosaic in Brazil. Plant Dis 75(4):336–342

    Article  CAS  Google Scholar 

  17. Barbara DJ, Clark MF (1982) A simple indirect elisa using f(ab′)2 fragments of immunoglobulin. J Gen Virol 58(Pt 2):315–322

    Article  PubMed  CAS  Google Scholar 

  18. Mowat WP, Dawson S (1987) Detection and identification of plant viruses by elisa using crude sap extracts and unfractionated antisera. J Virol Methods 15:233–247

    Article  PubMed  CAS  Google Scholar 

  19. Brakke MK (1951) Density gradient centrifugation: a new separation technique. J Am Chem Soc 74(4):1847–1848

    Article  Google Scholar 

  20. Tomlinson JA, Shepherd RJ, Walker JC (1958) Purification and serology of cucumber mosaic virus. Nature 182(4649):1616

    Article  PubMed  CAS  Google Scholar 

  21. Adkins S, Hammond J, Gera A, Maroon-Lango CJ, Sobolev I, Harness A, Zeidan M, Spiegel S (2006) Biological and molecular characterization of a novel carmovirus isolated from angelonia. Phytopathology 96(5):460–467

    Article  PubMed  CAS  Google Scholar 

  22. Schubert J, Habekuss A, Kazmaier K, Jeske H (2007) Surveying cereal-infecting geminiviruses in Germany—diagnostics and direct sequencing using rolling circle amplification. Virus Res 127(1):61–70

    Article  PubMed  CAS  Google Scholar 

  23. La Scola B, Desnues C, Pagnier I, Robert C, Barrassi L, Fournous G, Merchat M, Suzan-Monti M, Forterre P, Koonin E, Raoult D (2008) The virophage as a unique parasite of the giant mimivirus. Nature 455(7209):100–104

    Article  PubMed  Google Scholar 

  24. 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

    Article  PubMed  CAS  Google Scholar 

  25. Lovoll M, Wiik-Nielsen J, Grove S, Wiik-Nielsen CR, Kristoffersen AB, Faller R, Poppe T, Jung J, Pedamallu CS, Nederbragt AJ, Meyerson M, Rimstad E, Tengs T (2010) A novel totivirus and piscine reovirus (prv) in Atlantic salmon (Salmo salar) with cardiomyopathy syndrome (cms). Virol J 7:309

    Article  PubMed  Google Scholar 

  26. 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  PubMed  CAS  Google Scholar 

  27. Hagen C, Frizzi A, Kao J, Jia L, Huang M, Zhang Y, Huang S (2011) Using small RNA sequences to diagnose, sequence, and investigate the infectivity characteristics of vegetable-infecting viruses. Arch Virol 156:1209–1216

    Article  PubMed  CAS  Google Scholar 

  28. Wu Q, Luo Y, Lu R, Lau N, Lai EC, Li WX, Ding SW (2010) Virus discovery by deep sequencing and assembly of virus-derived small silencing RNAs. Proc Natl Acad Sci USA 107(4):1606–1611

    Article  PubMed  CAS  Google Scholar 

  29. Dellaporta SL, Wood J, Hicks JB (1983) A plant DNA minipreparation: version ii. Plant Mol Biol Rep 1:19–21

    Article  CAS  Google Scholar 

  30. Hagen C, Rojas MR, Sudarshana MR, Xoconostle-Cazares B, Natwick ET, Turini TA, Gilbertson RL (2008) Biology and molecular characterization of cucurbit leaf crumple virus, an emergent cucurbit-infecting begomovirus in the imperial valley of California. Plant Dis 92(5):781–793

    Article  CAS  Google Scholar 

  31. Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A, Team G (2010) Manipulation of FASTQ data with galaxy. Bioinformatics 26(14):1783–1785

    Article  PubMed  CAS  Google Scholar 

  32. Mueller LA, Tanksley SD, Giovannoni JJ, van Eck J, Stack S, Choi D, Kim BD, Chen M, Cheng Z, Li C, Ling H, Xue Y, Seymour G, Bishop G, Bryan G, Sharma R, Khurana J, Tyagi A, Chattopadhyay D, Singh NK, Stiekema W, Lindhout P, Jesse T, Lankhorst RK, Bouzayen M, Shibata D, Tabata S, Granell A, Botella MA, Giuliano G, Frusciante L, Causse M, Zamir D (2005) The tomato sequencing project, the first cornerstone of the international solanaceae project (sol). Comp Funct Genomics 6(3):153–158

    Article  PubMed  CAS  Google Scholar 

  33. Li H, Durbin R (2010) Fast and accurate long-read alignment with burrows-wheeler transform. Bioinformatics 26(5):589–595

    Article  PubMed  Google Scholar 

  34. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215(3):403–410

    PubMed  CAS  Google Scholar 

  35. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2009) Genbank. Nucleic Acids Res 37(Database issue):D26–D31

    Article  PubMed  CAS  Google Scholar 

  36. Park M, Jo S, Kwon JK, Park J, Ahn JH, Kim S, Lee YH, Yang TJ, Hur CG, Kang BC, Kim BD, Choi D (2010) Comparative analysis of pepper and tomato reveals euchromatin expansion of pepper genome caused by differential accumulation of ty3/gypsy-like elements. BMC Genomics 12:85

    Article  Google Scholar 

  37. Ramaraj T (2010) Development and testing of algorithmic solutions for problems in computational genomics and proteomics. University of Montana, Bozeman

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Monsanto company, Calgene campus, Davis, CA, USA

    Charles Hagen, Alessandra Frizzi & Shihshieh Huang

  2. Monsanto Vegetable Seeds, Wageningen, The Netherlands

    Suzan Gabriels

  3. Monsanto company, Creve Coeur, MO, USA

    Mingya Huang

  4. Monsanto Vegetable Seeds, San Juan Bautista, CA, USA

    Raquel Salati

  5. Monsanto Vegetable Seeds, Woodland, CA, USA

    Brad Gabor

Authors
  1. Charles Hagen
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Alessandra Frizzi
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Suzan Gabriels
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Mingya Huang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Raquel Salati
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Brad Gabor
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Shihshieh Huang
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Charles Hagen.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Hagen, C., Frizzi, A., Gabriels, S. et al. Accurate and sensitive diagnosis of geminiviruses through enrichment, high-throughput sequencing and automated sequence identification. Arch Virol 157, 907–915 (2012). https://doi.org/10.1007/s00705-012-1253-7

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00705-012-1253-7

Keywords

Search

Navigation