The Genetic Structure of Populations of Potato virus Y in Japan; Based on the Analysis of 20 Full Genomic Sequences

Journal of Phytopathology

Volumn 160, Issue 11-12, 2012, Pages 661-673

  Ogawa, Tetsuji ^a,b,c   Nakagawa, Akio ^d   Hataya, Tatsuji ^e   Ohshima, Kazusato ^a,b  

^a SAGA UNIVERSITY   (Japan)

^b KAGOSHIMA UNIVERSITY   (Japan)

^c Nagasaki Prefectural Government   (Japan)

^d NATIONAL AGRICULTURAL RESEARCH CENTER   (Japan)

^e HOKKAIDO UNIVERSITY   (Japan)

Author keywords

Genetic structure; Japan; Population; Potato virus Y

Indexed keywords

DATABASE; GENETIC STRUCTURE; PHYLOGENETICS; RECOMBINATION; VIRUS;

EUROPE; JAPAN; NORTH AMERICA;

POTATO VIRUS Y; POTYVIRUS;

EID: 84868214965     PISSN: 09311785     EISSN: 14390434     Source Type: Journal    
DOI: 10.1111/j.1439-0434.2012.01959.x     Document Type: Article

References (55)

1. Ahn HI, Yoon JY, Hong JS, Yoon HI, Kim MJ, Ha JH, Rhie MJ, Choi JK, Park WM, Ryu KH. (2006) The complete genome sequence of pepper severe mosaic virus and comparison with other potyviruses. Arch Virol 151:2037-2045.
2. NTN-NW, by multiplex PCR assay. J Virol Methods 165:15-20.
3. NTN-NW, a novel recombinant strain of Potato virus Y predominating in potato field in Syria. Plant Pathol 59:31-41.
4. Chung BY-W, Miller WA, Atkins JF, Firth AE. (2008) An overlapping essential gene in the Potyviridae. Proc Natl Acad Sci USA 105:5897-5902.
5. Dayhoff MO, Barker WC, Hunt LT. (1983) Establishing homologies in protein sequences. Methods Enzymol 91:524-545.
6. Felsenstein J. (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791.
7. Felsenstein J. (1993) PHYLIP (Phylogeny Interference Package), Version 3.5. Seattle, WA, USA, Department of Genetics, University of Washington.
8. E. Plant Pathol 61:388-398.
9. García-Arenal F, Fraile A, Malpica JM. (2001) Variability and genetic structure of plant virus populations. Ann Rev Phytopathol 39:157-186.
10. Gibbs AJ, Ohshima K. (2010) Potyviruses and the digital revolution. Annu Rev Phytopathol 48:205-223.
11. Gibbs MJ, Armstrong JS, Gibbs AJ. (2000) Sister-scanning: a Monte Carlo procedure for assessing signals in recombinant sequences. Bioinformatics 16:573-582.
12. Gibbs AJ, Ohshima K, Gibbs M, García-Arenal F. (2008) More about plant virus evolution; past, present and future. In: Domingo E, Parrish CR, Holland JJ. (eds) Origin and Evolution of Viruses, 2nd edn. Waltham, MA, USA: Elsevier Academic Press, pp 229-249.
13. NTN isolates. Arch Virol 147:363-378.
14. Gray SM, DeBoer SH, Lorenzen J, Karasev AV, Whitworth J, Nolte P, Singh RP, Boucher A, Xu H. (2010) Potato virus Y: a significant and evolving treat to potato crops in the United States and Canada. Plant Dis 94:1384-1397.
15. Guindon S, Gascuel O. (2003) A simple fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52:696-704.
16. Hall TA. (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95-98.
17. Hataya T, Sano T, Ohshima K, Shikata E. (1990) Polymerase chain reaction-mediated cloning and expression of the coat protein gene of potato virus Y in Escherichia coli. Virus Genes 4:339-350.
18. Hataya T, Inoue AK, Ohshima K, Shikata E. (1994) