Genetic structure and molecular variability of Grapevine fanleaf virus populations

Virus Research

Volumn 152, Issue 1-2, 2010, Pages 30-40

  Oliver, J E ^a   Vigne, E ^b,c   Fuchs, M ^a  

^a New York State Agricultural Experiment Station   (United States)

^b UNIVERSITÉ DE STRASBOURG   (France)

^c UNIVERSITÉ DE STRASBOURG   (France)

Author keywords

Arabis mosaic virus; Genetic structure; Grapevine fanleaf virus; Phylogenetic analysis; Recombination; Selection pressure

Indexed keywords

ARTICLE; CONTROLLED STUDY; GENE SEQUENCE; GENE TARGETING; GENETIC CODE; GENETIC VARIABILITY; GENOTYPE; GRAPEVINE FANLEAF VIRUS; NEPOVIRUS; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; PROMOTER REGION; RHIZOME; RNA SEQUENCE; UNITED STATES; VINEYARD; VIRUS GENOME; VIRUS ISOLATION; CLASSIFICATION; GENETICS; ISOLATION AND PURIFICATION; MOLECULAR GENETICS; PLANT DISEASE; VIROLOGY; VITIS;

ARABIS MOSAIC VIRUS; GRAPEVINE FANLEAF VIRUS; NEPOVIRUS;

VIRUS PROTEIN;

GENETIC VARIATION; MOLECULAR SEQUENCE DATA; NEPOVIRUS; PHYLOGENY; PLANT DISEASES; VIRAL PROTEINS; VITIS;

EID: 77955279752     PISSN: 01681702     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.virusres.2010.05.017     Document Type: Article

References (50)

