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

Archives of Virology

Volumn 157, Issue 5, 2012, Pages 907-915

  Hagen, Charles ^a   Frizzi, Alessandra ^a   Gabriels, Suzan ^b   Huang, Mingya ^a   Salati, Raquel ^c   Gabor, Brad ^c   Huang, Shihshieh ^a  

^a MONSANTO COMPANY   (United States)

^b Monsanto Vegetable Seeds   (Netherlands)

^c Monsanto Vegetable Seeds   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CLASSIFICATION; DNA SEQUENCE; EVALUATION; GEMINIVIRUS; GENETICS; HIGH THROUGHPUT SCREENING; ISOLATION AND PURIFICATION; METHODOLOGY; MOLECULAR GENETICS; PLANT DISEASE; TOMATO; VIROLOGY;

GEMINIVIRIDAE; HIGH-THROUGHPUT SCREENING ASSAYS; LYCOPERSICON ESCULENTUM; MOLECULAR SEQUENCE DATA; PLANT DISEASES; SEQUENCE ANALYSIS, DNA;

DNA VIRUSES; GEMINIVIRIDAE; LYCOPERSICON ESCULENTUM; TOMATO YELLOW LEAF CURL VIRUS;

EID: 84862787087     PISSN: 03048608     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00705-012-1253-7     Document Type: Article

References (37)

1. Bock KR (1982) Geminivirus diseases of tropical crops. Plant Dis 66(3): 266-270.
2. Saunders K, Bedford ID, Yahara T, Stanley J (2003) Aetiology: the earliest recorded plant virus disease. Nature 422(6934): 831.
3. Storey HH, Nichols RW (1938) Studies of the mosaic diseases of cassava. Ann Appl Biol 25: 790-806.
4. Legg JP, Fauquet CM (2004) Cassava mosaic geminiviruses in africa. Plant Mol Biol 56(4): 585-599.
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.
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.
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.
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.
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.
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.
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.
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.
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.
14. Mansoor S, Briddon RW, Zafar Y, Stanley J (2003) Geminivirus disease complexes: an emerging threat. Trends Plant Sci 8(3): 128-134.
15. Maniatis T, Fritsch EF, Sambrook J (1982) Molecular cloning, a laboratory manual, vol 1. Cold Spring Harbor Laboratory, New York.
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.
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.
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.
19. Brakke MK (1951) Density gradient centrifugation: a new separation technique. J Am Chem Soc 74(4): 1847-1848.
20. Tomlinson JA, Shepherd RJ, Walker JC (1958) Purification and serology of cucumber mosaic virus. Nature 182(4649): 1616.
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.
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.
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.
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.
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.
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.
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.
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.
29. Dellaporta SL, Wood J, Hicks JB (1983) A plant DNA minipreparation: version ii. Plant Mol Biol Rep 1: 19-21.
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.
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.
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.
33. Li H, Durbin R (2010) Fast and accurate long-read alignment with burrows-wheeler transform. Bioinformatics 26(5): 589-595.
34. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215(3): 403-410.
35. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2009) Genbank. Nucleic Acids Res 37(Database issue): D26-D31.
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.
37. Ramaraj T (2010) Development and testing of algorithmic solutions for problems in computational genomics and proteomics. University of Montana, Bozeman.