Association of a novel DNA virus with the grapevine vein-clearing and vine decline syndrome

Phytopathology

Volumn 101, Issue 9, 2011, Pages 1081-1090

  Zhang, Yu ^a   Singh, Kashmir ^a,b   Kaur, Ravneet ^a,c   Qiu, Wenping ^a  

^a MISSOURI STATE UNIVERSITY   (United States)

^b PANJAB UNIVERSITY   (India)

^c Government College   (India)

Author keywords

[No Author keywords available]

Indexed keywords

CIRCULAR DNA; SMALL INTERFERING RNA; VIRUS DNA; VIRUS RNA;

ARTICLE; BADNAVIRUS; CLASSIFICATION; DNA SEQUENCE; DNA VIRUS; GENE LIBRARY; GENETICS; HIGH THROUGHPUT SEQUENCING; HISTOLOGY; ISOLATION AND PURIFICATION; METHODOLOGY; OPEN READING FRAME; PHYLOGENY; PLANT; PLANT DISEASE; PLANT LEAF; PLANT VIRUS; UNITED STATES; VIROLOGY; VIRUS GENOME; VITIS;

BADNAVIRUS; DNA VIRUSES; DNA, CIRCULAR; DNA, VIRAL; GENE LIBRARY; GENOME, VIRAL; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MIDWESTERN UNITED STATES; OPEN READING FRAMES; PHYLOGENY; PLANT DISEASES; PLANT LEAVES; PLANT SHOOTS; PLANT VIRUSES; RNA, SMALL INTERFERING; RNA, VIRAL; SEQUENCE ANALYSIS, DNA; VITIS;

BADNAVIRUS; CAULIMOVIRIDAE; DNA VIRUSES; VITACEAE; VITIS; VITIS VINIFERA;

EID: 80052640945     PISSN: 0031949X     EISSN: None     Source Type: Journal    
DOI: 10.1094/PHYTO-02-11-0034     Document Type: Article

References (27)

