DOI QR코드

DOI QR Code

Molecular Evidence of Recombination on Korean Isolates of Tomato yellow leaf curl virus by Nucleotide Transversions and Transitions

  • Lee, Hye-Jung (Department of Genetic Engineering, Sungkyunkwan University) ;
  • Park, Jung-An (Department of Genetic Engineering, Sungkyunkwan University) ;
  • Auh, Chung-Kyoon (Department of Biological Sciences, Mokpo National University) ;
  • Lee, Kyeong-Yeoll (Department of Agriculture Biology, Kyungpook National University) ;
  • Kim, Chang-Seok (Department of Agricultural Biology, National Academy of Agricultural Science) ;
  • Lee, Gwan-Seok (Department of Agricultural Biology, National Academy of Agricultural Science) ;
  • Soh, Hyun-Cheol (Department of Genetic Engineering, Sungkyunkwan University) ;
  • Choi, Hong-Soo (Department of Agricultural Biology, National Academy of Agricultural Science) ;
  • Lee, Suk-Chan (Department of Genetic Engineering, Sungkyunkwan University)
  • Received : 2011.07.20
  • Accepted : 2011.08.28
  • Published : 2011.12.01

Abstract

Tomato yellow leaf curl virus (TYLCV), a member of genus Begomovirus, was isolated in Korea in 2008. We sequenced and analyzed the DNA-A of 51 TYLCV isolates from Korea, and 13 of the TYLCV isolates were selected as type representatives of TYLCV from six Korean provinces. The 13 TYLCV isolates were classified into Korea Group 1 (KG1, nine isolates) and Korea Group 2 (KG2, four isolates) based on the results of phylogenetic analysis and genome size (2774 and 2781 nucleotides, respectively). A recombination detection program 3 (RDP3) revealed two recombinations between the TYLCV Korea isolates and other TYLCV isolates [Thailand (AF206674), Iran (AJ132711), and Israel (X76319)]. TYLCV Jeju isolate was characterized by two recombination events (E1 and E2) caused by the presence of E1 in ORF V1 and C3, which may seem to be the mutations of the high nucleotide transversion and transition rate. Collectively, our results suggest that the occurrence of nucleotide transversions and transitions in TYLCV DNA-A might have induced novel recombination events within the TYLCV Korea isolates.