1. Andret-Link P., Laporte C., Valat L., Ritzenthaler C., Demangeat G., Vigne E., Laval V., Pfeiffer P., Stussi-Garaud C., Fuchs M. Grapevine fanleaf virus: still a major threat to the grapevine industry. J. Plant Pathol. 2004, 86:183-195.
2. Andret-Link P., Schmitt-Keichinger C., Demangeat G., Komar V., Fuchs M. The specific transmission of Grapevine fanleaf virus by its nematode vector Xiphinema index is solely determined by the viral coat protein. Virology 2004, 320:12-22.
3. Bashir N.S., Zarghani S.N., Hejazi M.S. Diversity of Grapevine fanleaf virus isolates from Iran. Virus Res. 2007, 128:144-148.
4. Belin C., Schmitt C., Gaire F., Walter B., Demangeat G., Pinck L. The nine C-terminal residues of the grapevine fanleaf nepovirus movement protein are critical for systemic virus spread. J. Gen. Virol. 1999, 80:1347-1356.
5. Boulila M. Phylogeny and genetic recombination of Grapevine fanleaf virus isolates from naturally infected vineyards in Tunisia. Phytopathol. Mediterr. 2007, 46:285-294.
6. Demangeat G., Voisin R., Minot J.-C., Bosselut N., Fuchs M., Esmenjaud D. Survival of Xiphinema index in vineyard soil and retention of Grapevine fanleaf virus over extended time in the absence of host plants. Phytopathology 2005, 95:1151-1156.
7. Fattouch S., Acheche H., M'hirsi S., Mellouli L., Bejar S., Marrakchi M., Marzouki N. RT-PCR-RFLP for genetic diversity analysis of Tunisian Grapevine fanleaf virus isolates in their natural host plants. J. Virol. Methods 2005, 127:126-132.
8. Galtier N., Gouy M., Gautier C. SEAVIEW and PHYLO_W: two graphic tools for sequence alignment and molecular phylogeny. Comput. Appl. Biosci. 1996, 12:543-548.
9. Garcia-Arenal F., Fraile A., Malpica J.M. Variability and genetic structure of plant virus populations. Ann. Rev. Phytopathol. 2001, 39:157-186.
10. Ghanem-Sabanadzovic N.A., Sabanadzovic S., Digiaro M., Martelli G.P. Complete nucleotide sequence of the RNA-2 of Grapevine deformation and Grapevine anatolian ringspot viruses. Virus Genes 2005, 30:335-340.
11. Gibbs M.J., Armstrong J.S., Gibbs A.J. Sister-scanning: a monte carlo procedure for assessing signals in recombinant sequences. Bioinformatics 2000, 16:573-582.
12. Harris A.R. Resistance of some vitis rootstocks to Xiphinema index. J. Nematol. 1983, 15:405-409.
13. Hewitt W.B., Raski D.J., Goheen A.C. Nematode vector of soil-borne fanleaf virus of grapevines. Phytopathology 1958, 48:586-595.
14. Huynen M.A., Stadler P.F., Fontana W. Smoothness within ruggedness: the role of neutrality in adaptation. Proc. Natl. Acad. Sci. U.S.A. 1996, 93:397-401.
15. Jawhar, J., Minafra, A., La Notte P., Pirolo, C., Saldarelli, P., Boscia, D., Savino, V., Martelli, G.P., 2009. Recombination events in RNA-2 of Grapevine fanleaf virus and Arabis mosaic virus in grapevines affected by yellow mosaic. Le Progrès Agricole et Viticole, hors série, pp. 73-74, Extended abstracts 16th Meeting of ICVG, Dijon, France, August 31-September 4.
16. Komar V., Vigne E., Demangeat G., Lemaire O., Fuchs M. Cross-protection as control strategy against Grapevine fanleaf virus in naturally infected vineyards. Plant Dis. 2008, 92:1689-1694.
17. Koonin E.V. The phylogeny of RNA-dependent RNA polymerases of positive-strand RNA viruses. J. Gen. Virol. 1991, 72:2197-2206.
18. Korber B. HIV signatures and sequence variation analysis. Computational Analysis of HIV Molecular Sequences 2000, 55-72. Kluwer Academic Publishers, Dordrecht, Netherlands. A.G. Rodrigo, G.H. Learn (Eds.).
19. Kunde R.M., Lider L.A., Schmitt R.V. A test of Vitis resistance to Xiphinema index. Am. J. Enol. Vitic. 1968, 19:30-36.
20. Le Gall O., Lanneau M., Candresse T., Dunez J. The nucleotide sequence of the RNA-2 of an isolate of the English serotype of Tomato black ring virus: RNA recombination in the history of nepoviruses. J. Gen. Virol. 1995, 76:1279-1283.
21. Legin R., Bass P., Etienne L., Fuchs M. Selection of mild virus strains of fanleaf degeneration by comparative field performance of infected grapevines. Vitis 1993, 32:103-110.
22. Liebenberg A., Freeborough M.-J., Visser C.J., Bellstedt D.U., Burger J.T. Genetic variability within the coat protein gene of Grapevine fanleaf virus isolates from South Africa and the evaluation of RT-PCR, DAS-ELISA and immunostrips as virus diagnostic assays. Virus Res. 2009, 142:28-35.
23. Loudes A.M., Ritzenthaler C., Pinck M., Serghini M.A., Pinck L. The 119kDa and 124kDa polyproteins of arabis mosaic nepovirus (isolate S) are encoded by two distinct RNA2 species. J. Gen. Virol. 1995, 76:899-906.
24. Lunden S., Meng B., Avery J., Qiu W. Association of Grapevine fanleaf virus, Tomato ringspot virus and Grapevine rupestris stem pitting-associated virus with grapevine vein-clearing complex on var. Chardonnay. Eur. J. Plant Pathol. 2010, 126:135-144.
25. Martelli G.P., Hewitt W.B. Comparative studies on some Italian and Californian virus diseases of grapevine. Phytopathol. Mediterr. 1963, 2:275-284.
