Identification and characterization of Citrus yellow vein clearing virus, a putative new member of the genus Mandarivirus

Phytopathology

Volumn 102, Issue 12, 2012, Pages 1168-1175

  Loconsole, G ^a   Onelge N ^b   Potere, O ^a   Giampetruzzi, A ^a   Bozan, O ^b   Satar, S ^b   De Stradis, A ^c   Savino, V ^a   Yokomi, R K ^d   Saponari, M ^c  

^a UNIVERSITY OF BARI   (Italy)

^b CUKUROVA UNIVERSITY   (Turkey)

^c INSTITUTE FOR SUSTAINABLE PLANT PROTECTION   (Italy)

^d United States Department of Agriculture Agricultural Research Service ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CITRUS; CLASSIFICATION; FLEXIVIRIDAE; GENE EXPRESSION REGULATION; GENETICS; PHYLOGENY; PLANT DISEASE; VIROLOGY; VIRUS GENOME;

CITRUS; FLEXIVIRIDAE; GENE EXPRESSION REGULATION, VIRAL; GENOME, VIRAL; PHYLOGENY; PLANT DISEASES;

CITRUS; CITRUS LIMON; INDIAN CITRUS RINGSPOT VIRUS; MANDARIVIRUS; PHASEOLUS VULGARIS;

EID: 84871741290     PISSN: 0031949X     EISSN: None     Source Type: Journal    
DOI: 10.1094/PHYTO-06-12-0140-R     Document Type: Article

References (40)