1. Adams, I. P., Glover, R. H., Monger, W. A., Mumford, R., Jackeviciene, E., Navalinkiene, M., Samuitiene, M., and Boonham, N. 2009. Nextgeneration sequencing and metagenomic analysis: A universal diagnostic tool in plant virology. Mol. Plant Pathol. 10:537-545.
2. Al Rwahnih, M., Daubert, S., Golino, D., and 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 387:395-401.
3. Bertsch, C., Beuve, M., Dolja, V., Wirth, M., Pelsy, F., Herrbach, E., and Lemaire, O. 2009. Retention of the virus-derived sequences in the nuclear genome of grapevine as a potential pathway to virus resistance. Biol. Direct 4:21.
4. Carra, A., Mica, E., Gambino, G., Pindo, M., Moser, C., Pè, M. E., and Schubert, A. 2009. Cloning and characterization of small non-coding RNAs from grape. Plant J. 59:750-763.
5. Coetzee, B., Freeborough, M.-J., Maree, H. J., Celton, J.-M., Rees, D. J. G., and Burger, J. T. 2010. Deep sequencing analysis of viruses infecting grapevines: virome of a vineyard. Virology 400:157-163.
6. Ding, S.-W., and Voinnet, O. 2007. Antiviral immunity directed by small RNAs. Cell 130:413-426. (Pubitemid 47198311)
7. Donaire, L., Wany, Y., Gonzalez-Ibeas, D., Mayer, K. F., Aranda, M. A., and Llave, C. 2009. Deep sequencing of plant viral small RNAs reveals effective and widespread targeting of viral genomes. Virology 392:203-214.
8. Fung, R. W. M., Gonzalo, M., Fekete, C., Kovacs, L. G., He, Y., Marsh, E., McIntyre, L. M., Schachtman, D. P., and Qiu, W. P. 2008. Powdery mildew induces defense-oriented reprogramming of the transcriptome in a susceptible but not in a resistant grapevine. Plant Physiol. 146:236-249. (Pubitemid 351380052)
9. Harper, G., Hart, D., Moult, S., and Hull, R. 2004. Banana streak virus is very diverse in Uganda. Virus Res. 100:51-56. (Pubitemid 38230816)
10. Hull, R., Geering, A., Harper, G., Lockhart, B. E., and Schoelz, J. E. 2005. Genus Badnavirus. Pages 392-396 in: Virus Taxonomy: 8th Report of the International Committee for Taxonomy of Viruses. C. M. Fauquet, M. A. Mayo, J. Maniloff, U. Desselberger, and L. A. Ball, eds. Elsevier Academic Press, San Diego, CA.
11. Jones, R. A. C. 2009. Plant virus emergence and evolution: origins, new encounter scenarios, factors driving emergence, effects of changing world conditions, and prospects for control. Virus Res. 141:113-130.
12. Kasschau, K. D., Fahlgren, N., Chapman, E. J., Sullivan, C. M., Cumbie, J. S., Givan, S. A., and Carrington, J. C. 2007. Genome-wide profiling and analysis of Arabidopsis siRNAs. PLoS Biol. 5:e57.
13. Komar, V., Vigne, E., Demangeat, G., Cornuet, P., and Fuchs, M. 2006. Effect of virus combinations on the performance of Vitis vinifera var. Chardonnay. Pages 134-135 in: Extended Abstr. XIV Meet. Int. Counc. Study of Viruses and Virus-like Disease of the Grapevine, Stellenbosch, South Africa.
14. Kreuze, J. F., Perez, A., Untiveros, M., Quispe, D., Fuentes, S., Barker, I., and Simon, R. 2009. Complete viral genome sequence and discovery of novel viruses by deep sequencing of small RNAs: a generic method diagnosis, discovery and sequencing of viruses. Virology 388:1-7.
15. Li, H., Ruan, J., and Durbin, R. 2008. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 18:1851-1858.
16. Lunden, S., Meng, B., Avery, J. D., and Qiu, W. P. 2009. Characterization of a grapevine vein-clearing complex on Chardonnay. Eur. J. Plant Pathol. 126:135-144.
17. Martelli, G. P., and Boudon-Padieu, E. 2006. Directory of infectious diseases of grapevines and viruses and virus-like diseases of the grapevine: Bibliographic report of 1998-2004. In: Options Mediterraneennes, Serie B: N.55. CIHEAM, Bari, Italy.
18. Medberry, S. L., Lockhart, B. E., and Olszewski, N. E. 1990. Properties of Commelina yellow mottle virus's complete DNA sequence, genomic discontinuities and transcript suggest that it is a pararetrovirus. Nucleic Acid Res. 18:5505-5513.
19. Meng, B., Rebelo, A. R., and Fisher, H. 2006. Genetic diversity analyses of grapevine Rupestris stem pitting-associated virus reveal distinct population structures in scion versus rootstock. J. Gen. Virol. 87:1725-1733. (Pubitemid 43827228)
20. Mlotshwa, S., Pruss, G. J., and Vance, V. 2008. Small RNAs in viral infection and host defense. Trends Plant Sci. 13:375-382.
21. Navarro, B., Pantaleo, V., Gisel, A., Moxon, S., Dalmay, T., et al. 2009. Deep sequencing of viroid-derived small RNAs from grapevine provides new insights on the role of RNA silencing in plant-viroid interaction PLoS ONE 4. doi: 10.1371/journal.pone.0007686.
22. Prosser, S. W., Goszczynski, D. E., and Meng, B. 2007. Molecular analysis of double-stranded RNAs reveals complex infection of grapevines with multiple viruses. Virus Res. 124:151-159. (Pubitemid 46216568)
23. Qiu, W. P., Avery, J. D., and Lunden, S. 2007. Characterization of a severe virus-like disease in Chardonnay grapevines in Missouri. Plant Health Progress. doi: 10.1094/PHP-2007-1119-01-BR.
24. Rowhani, A., Uyemoto, J. K., Golino, D. A., and Martelli, G. P. 2005. Pathogen testing and certification of Vitis and Prunus species. Annu. Rev. Phytopathol. 43:261-278. (Pubitemid 41318873)
25. Rwahnih, M. A., Daubert, S., Golino, D., and 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 387:395-401.
26. Warren, R. L., Sutton, G. G., Jones, S. J., and Holt, R. A. 2007. Assembling millions of short DNA sequences using SSAKE. Bioinformatics 23:500-501. (Pubitemid 46323134)
27. Wu, Q., Luo, Y., Lu, R., Lau, N., Lai, E. C., Li, W.-X., and Ding, S.-W. 2010. Virus discovery by deep sequencing and assembly of virus-derived small silencing RNAs. Proc. Natl. Acad. Sci. USA 107:1606-1611.