The Plant Pathology Journal

The Korean Society of Plant Pathology (한국식물병리학회)
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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)
  • Received : 2018.08.08
  • Accepted : 2018.10.04
  • Published : 2019.02.01
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Abstract

Sugarcane bacilliform viruses (SCBV), which belong to the genus Badnavirus, family Caulimoviridae, are an important DNA virus complex that infects sugarcane. To explore the genetic diversity of the sugarcane-infecting badnavirus complex in China, we tested 392 sugarcane leaf samples collected from Fujian, Yunnan, and Hainan provinces for the occurrence of SCBV by polymerase chain reaction (PCR) assays using published primers SCBV-F and SCBV-R that target the reverse transcriptase/ribonuclease H (RT/RNase H) regions of the viral genome. A total of 111 PCR-amplified fragments (726 bp) from 63 SCBV-positive samples were cloned and sequenced. A neighbor-joining phylogenetic tree was constructed based on the SCBV sequences from this study and 34 published sequences representing 18 different phylogroups or genotypes (SCBV-A to -R). All SCBV-tested isolates could be classified into 20 SCBV phylogenetic groups from SCBV-A to -T. Of nine SCBV phylogroups reported in this study, two novel phylogroups, SCBV-S and SCBV-T, that share 90.0-93.2% sequence identity and show 0.07-0.11 genetic distance with each other in the RT/RNase H region, are proposed. SCBV-S had 57.6-92.2% sequence identity and 0.09-0.66 genetic distance, while SCBV-T had 58.4-90.0% sequence identity and 0.11-0.63 genetic distance compared with the published SCBV phylogroups. Additionally, two other Badnavirus species, Sugarcane bacilliform MO virus (SCBMOV) and Sugarcane bacilliform IM virus (SCBIMV), which originally clustered in phylogenetic groups SCBV-E and SCBV-F, respectively, are first reported in China. Our findings will help to understand the level of genetic heterogeneity present in the complex of Badnavirus species that infect sugarcane.

Keywords

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Fig. 2. Geographical distribution of sugarcane bacilliform virus phylogenetic groups (genotypes) in China and other countries.

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Fig. 1. Phylogenetic analysis of sugarcane bacilliform virus (SCBV) isolates based on the partial DNA sequences of the reverse transcriptase/ribonuclease H (RT/RNase H) genomic region (480 nt). (a) The phylogeny was constructed by using the neighbor-joining (NJ) with the Tamura-Nei model. The bootstrap consensus tree was inferred from 1,000 replicates, and branches present in < 60% of the bootstrap replicates were collapsed. The analysis included 146 SCBV nucleotide sequences; 111 SCBV nucleotide sequences from this study, 34 SCBV nucleotide sequences from GenBank (bold type), and one corresponding nucleotide sequence of ComYMV (Commelina yellow mottle virus) as an outgroup. Newlyidentified SCBV groups (genotypes) are denoted by grey boxes. Phylogenetic trees of the SCBV-E (b) and SCBV-F (c) groups were also constructed using the NJ method.

Table 1. The occurrence of sugarcane bacilliform viruses in the Chinese sugarcane-producing regions of Fujian and Yunnan provinces and in a germplasm resource nursery in Hainan province

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Table 2. Nucleotide identities (%, lower left) and genetic distances (upper right) among and between sugarcane bacilliform virus (SCBV) phylogenetic groups from Fujian, Yunnan, and Hainan provinces based on the 480 nucleotide sequences of RT/RNase H regionsa

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References

  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. https://doi.org/10.1007/s00705-012-1299-6
  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. https://doi.org/10.1007/s00705-016-2977-6
  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. https://doi.org/10.1099/0022-1317-74-1-15
  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. https://doi.org/10.1007/s00705-008-0095-9
  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. https://doi.org/10.1094/PD-79-0792
  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. https://doi.org/10.1094/PD-74-0530F
  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. https://doi.org/10.1007/s40858-015-0033-9
  11. Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791. https://doi.org/10.1111/j.1558-5646.1985.tb00420.x
  12. 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.
  13. 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. https://doi.org/10.1007/s00705-002-0879-2
  14. Haible, D., Kober, S. and Jeske, H. 2006. Rolling circle amplification revolutionizes diagnosis and genomics of geminiviruses. J. Virol. Methods 135:9-16. https://doi.org/10.1016/j.jviromet.2006.01.017
  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. https://doi.org/10.1016/j.virusres.2014.01.005
  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. https://doi.org/10.1007/s11262-013-0890-6
  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. 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.
  19. 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.
  20. 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. https://doi.org/10.1093/bioinformatics/btq467
  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. https://doi.org/10.1016/j.virusres.2011.06.016
  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. https://doi.org/10.1111/jph.12270
  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. https://doi.org/10.1007/s11262-015-1179-8
  24. 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. https://doi.org/10.1007/s10658-015-0851-0
  25. 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. https://doi.org/10.1093/molbev/mst197
  26. Viswanathan, R., Alexander, K. C. and Garg, I. D. 1996. Detection of sugarcane bacilliform virus in sugarcane germplasm. Acta Virol. 40:5-8.
  27. 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. https://doi.org/10.1111/jph.12483
  28. 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). https://doi.org/10.3969/j:issn.2095-1191.2015.11.1980
  29. 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. https://doi.org/10.1007/s00705-003-0163-0