1. Adams, M. J., Candresse, T., Hammond, J., Kreuze, J. F., Martelli, G. P., Namba, S., Pearson, M. N., Ryu, K. H., and Vaira, A. M. 2011. Family Alphaflexiviridae. Pages 904-919 in: Virus Taxonomy. Ninth Report of 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, Amsterdam, The Netherlands.
2. Alshami, A. A. A., Ahlawat, Y. S., and Pant, R. P. 2003. A hitherto unreported yellow vein clearing disease of citrus in India and its viral aetiology. Indian Phytopathol. 56:422-427.
3. Bratlie, M. S., and Drabløs, F. 2005. Bioinformatic mapping of AlkB homology domains in viruses. BMC Genomics 6:1. http://www.biomedcentral. com/1471-2164/6/1. doi:10.1186/1471-2164-6-1
4. Caruthers, J. M., and McKay, D. B. 2002. Helicase structure and mechanism. Curr. Opin. Struc. Biol. 12:123-133.
5. Catara, A., Azzaro, A., Davino, M., and Polizzi, G. 1993. Yellow vein clearing of lemon in Pakistan. Pages 364-367 in: Proc. 12th Conf. IOCV. IOCV, Riverside, CA.
6. Deleris, A., Gallego-Bartolome, J., Bao, J., Kasschau, K. D., Carrington, J. C., and Voinnet, O. 2006. Hierarchical action and inhibition of plant dicer-like proteins in antiviral defense. Science 313:68-71.
7. Ding, S. W. 2010. RNA-based antiviral immunity. Nat. Rev. Immunol. 10:632-44.
8. Dolja, V. V., Boyko, V. P., Agranowsky, A. A., and Koonin, E. V. 1991. Phylogeny of capsid proteins of rod-shaped and filamentous RNA plant viruses: Two families with distinct patterns of sequence and probably structure conservation. Virology 184:79-86.
9. Giampetruzzi, A., Roumi, V., Roberto, R., Malossini, U., Yoshikawa, N., La Notte, P., Terlizzi, F., Credi, R., and Saldarelli, P. 2012. A new grapevine virus discovered by deep sequencing of virus- and viroidderived small RNAs in cv. Pinot Gris. Virus Res. 163:262-268.
10. Gramstat, A., Courtpozanis, A., and Rohde, W. 1990. The 12 kDa protein of potato virus M displays properties of a nucleic acid-binding regulatory protein. FEBS Lett. 276:34-38.
11. Grimaldi, V., and Catara, A. 1996. Association of a filamentous virus with yellow vein clearing of lemon. Pages 343-345 in: Proc. 13th Conf. IOCV. IOCV, Riverside, CA.
12. Hammond, J. 1990. Western blotting and the use of membranes to absorb antisera and to affinity purify antibodies. Pages 269-281 in: Serological Methods for Detection and Identification of Viral and Bacterial Plant Pathogens, A Laboratory Manual. R. O. Hampton, E. M. Ball, and S. H. DeBoer, eds. American Phytopathological Society, St. Paul, MN.
13. Haylor, M. T. M., Brunt, A. A., and Coutts, R. H. A. 1990. Conservation of the 30 terminal nucleotide sequence in five carlaviruses. Nucleic Acids Res. 18:6-127.
14. Hoa, N. V., and Ahlawat, Y. S. 2004. Characterization of four isolates of Indian citrus ringspot virus. Indian Phytopathol. 57:296-302.
15. Iftikhar, Y., Iqbal, Z., Ahmed, S., Awan, A. R., Saleem, U., Sarwar, G., and Moeen-ud-Din. 2010. Effect of environmental factors on Yellow vein clearing virus incidence in lemon. J. Agric. Res. 48:87-92.
16. Jelkmann, W. 1994. Nucleotide sequences of apple stem pitting virus and of the coat protein gene of a similar virus from pear associated with vein yellows disease and their relationship with potex- and carlaviruses. J. Gen. Virol. 75:1535-1542.
17. Koonin, E. V. 1991. The phylogeny of RNA-dependent RNA polymerases of positive strand RNA viruses. J. Gen. Virol. 72:2197-2206.
18. 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.
19. Loconsole, G., Saldarelli, P., Doddapaneni, H., Savino, V., Martelli, G. P., and Saponari, M. 2012. Identification of a single-stranded DNA virus associated with citrus chlorotic dwarf disease, a new member in the family Geminiviridae. Virology. DOI: 10.1016/j.virol.2012.06.005
20. Lu, C., Meyers, B. C., and Green, P. J. 2007. Construction of small RNA cDNA libraries for deep sequencing. Methods 47:110-117.
21. Milne, R. G. 1993. Electron-microscopy of in vitro preparations. Pages 229-233 in: Diagnosis of Plant Viruses. R. E. F. Matthews, ed. CRC Press, Boca Raton, FL.
22. Morozov, S. Y., and Solovyev, A. G. 2003. Triple gene block: Modular design of a multifunctional machine for plant virus movement. J. Gen. Virol. 84:1351-1366.
23. Moxon, S., Schwach, F., MacLean, D., Dalmay, T., Studholme, D. J., and Moulton, V. 2008. A toolkit for analyzing large-scale plant small RNA datasets. Bioinformatics 24:2252-2253.
24. Murray, M. G., and Thompson, W. F. 1980. Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res. 8:4321-4325.
25. Mushegian, A. R., and Koonin, E. V. 1993. Cell-to-cell movement of plant viruses. Insights from amino acid sequence comparisons of movement proteins and from analogies with cellular transport systems. Arch. Virol. 133:239-257.
26. Önelge, N. 2002. First report of yellow vein clearing of lemons in Turkey. J. Turk. Phytopathol. 32:53-55.
27. Önelge, N., Bozan, O., Gök, M., and Satar, S. 2010. Yellow vein clearing of lemons in Turkey. Pages 227-228 in: Proc. 17th Conf. IOCV. IOCV, Riverside, CA.
28. Önelge, N., Kersting, U., Guang, Y., Bar Joseph, M., and Bozan, O. 2000. Nucleotide sequences of citrus viroids CVd-IIIa and CVd-IV obtained from dwarfed Meyer lemon trees grafted on sour orange. J. Plant Dis. Prot. 107:387-391.
29. Önelge, N., Satar, S., Elibüyük, Ö., and Bozan, O. 2011. Citrus yellow vein clearing virus: A new aphid-transmitted citrus virus? Citrograph, January/February 2011:22-24.
30. Önelge, N., Satar, S., Elibüyük, Ö., Bozan, O., and Kamberoǧlu, M. 2011. Transmission studies on Citrus yellow vein clearing virus. Proc. 18th Conf. IOCV. IOCV, Riverside, CA.
31. Rozanov, M. N., Koonin, E. V., and Gorbalenya, A. E. 1992. Conservation of the putative methyltransferase domain: A hallmark of the 'Sindbis-like' supergroup of positive-strand RNA viruses. J. Gen. Virol. 73:2129-2134.
32. Rustici, G., Accotto G. P., Noris, E., Masenga, V., Luisoni, E., and Milne, R. G. 2000. Indian citrus ringspot virus: A proposed new species with some affinities to potex-, carla-, fovea- and allexiviruses. Arch. Virol. 145:1895-1908.
33. Rustici, G., Milne, R. G., and Accotto, G. P. 2002. Nucleotide sequence, genome organization and phylogenetic analysis of Indian citrus ringspot virus. Arch. Virol. 147:2215-2224.
34. Skryabin, K. G., Morozov, S. Y., Kraev, A. S., Rozanov, M. N., Chernov, B. K., Lukasheva, L. I., and Atabekov, J. G. 1988. Conserved and variable elements in RNA genomes of potexviruses. FEBS 240:33-40.
35. Sumi, S., Tsuneyoshi, T., and Furutani, H. 1993. Novel rod-shaped viruses isolated from garlic, Allium sativum, possessing a unique genome organisation. J. Gen. Virol. 74:1879-1885.
36. Van Oosten, H. J. 1972. Purification of plum pox (sharka) virus with the use of Triton X-100. Eur. J. Plant. Pathol. 78:33-34.
37. Zerbino, D. R., and Birney, E. 2008. Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18:821-829.
38. Zhang, Y., Singh, K., Kaur, R., and Qiu, W. 2011. Association of a novel DNA virus with the grapevine vein-clearing and vine decline syndrome. Phytopathology 101:1081-1090.
39. Zhang, Y.-P., Kirkpatrick, B. C., Smart, C. D., and Uyemoto, J. K. 1998. cDNA cloning and molecular characterization of Cherry green ring mottle virus. J. Gen. Virol. 79:2275-2281.
40. Zhou, C., and Li, Z. 2010. Current occurrence and research status of graft-transmissible citrus diseases in P.R. China. Page 44 in: Proc. 18th Conf. IOCV. IOCV, Riverside, CA.