Whole genome characterization of Potato virus Y isolates collected in the western USA and their comparison to isolates from Europe and Canada

Archives of Virology

Volumn 151, Issue 6, 2006, Pages 1055-1074

  Lorenzen, J H ^a   Meacham, T ^a   Berger, P H ^a   Shiel, P J ^a   Crosslin, J M ^b   Hamm, P B ^c   Kopp, H ^a  

^a UNIVERSITY OF IDAHO   (United States)

^b AGRICULTURAL RESEARCH SERVICE   (United States)

^c OREGON STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CAPSID PROTEIN; VIRUS RNA;

ARTICLE; CANADA; CLASSIFICATION; COMPARATIVE STUDY; DNA SEQUENCE; EUROPE; GENETIC RECOMBINATION; GENETICS; ISOLATION AND PURIFICATION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLANT DISEASE; POTYVIRUS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SEQUENCE HOMOLOGY; SEROTYPING; UNITED STATES; VIRUS GENOME;

CANADA; CAPSID PROTEINS; EUROPE; GENOME, VIRAL; MOLECULAR SEQUENCE DATA; PHYLOGENY; PLANT DISEASES; POTYVIRUS; RECOMBINATION, GENETIC; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, VIRAL; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY; SEROTYPING; UNITED STATES;

NICOTIANA TABACUM; POTATO VIRUS Y; POTYVIRUS; SOLANUM TUBEROSUM;

EID: 33744498350     PISSN: 03048608     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00705-005-0707-6     Document Type: Article

References (54)