26. Martin D.P., Williamson C., Posada D. RDP2: recombination detection and analysis from sequence alignments. Bioinformatics 2005, 21:260-262.
27. McKenry M.V., Kretsch J.O., Anwar S.A. Interactions of selected rootstocks with ectoparasitic nematodes. Am. J. Enol. Vitic. 2001, 52:304-309.
28. Mekuria T.A., Gutha L.R., Martin R.R., Naidu R.A. Genome diversity and intra- and interspecies recombination events in Grapevine fanleaf virus. Phytopathology 2009, 99:1394-1402.
29. Moury B., Desbiez C., Jacquemond M., Lecoq H. Genetic diversity of plant virus populations: toward hypothesis testing in molecular epidemiology. Adv. Virus Res. 2006, 67:49-87.
30. Mushegian A.R. The putative movement domain encoded by nepovirus RNA-2 is conserved in all sequenced nepoviruses. Arch. Virol. 1994, 135:437-441.
31. Naraghi-Arani P., Daubert S., Rowhani A. Quasispecies nature of the genome of Grapevine fanleaf virus. J. Gen. Virol. 2001, 82:1791-1795.
32. Page R.D.M. TreeView: an application to display phylogenetic trees on personal computers. Bioinformatics 1996, 12:357-358.
33. Pinney T. A History of Wine in America: From the Beginnings to Prohibition 1989, University of California Press, Berkeley.
34. Pompe-Novak M., Gutiérrez-Aguirre I., Vojvoda J., Blas M., Tomažič I., Vigne E., Fuchs M., Ravnikar M., Petrovič N. Genetic variability within RNA2 of Grapevine fanleaf virus. Eur. J. Plant Pathol. 2007, 117:307-312.
35. Pourrahim R., Farzadfar S.H., Golnaraghi A.R., Ahoonmanesh A. Partial molecular characterization of some Grapevine fanleaf virus isolates from North-east of Iran. J. Phytopathol. 2007, 155:754-757.
36. Ritzenthaler C., Viry M., Pinck M., Margis R., Fuchs M., Pinck L. Complete nucleotide sequence and genetic organization of grapevine fanleaf nepovirus RNA1. J. Gen. Virol. 1991, 72:2357-2365.
37. Sanchez F., Chay C., Borja M.J., Rowhani A., Romero J., Bruening G., Ponz F. cDNA sequence of the capsid protein gene and 3' untranslated region of a fanleaf isolate of grapevine fanleaf virus. Nucleic Acids Res. 1991, 19:5440.
38. Sanfaçon H., Wellink J., LeGall O., Karasev A., van der Vlugt R., Wetzel T. Secoviridae: a proposed family of plant viruses within the order Picornavirales that combines the families Sequiviridae and Comoviridae, the unassigned genera Cheravirus and Sadwavirus, and the proposed genus Torradovirus. Arch. Virol. 2009, 154:889-907.
39. Serghini M.A., Fuchs M., Pinck M., Reinbolt J., Walter B., Pinck L. RNA2 of grapevine fanleaf virus: sequence analysis and coat protein cistron location. J. Gen. Virol. 1990, 71:1433-1441.
40. Taylor R.H., Hewitt W.B. Properties and serological relationships of Australian and Californian soil-borne viruses of the grapevine and arabis mosaic virus. Aust. J. Agric. Res. 1964, 15:571-585.
41. Van Lent J.W.M., Schmitt-Keichinger C. Viral movement proteins induce tubule formation in plant and insect cells. Cell-Cell Channels 2006, 160-174. Landes Bioscience, Austin, TX. Baluska, D. Volkmann, P.W. Barlow (Eds.).
42. Villate L., Fievet V., Hanse B., Delemarre F., Plantard O., Esmenjaud D., van Helden M. Spatial distribution of the dagger nematode Xiphinema index and its associated Grapevine fanleaf virus in French vineyard. Phytopathology 2008, 98:942-948.
43. Vigne E., Marmonier A., Komar V., Lemaire O., Fuchs M. Genetic structure and variability of virus populations in cross-protected grapevines superinfected by Grapevine fanleaf virus. Virus Res. 2009, 144:154-162.
44. Vigne E., Marmonier A., Fuchs M. Multiple interspecies recombination events within RNA2 of Grapevine fanleaf virus and Arabis mosaic virus. Arch. Virol. 2008, 153:1771-1776.
45. Vigne E., Demangeat G., Komar V., Fuchs M. Characterization of a naturally occurring recombinant isolate of Grapevine fanleaf virus. Arch. Virol. 2005, 150:2241-2255.
46. Vigne E., Bergdoll M., Guyader S., Fuchs M. Population structure and genetic variability within isolates of Grapevine fanleaf virus from a naturally infected vineyard in France: evidence for mixed infection and recombination. J. Gen. Virol. 2004, 85:2435-2445.
47. Wetzel T., Beck A., Wegener U., Krczal G. Complete nucleotide sequence of the RNA1 of a grapevine isolate of Arabis mosaic virus. Arch. Virol. 2004, 149:989-995.
48. Wetzel T., Jardak R., Meunier L., Ghorbel A., Reustle G.M., Krczal G. Simultaneous RT/PCR detection and differentiation of arabis mosaic and grapevine fanleaf nepoviruses in grapevines with a single pair or primers. J. Virol. Methods 2002, 101:63-69.
49. Wetzel T., Meunier L., Jaeger U., Reustle G.M., Krczal G. Complete nucleotide sequences of the RNAS 2 of German isolates of Grapevine fanleaf and Arabis mosaic nepoviruses. Virus Res. 2001, 75:139-145.
50. Wylie S.J., Jones R.A.C. Role of recombination in the evolution of host specialization within Bean yellow mosaic virus. Phytopathology 2009, 99:512-518.