Keywords

References

  1. Bonilla-Ramirez, G. M., Guevara-Gonzalez, R. G., Garzon- Tiznado, J. A., Ascencio-Ibanez, J. T., Torres-Pacheco, I. and Rivera-Bustamante, R. F. 1997. Analysis of the infectivity of monomeric clones of Pepper huasteco virus. J. Gen. Virol. 78:947-951. https://doi.org/10.1099/0022-1317-78-4-947
  2. Briddon, R. W., Bedford, I. D., Tsai, J. H. and Markham, P. G. 1996. Analysis of the nucleotide sequence of the treehoppertransmitted geminivirus, Tomato pseudo-curly top virus, suggests a recombinant origin. Virology 219:387-394. https://doi.org/10.1006/viro.1996.0264
  3. Garcia-Andres, S., Tomas, D. M., Sanchez-Campos, S., Navas-Castillo, J. and Moriones, E. 2007. Frequent occurrence of recombinants in mixed infections of tomato yellow leaf curl disease associated begomoviruses. Virology 365:210-219. https://doi.org/10.1016/j.virol.2007.03.045
  4. Choi, K. J., Kim, W. G., Kim, H. G., Choi, H. W., Lee, Y. K., Lee, B. D., Lee, S. Y. and Hong, S. K. 2011. Morphology, molecular phylogeny and pathogenecity of Colletotrichum panacicola causing anthracnose of Korean ginseng. Plant Pathol. J. 27:1-7. https://doi.org/10.5423/PPJ.2011.27.1.001
  5. Davino, S., Napoli, C., Dellacroce, C., Miozzi, L., Noris, E., Davino, M. and Accotto, G. P. 2009. Two new natural begomovirus recombinants associated with the Tomato yellow leaf curl disease co-exist with parental viruses in tomato epidemics in Italy. Virus Res. 143:15-23. https://doi.org/10.1016/j.virusres.2009.03.001
  6. Duffy, S. and Holmes, E. C. 2008. Phylogenetic evidence for rapid rates of molecular evolution in the single-stranded DNA begomovirus Tomato yellow leaf curl virus. J. Virol. 82:957-965. https://doi.org/10.1128/JVI.01929-07
  7. Edgar, R. C. 2004. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinform. 5:113. https://doi.org/10.1186/1471-2105-5-113
  8. Fondong, V. N., Pita, J. S., Rey, M. E., de Kochko, A., Beachy, R. N. and Fauquet, C. M. 2000. Evidence of synergism between African cassava mosaic virus and a new double recombinant geminivirus infecting cassava in Cameroon. J. Gen. Virol. 81:287-297. https://doi.org/10.1099/0022-1317-81-1-287
  9. Ge, L., Zhang, J., Zhou, X. and Li, H. 2007. Genetic structure and population variability of Tomato yellow leaf curl China virus. J. Virol. 81:5902-5907. https://doi.org/10.1128/JVI.02431-06
  10. Hagelberg, E., Goldman, N., Lio, P., Whelan, S., Schiefenhöel, W., Clegg, J. B. and Bowden, D. K. 1999. Evidence for mitochondrial DNA recombination in a human population of island Melanesia. Proc. Biol. Sci. 266:485-492. https://doi.org/10.1098/rspb.1999.0663
  11. Idris, A. M. and Brown, J. K. 2005. Evidence for interspecificrecombination for three monopartite begomoviral genomes associated with the Tomato leaf curl disease from central Sudan. Arch. Virol. 150:1003-1012. https://doi.org/10.1007/s00705-004-0484-7
  12. Jonson, M. G., Seo, J. K., Choi, H. S., Kim, J. S. and Kim, K. H. 2009. Effects of recombination on the pathogenicity and evolution of Pepper mottle virus. Plant Pathol. J. 25:417-421. https://doi.org/10.5423/PPJ.2009.25.4.417
  13. Kim, J. S., Cho, J. D., Choi, H. S., Lee, S. H., Choi, G. S., Lee, S. Y., Kim, H. J. and Yoon, M. K. 2010. Ribgrass mosaic Tobamovirus occurred on chinese cabbage in Korea. Plant Pathol. J. 26:328-339. https://doi.org/10.5423/PPJ.2010.26.4.328
  14. Klute, K. A., Nadler, S. A. and Stenger, D. C. 1996. Horseradish curly top virus is a distinct subgroup II geminivirus species with rep and C4 genes derived from a subgroup III ancestor. J. Gen. Virol. 77:1369-1378. https://doi.org/10.1099/0022-1317-77-7-1369
  15. Lefeuvre, P., Martin, D. P., Harkins, G., Lemey, P. and Gray, A. J. A. 2010. The spread of Tomato yellow leaf curl virus from the Middle East to the world. PLoS Pathog. 6:e1001164. https://doi.org/10.1371/journal.ppat.1001164
  16. Lee, H., Song, W., Kwak, H. R., Kim, J. D., Park, J., Auh, C. K., Kim, D. H., Lee, K. Y., Lee, S. and Choi, H. S. 2010. Phylogenetic analysis and inflow route of Tomato yellow leaf curl virus (TYLCV) and Bemisia tabaci in Korea. Mol. Cells 30:467-476. https://doi.org/10.1007/s10059-010-0143-7
