Association of Little cherry virus 1 (LChV1) with the Shirofugen stunt disease and characterization of the genome of a divergent LChV1 isolate

Phytopathology

Volumn 103, Issue 3, 2013, Pages 293-298

  Candresse, Thierry ^a   Marais, Armelle ^a   Faure, Chantal ^a   Gentit, Pascal ^b  

^a UNIVERSITÉ DE BORDEAUX   (France)

^b Ctifl   (France)

Author keywords

Closteroviridae; Deep sequencing; Double stranded RNA

Indexed keywords

COMPLEMENTARY DNA; DOUBLE STRANDED RNA; VIRUS RNA;

ARTICLE; CHEMISTRY; CLOSTEROVIRIDAE; DNA SEQUENCE; GENETICS; HIGH THROUGHPUT SEQUENCING; ISOLATION AND PURIFICATION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLANT DISEASE; PLANT LEAF; POLYMERASE CHAIN REACTION; PRUNUS; VIROLOGY; VIRUS GENOME;

BASE SEQUENCE; CLOSTEROVIRIDAE; DNA, COMPLEMENTARY; GENOME, VIRAL; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MOLECULAR SEQUENCE ANNOTATION; MOLECULAR SEQUENCE DATA; PHYLOGENY; PLANT DISEASES; PLANT LEAVES; POLYMERASE CHAIN REACTION; PRUNUS; RNA, DOUBLE-STRANDED; RNA, VIRAL; SEQUENCE ANALYSIS, DNA;

EID: 84874364001     PISSN: 0031949X     EISSN: None     Source Type: Journal    
DOI: 10.1094/PHYTO-10-12-0275-R     Document Type: Article

References (35)

