Presence of Diverse Sugarcane Bacilliform Viruses Infecting Sugarcane in China Revealed by Pairwise Sequence Comparisons and Phylogenetic Analysis |
Ahmad, Kashif
(National Engineering Research Center of Sugarcane, Fujian Agricultural and Forestry University)
Sun, Sheng-Ren (National Engineering Research Center of Sugarcane, Fujian Agricultural and Forestry University) Chen, Jun-Lu (Guangzhou Sugarcane Industry Research Institute) Huang, Mei-Ting (National Engineering Research Center of Sugarcane, Fujian Agricultural and Forestry University) Fu, Hua-Ying (National Engineering Research Center of Sugarcane, Fujian Agricultural and Forestry University) Gao, San-Ji (National Engineering Research Center of Sugarcane, Fujian Agricultural and Forestry University) |
1 | Adams, M. J. and Carstens, E. B. 2012. Ratification vote on taxonomic proposals to the international committee on taxonomy of viruses (2012). Arch. Virol. 157:1411-1422. DOI |
2 | Adams, M. J., Lefkowitz, E. J., King, A. M., Harrach, B., Harrison, R. L., Knowles, N. J., Kropinski, A. M., Krupovic, M., Kuhn, J. H., Mushegian, A. R., Nibert, M., Sabanadzovic, S., Sanfacon, H., Siddell, S. G., Simmonds, P., Varsani, A., Zerbini, F. M., Gorbalenya, A. E. and Davison., A. J. 2016. Ratification vote on taxonomic proposals to the international committee on taxonomy of viruses (2016). Arch. Virol. 161:2921-2949. DOI |
3 | Autrey, L., Boolell, S., Jones, P., Lockhart, B. and Nadif, A. 1995. Distribution of sugarcane bacilliform virus in various geographical regions. In: Proceedings of XXI International Society of Sugarcane Technologists, eds. by B. Napompeth and P. Wisarath, pp. 527-541. Kasetsart University, Bangkok, Thailand. |
4 | Bouhida, M., Lockhart, B. E. L. and Olszewski, N. E. 1993. An analysis of the complete sequence of a sugarcane bacilliform virus genome infectious to banana and rice. J. Gen. Virol. 74:15-22. DOI |
5 | Bousalem, M., Douzery, E. J. and Seal, S. 2008. Taxonomy, molecular phylogeny and evolution of plant reverse transcribing viruses (family caulimoviridae) inferred from full-length genome and reverse transcriptase sequences. Arch. Virol. 153:1085-1102. DOI |
6 | Braithwaite, K. S., Egeskov, N. M. and Smith, G. R. 1995. Detection of sugarcane bacilliform virus using the polymerase chain reaction. Plant Dis. 79:792-796. DOI |
7 | Cai, Y. Q., Xu, D. L. and Zhou, G. H. 2009. Evidence of sugarcane bacilliform virus DNA fragment integrated into the saccharum inter-specific hybrids genome. J. South China Agric. Univ. 30:19-23 (in Chinese). |
8 | Comstock, J. C. and Lockhart, B. E. L. 1990. Widespread occurrence of sugarcane bacilliform virus in U.S. sugarcane germ plasm collections. Plant Dis. 74:530. DOI |
9 | D'Hont, A., Grivet, L., Feldmann, P., Glaszmann, J. C., Rao, S. and Berding, N. 1996. Characterisation of the double genome structure of modern sugarcane cultivars (Saccharum spp.) by molecular cytogenetics. Mol. Gen. Genet. 250:405-413. |
10 | da Silva, J. M., Jobim, L. J., Ramos-Sobrinho, R., Lima, J. S., Assuncao, I. P., Cruz, M. M. and Lima, G. S. 2015. Incidence and species diversity of badnaviruses infecting sugarcane from a germplasm collection in Brazil. Trop. Plant Pathol. 40:212-217. DOI |
11 | Haible, D., Kober, S. and Jeske, H. 2006. Rolling circle amplification revolutionizes diagnosis and genomics of geminiviruses. J. Virol. Methods 135:9-16. DOI |
12 | Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791. DOI |
13 | Geering, A. D. W. and Hull, R. 2012. Family Caulimoviridae. In: Virus Taxonomy: Ninth report of the international committee on taxonomy of viruses, eds. by A. M. Q. King, M. J. Adams, E. B. Carestens and E. J. Lefkowitz, pp. 424-443. Elsevier Academic Press, San Diego, CA, USA. |