1. PH Berge PJ Shiel 1998 Potyvirus isolation and RNA extraction GD Foster SC Taylor Plant virology protocols Humana Press Inc. Totowa, NJ, USA 151 160
2. B Blanco-Urgoiti F Sanchez J Dopazo F Ponz 1996 A strain-type clustering of potato virus Y based on the genetic distance between isolates calculated by RFLP analysis of the amplified CP gene Arch Virol 141 2425 2442
3. B Blanco-Urgoiti F Sanchez C Perez de San Roman J Dopazo F Ponz 1998a Potato virus Y group C isolates are a homogenous pathotype but two different genetic strains J Gen Virol 79 2037 2042
4. B Blanco-Urgoiti M Tribodet S Leclere F Ponz C Perez de San Roman FJ Legorburu C Kerlan 1998b Characterisation of Potato virus Y (PVY) isolates from seed potato batches. Situation of the NTN, Wilga and Z isolates Eur J Plant Pathol 104 811 819
5. N Boonham K Walsh M Hims S Preston J North I Barker 2002a Biological and sequence comparison of Potato virus Y isolates associated with potato tuber necrotic ringspot disease Plant Pathol 51 117 126
6. C strains using RT-PCR J Virol Methods 102 103 112
7. AA Brunt 2001 Potyviruses G Loebenstein PH Berger AA Brunt RH Lawson Virus and virus-like diseases of potatoes and production of seed-potatoes Kluwer Academic Publishers Dordrecht 77 86
8. N Cerovska T Moravec M Filigarova K Petrzik 2001 Nucleotide sequences of 5′-terminal parts of coat protein genes of various isolates of NTN strain of Potato virus Y Acta Virol 45 55 59
9. AM Chachulska M Chrzanowska C Robaglia W Zagorski 1997 Tobacco veinal necrosis determinants are unlikely to be located within the 5′- and 3′-terminal sequences of the potato virus Y genome Archiv Virol 142 765 779
10. N) found recently in Poland Potato Res 34 179 182
11. N) potyvirus on potatoes in the northwestern United States Plant Dis 86 1177
12. N) from potatoes grown in the western United States Amer J Potato Res 82 263 269
13. De Bokx JA, Huttinga H (1981) Potato Virus Y. Descriptions of plant viruses, No. 242. Commonw Mycol Inst/Assoc Appl Biol, Kew, England
14. P Ellis R Stace-Smith G Gowler DJ [tmp] MacKenzie 1996 Production of monoclonal antibodies for detection and identification of strains of Potato virus Y Can J Plant Pathol 18 64 70
15. P Ellis R Stace-Smith G de Villiers 1997 Identification and geographic distribution of serotypes of Potato virus Y Plant Dis 81 481 484
16. A Fanigliulo S Comes R Pacella B Harrach DP Martin A Crescenzi 2005 Characterization of Potato virus Y nnp strain inducing veinal necrosis in pepper: a naturally occurring recombinant strain of PVY Arch Virol 150 709 720
17. GD Franc 2001 Seed certification as a virus management tool G Loebenstein PH Berger AA Brunt RH Lawson Virus and virus-like diseases of potatoes and production of seed-potatoes Kluwer Academic Publishers Dordrecht 407 420
18. MJ Gibbs JS Armstrong AJ Gibbs 2000 Sister-scanning: a Monte Carlo procedure for assessing signals in recombinant sequences Bioinformatics 16 573 582
19. L Glais M Tribodet JP Gauthier S Astier-Manifacier C Robaglia C Kerlan 1998 RFLP mapping of the whole genome of ten viral isolates representative of different biological groups of potato virus Y Arch Virol 143 2077 2091
20. N isolates Arch Virol 147 363 378
21. D Gordon C Abajian P Green 1998 Consed: a graphical tool for sequence finishing Genome Res 8 195 202
22. DC Hane PB Hamm 1999 Effects of seedborne Potato virus Y infection in two potato cultivars expressing mild disease symptoms Plant Dis 83 43 45
23. AK Inoue-Nagata MEN Fonseca TOTA Lobo AC de Avila DC Monte 2001 Analysis of the nucleotide sequence of the coat protein and 3′-untranslated region of two Brazilian Potato virus Y isolates Fitopatol Bras 26 45 52
24. G Jakab E Droz G Brigneti D Baulcombe P Malnoe 1997 Infectious in vivo and in vitro transcripts from a full-length cDNA clone of PVY-N605, a Swiss necrotic isolate of potato virus Y J Gen Virol 78 3141 3145
25. R Jordan J Hammond 1991 Comparison and differentiation of potyvirus isolates and identification of strain-, virus-, subgroup-specific and potyvirus group-common epitopes using monoclonal antibodies J Gen Virol 72 25 36
26. Kalendar R (2004) FastPCR, PCR primer design, DNA and protein tools, repeats and own database searches program. www.biocenter.helsinki.fi/bi/bare- 1_html/fastpcr.htm
27. C Kerlan M Tribodet L Glais M Guillet 1999 Variability of potato virus Y in potato crops in France J Phytopathol 147 643 651
28. M Le Romancer C Kerlan M Nedellec 1994 Biological characterization of various geographical isolates of potato virus Y inducing superficial necrosis on potato tubers Plant Pathol 43 138 144
29. D Martin E Rybicki 2000 RDP: detection of recombination amongst aligned sequences Bioinformatics 16 562 563
30. DP Martin D Posada C Williamson 2005 RDP2: Recombination detection and analysis from sequence alignments Bioinformatics 21 260 262
31. N in North America Plant Dis 77 87 89
32. O strain groups Am Potato J 7 309 315
33. NTN Am Potato J 73 317 323
34. B Moury C Morel E Johansen M Jacquemond 2002 Evidence for diversifying selection in Potato virus Y and in the coat protein of other potyviruses J Gen Virol 83 2563 2573
35. X Nie RP Singh 2002 A new approach for the simultaneous differentiation of biological and geographical strains of Potato virus Y by uniplex and multiplex RT-PCR J Virol Methods 104 41 54
36. NTN strain Tu 660 by mutation rather than recombination Virus Genes 26 39 47
37. NTN isolates by multiplex RT-PCR J Virol Methods 113 69 77
38. X Nie RP Singh M Singh 2004 Molecular and pathological characterization of N:O isolates of the Potato virus Y from Manitoba, Canada Can J Plant Pathol 26 573 583
39. LM Piche RP Singh X Nie NC Gudmestad 2004 Diversity among PVY field isolates obtained from potatoes grown in the United States Phytopathology 94 1368 1375
40. F Revers O Le Gall T Candresse M Le Romancer J Dunez 1996 Frequent occurrence of recombinant potyvirus isolates J Gen Virol 77 1953 1965
41. JL Riechmann S Lán JA Garáa 1992 Highlights and prospects of potyvirus molecular biology J Gen Virol 73 1 16
42. DG Rose AL Hubbard 1986 Production of monoclonal antibodies for the detection of potato virus Y Ann Appl Biol 109 317 321
43. NTN by unique single-restriction cleavage of PCR products Potato Res 42 215 221
44. K Silberschmidt 1960 Types of Potato virus Y necrotic to tobacco: history and recent observation Am Potato J 37 151 159
45. L Simon-Buela HS Guo JA Garáa 1997 Long sequences in the 5′ noncoding region of Plum Pox Virus are not necessary for viral infectivity but contribute to viral competitiveness and pathogenesis Virology 233 157 162
46. RP Singh J Kurz G Boiteau 1996 Detection of stylet-borne and circulative potato viruses in aphids by duplex reverse transcription polymerase chain reaction J Virol Methods 59 189 196
47. RP Singh DL [tmp] McLaren X Nie M Singh 2003 Possible escape of a recombinant isolate of Potato virus Y by seriological indexing and methods of its detection Plant Dis 87 679 685
48. O) Can J Plant Pathol 18 209 214
49. C Spetz AM Taboada S Darwich J Ramsell LF Salazar JP Valkonen 2003 Molecular resolution of a complex of potyviruses infecting solanaceous crops at the centre of origin in Peru J Gen Virol 84 2565 2578
50. V Thole T Dalmay J Burgyan E Balazs 1993 Cloning and sequencing of potato virus Y (Hungarian isolate) genomic RNA Gene 123 149 156
51. JD Thompson TJ Gibson F Plewniak F Jeanmougin DG Higgins 1997 The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools Nucleic Acids Res 24 4876 4882
52. N isolates in infected Nicotiana tabacum cv. Xanthi J Gen Virol 86 2101 2105
53. JFJM van den Heuvel RAA van der Vlugt M Verbeek PT de Haan H Huttinga 1994 Characteristics of a resistance-breaking isolate of Potato virus Y causing potato tuber necrotic ringspot disease Eur J Plant Pathol 100 347 356
54. K Walsh J North I Barker N Boonham 2001 Detection of different strains of Potato virus Y and their mixed infections using competive fluorescent RT-PCR J Virol Methods 91 167 173