1. Adams, I. P., Glover, R. H., Monger, W. A., Mumford, R., Jackeviciene, E., Navalinskiene, 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. Al Rwahnih, M., Daubert, S., Urbez-Torres, J. R., Cordero, F., and Rowhani, A. 2011. Deep sequencing evidence from single grapevine plants reveals a virome dominated by mycoviruses. Arch. Virol. 156:397-403.
4. Bajet, N. B., Unruh, T. R., Druffel, K. L., and Eastwell, K. C. 2008. Occurrence of two little cherry viruses in sweet cherry in Washington State. Plant Dis. 92:234-238.
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. Desvignes, J. C. 1999. Virus diseases of fruit trees. CTIFL Editions, France.
7. Eastwell, K. C., and Bernardy, M. G. 2001. Partial characterization of a closterovirus associated with apple mealybug-transmitted little cherry disease in North America. Phytopathology 91:268-273.
8. Foissac, X., Svanella-Dumas, L., Gentit, P., Dulucq, M.-J., Marais, A., and Candresse, T. 2005. Polyvalent degenerate oligonucleotides reverse transcription-polymerase chain reaction: a polyvalent detection and characterization tool for Trichoviruses, Capilloviruses, and Foveaviruses. Phytopathology 95:617-625.
9. Gentit, P., Foissac, X., Svanella-Dumas, L., Peypelut, M., and Candresse, T. 2001. Characterization of two different apricot latent virus variants associated with peach asteroid spot and peach sooty ringspot diseases. Arch. Virol. 146:1453-1464.
10. Howell, W. E., Thompson, D., and Scott, S., 2012. Virus-like disorders of fruit trees with undetermined etiology. Pages 259-266 in: Virus and Virus-Like Diseases of Pome and Stone Fruits. A. Hadidi, M. Barba, T. Candresse, and W. Jelkmann, eds. American Phytopathological Society Press, St Paul MN.
11. James, D., Varga, A., Pallas, V., and Candresse, T. 2006. Strategies for simultaneous detection of multiple plant viruses. Can. J. Plant Pathol. 28:16-29.
12. Jelkmann, W., and Eastwell, K. C. 2011. Little cherry virus-1 and -2. Pages 153-159 in: Virus and Virus-Like Diseases of Pome and Stone Fruits. A. Hadidi, M. Barba, T. Candresse, and W. Jelkmann, eds. American Phytopathological Society Press, St. Paul, MN.
13. Jelkmann, W., Fechtner, B., and Agranovsky, A. A. 1997. Complete genome structure and phylogenetic analysis of little cherry virus, a mealybug transmissible closterovirus. J. Gen. Virol. 78:2067-2071.
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 for diagnosis, discovery and sequencing of viruses. Virology 388:1-7.
15. Kunze, L., 1982. Experiments with Shirofugen stunt virus, a latent virus of sour cherry. Acta Hortic. 130:53-58.
16. Maccheroni, W., Alegria, M.C., Greggio, C. C., Piazza, J. P., Kamla, R. F., Zacharias, P. R., Bar-Joseph, M., Kitajima, E. W., Assumpção, L. C., Camarotte, G., Cardozo, J., Casagrande, E. C., Ferrari, F., Franco, S. F., Giachetto, P. F., Girasol, A., Jordão, H., Jr., Silva, V. H., Souza L. C., Aguilar-Vildoso, C. I., Zanca, A. S., Arruda, P., Kitajima, J. P., Reinach, F. C., Ferro, J. A., and da Silva, A. C. 2005. Identification and genomic characterization of a new virus (Tymoviridae family) associated with citrus sudden death disease. J. Virol. 79:3028-3037.
17. Marais, A., Svanella-Dumas, L., Barone, M., Gentit, P., Faure, C., Charlot, G., Ragozzino, A., and Candresse, T. 2011. Development of a polyvalent RT-PCR detection assay covering the genetic diversity of Cherry capillovirus A (CVA). Plant Pathol. 61:195-204.
18. Martelli, G. P., Agranovsky, A. A., Bar-Joseph, M., Boscia, D., Candresse, T., Coutts, R. H. A., Dolja, V. V., Hu, J. S., Jelkmann, W., Karasev, A. V., Martin, R. R., Minafra, A., Namba, S., and Vetten, H. J. 2012. Family Closteroviridae. Pages 987-1001 in: Virus Taxonomy - Ninth Report on the International Committee on Taxonomy of Viruses. A. M. Q. King, M. J. Adams, E. B. Carstens, and E. J. Lefkowitz, eds. Elsevier Academic Press, London.
19. Matic, S., Minafra, A., Sanchez-Navarro, J. A., Pallas, V., Myrta, A., and Martelli, G. P. 2009. 'Kwanzan Stunting' syndrome: detection and molecular characterization of an Italian isolate of Little cherry virus 1. Virus Res. 143:61-67.
20. Melcher, U., Muthukumar, V., Wiley, G. B., Min, B. E., Palmer, M. W., Verchot-Lubicz, J., Ali, A., Nelson, R. S., Roe, B. A., Thapa, V., and Pierce, M. L. 2008. Evidence for novel viruses by analysis of nucleic acids in virus-like particle fractions from Ambrosia psilostachya. J. Virol. Methods 152:49-55.
21. Nemeth, M. 1986. Virus, Mycoplasma and Rickettsia Diseases of Fruit Trees. Martinus Nijhoff/Dr W. Junk Publishers, Dordrecht/Boston/Lancaster.
22. Reeves, L., and Cheney, P. 1963. Flowering cherries as symptomless hosts of little cherry virus. Phytopathol. Mediterr. 2:184-190.
23. Reeves, E. L., Cheney, P. W., and Milbrath, J. A. 1955. Normal appearing Kwanzan and Shirofugen Oriental flowering cherries found to carry a virus of little cherry type. Plant Dis. Rep. 39:725-726.
24. Roossinck, M. J. 2011 The big unknown: Plant virus biodiversity. Curr. Opin. Virol. 1:63-67.
25. Roossinck, M. J., Saha, P., Wiley, G. B., Quan, J., White, J. D., Lai, H., Chavarría, F., Shen, G., and Roe, B. A. 2010. Ecogenomics: using massively parallel pyrosequencing to understand virus ecology. Mol. Ecol. 19:81-88.
26. Rott, M. E., and Jelkmann, W. 2001. Detection and partial characterization of a second closterovirus associated with little cherry disease, Little cherry virus-2. Phytopathology 91:261-267.
27. Studholme, D. J., Glover, R. H., and Boonham, N. 2011. Application of high-throughput DNA sequencing in phytopathology. Annu. Rev. Phytopathol. 49:87-105.
28. Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., and Kumar, S. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28:2731-2739.
29. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F., and Higgins, D. G. 1997. The Clustal X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 24:4876-4882.
30. Valverde, R. A., Dodds, J. A., and Heick, J. A. 1986. Double-stranded ribonucleic acid from plants infected with viruses having elongated particles and undivided genomes. Phytopathology 76:459-465.
31. Wilks, J. M., and Reeves, E. L. 1960. Flowering cherry, a reservoir of the little cherry virus. Phytopathology 50:188-190.
32. Wren, J. D., Roossinck, M. J., Nelson, R. S., Scheets, K., Palmer, M. W., and Melcher, U. 2006. Plant virus biodiversity and ecology. PLoS Biol. 4:e80.
33. Wylie, S. J., and Jones, M. G. 2011. The complete genome sequence of a Passion fruit woodiness virus isolate from Australia determined using deep sequencing, and its relationship to other potyviruses. Arch. Virol. 156:479-482.
34. Wylie, S. J., Luo, H., Li, H., and Jones, M. G. 2012. Multiple polyadenylated RNA viruses detected in pooled cultivated and wild plant samples. Arch. Virol. 157:271-284.
35. Youssef, F., Marais, A., Faure, C., Gentit, P., and Candresse, T. 2011. Strategies to facilitate the development of uncloned or cloned infectious full-length viral cDNAs: Apple chlorotic leaf spot virus as a case study. Virol. J. 8:488-500.