14 | Geijskes, R. J., Braithwaite, K. S., Dale, J. L., Harding, R. M. and Smith, G. R. 2002. Sequence analysis of an Australian isolate of sugarcane bacilliform badnavirus. Arch. Virol. 147:2393-2404. DOI |
15 | Iskra-Caruana, M. L., Chabannes, M., Duroy, P. O. and Muller, E. 2014. A possible scenario for the evolution of Banana streak virus in banana. Virus Res. 186:155-162. DOI |
16 | Karuppaiah, R., Viswanathan, R. and Kumar, V. G. 2013. Genetic diversity of sugarcane bacilliform virus isolates infecting saccharum spp. in India. Virus Genes. 46:505-516. DOI |
17 | Li, W. F., Huang, Y. K., Jiang, D. M., Zhang, Z. X., Zhang, B. L. and Li, S. F. 2010. Detection of sugarcane bacilliform virus isolate and its influence on yield and quality of cane in Yunnan. Acta Phytopathol. Sinica 40:651-654 (in Chinese). |
18 | Martin, D. P., Lemey, P., Lott, M., Moulton, V., Posada, D. and Lefeuvre, P. 2010. RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics 26:2462-2463. DOI |
19 | Lockhart, B. E. L., Irey, M. J. and Comstock, J. C. 1996. Sugarcane bacilliform virus, Sugarcane mild mosaic virus, and sugarcane yellow leaf syndrome. In: Sugarcane Germplasm Conservation and Exchange, eds. by B. J. Croft, C. T. Piggin, E. S. Wallis and D. M. Hogarth, pp. 108-112. Australian Centre for International Agricultural Research (ACIAR), Brisbane, Queensland, Australia. |
20 | Lockhart, B. E. L. and Autrey, L. J. C. 2000. Sugarcane bacilliform virus. In: A Guide to Sugarcane Diseases, eds. by P. Rott, R. A. Bailey, J. C. Comstock, B. J. Croft, A. S. and Saumtally, pp. 268-272. CIRAD and ISSCT Press, Montpellier, France. |
21 | Muller, E., Dupuy, V., Blondin, L., Bauffe, F., Daugrois, J. H., Nathalie, L. and Iskra-Caruana, M. L. 2011. High molecular variability of sugarcane bacilliform viruses in Guadeloupe implying the existence of at least three new species. Virus Res. 160:414-419. DOI |
22 | Rao, G. P., Sharma, S. K., Singh, D., Arya, M., Singh, P. and Baranwal, V. K. 2014. Genetically diverse variants of sugarcane bacilliform virus infecting sugarcane in India and evidence of a novel recombinant Badnavirus variant. J. Phytopathol. 162:779-787. DOI |
23 | Sharma, S. K., Vignesh, K. P., Geetanjali, A. S., Pun, K. B. and Baranwal, V. K. 2015. Subpopulation level variation of banana streak viruses in India and common evolution of banana and sugarcane badnaviruses. Virus Genes 50:450-465. DOI |
24 | Yang, I. C., Hafner, G. J., Revill, P. A., Dale, J. L. and Harding, R. M. 2003. Sequence diversity of South Pacific isolates of Taro bacilliform virus and the development of a PCR-based diagnostic test. Arch. Virol. 148:1957-1968. DOI |
25 | Sun, S. R., Damaj, M. B., Alabi, O. J., Wu, X. B., Mirkov, T. E., Fu, H. Y., Chen, R. K. and Gao, S. J. 2016. Molecular characterization of two divergent variants of sugarcane bacilliform viruses infecting sugarcane in China. Eur. J. Plant Pathol. 145:375-384. DOI |
26 | Tamura, K., Stecher, G., Peterson, D., Filipski, A. and Kumar, S. 2013. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol. Biol. Evol. 30:2725-2729. DOI |
27 | Viswanathan, R., Alexander, K. C. and Garg, I. D. 1996. Detection of sugarcane bacilliform virus in sugarcane germplasm. Acta Virol. 40:5-8. |
28 | Wu, X. B., Alabi, O. J., Damaj, M. B., Sun, S. R., Mirkov, T. E., Fu, H. Y., Chen, R. K. and Gao, S. J. 2016. Prevalence and RT/RNase H genealogy of sugarcane bacilliform virus isolates from China. J. Phytopathol. 164:595-607. DOI |
29 | Xu, Z. Y., Zhou, L. W., Tang, Y., Lu, B. L., Gui, C. Y., Bai, R. M., Wen, R. H. and Chen, B. S. 2015. Molecular detection and distribution of sugarcane bacilliform virus in Guangxi. J. Southern Agric. 46:1980-1984 (in Chinese). DOI |