  17. 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
  18. Monci, F., Sanchez-Campos, S., Navas-Castillo, J. and Moriones, E. 2002. A natural recombinant between the geminiviruses Tomato yellow leaf curl Sardinia virus and Tomato yellow leaf curl virus exhibits a novel pathogenic phenotype and is becoming prevalent in Spanish populations. Virology 303:317-326. https://doi.org/10.1006/viro.2002.1633
  19. Navas-Castillo, J., Sanchez-Campos, S., Noris, E., Louro, D., Accotto, G. P. and Moriones, E. 2000. Natural recombination between Tomato yellow leaf curl virus-Is and Tomato leaf curl virus. J. Gen. Virol. 81:2797-2801. https://doi.org/10.1099/0022-1317-81-11-2797
  20. Padidam, M., Sawyer, S. and Fauquet, C. M. 1999. Possible emergence of new geminiviruses by frequent recombination. Virology 265:218-225. https://doi.org/10.1006/viro.1999.0056
  21. Picketts, D. J., D'Souza, C., Bridge, P. J. and Lillicrap, D. 1992. An A to T transversion at position −5 of the factor IX promoter results in hemophilia B. Genomics 12:161-163. https://doi.org/10.1016/0888-7543(92)90421-N
  22. Saitou, N. and Nei, M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
  23. Sanz, A. I., Fraile, A., Garcia-Arenal, F., Zhou, X., Robinson, D. J., Khalid, S., Butt, T. and Harrison, B. D. 2000. Multiple infection, recombination and genome relationships among begomovirus isolates found in cotton and other plants in Pakistan. J. Gen. Virol. 81:1839-1849. https://doi.org/10.1099/0022-1317-81-7-1839
  24. Saunders, K. and Stanley, J. 1999. A nanovirus-like DNA component associated with yellow vein disease of Ageratum conyzoides: evidence for interfamilial recombination between plant DNA viruses. Virology 264:142-152. https://doi.org/10.1006/viro.1999.9948
  25. Schneider, W. L. and Roossinck, M. J. 2001. Genetic diversity in RNA virus quasispecies is controlled by host-virus interactions. J. Virol. 75:6566-6571. https://doi.org/10.1128/JVI.75.14.6566-6571.2001
  26. Smith, G. R. 1994. Hotspots of homologous recombination. Cell. Mol. Life Sci. 50:234-241. https://doi.org/10.1007/BF01924006
  27. Tamura, K. 1992. Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G+ C-content biases. Mol. Biol. Evol. 9:678.
  28. Tamura, K., Dudley, J., Nei, M. and Kumar, S. 2007. MEGA 4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24:1596-1599. https://doi.org/10.1093/molbev/msm092
  29. Torres-Pacheco, I., Garzon-Tiznado, J. A., Herrera-Estrella, L. and Rivera-Bustamante, R. F. 1993. Complete nucleotide sequence of Pepper huasteco virus: analysis and comparison with bipartite geminiviruses. J. Gen. Virol. 74:2225-2231. https://doi.org/10.1099/0022-1317-74-10-2225
  30. Umaharan, P., Padidam, M., Phelps, R. H., Beachy, R. N. and Fauquet, C. M. 1998. Distribution and diversity of geminiviruses in Trinidad and Tobago. Phytopathology 88:1262-1268. https://doi.org/10.1094/PHYTO.1998.88.12.1262
  31. Zhou, X., Liu, Y., Calvert, L., Munoz, C., Otim-Nape, G. W., Robinson, D. J. and Harrison, B. D. 1997. Evidence that DNA-A of a geminivirus associated with severe cassava mosaic disease in Uganda has arisen by interspecific recombination. J. Gen. Virol. 78:2101-2111. https://doi.org/10.1099/0022-1317-78-8-2101
  32. Zhou, X., Liu, Y., Robinson, D. J. and Harrison, B. D. 1998. Four DNA-A variants among Pakistani isolates of cotton leaf curl virus and their affinities to DNA-A of geminivirus isolates from okra. J. Gen. Virol. 79:915-923. https://doi.org/10.1099/0022-1317-79-4-915

Cited by

  1. Sweet pepper confirmed as a reservoir host for tomato yellow leaf curl virus by both agro-inoculation and whitefly-mediated inoculation vol.159, pp.9, 2014, https://doi.org/10.1007/s00705-014-2072-9
  2. Emergence and diversity of begomoviruses infecting solanaceous crops in East and Southeast Asia vol.186, 2014, https://doi.org/10.1016/j.virusres.2013.12.026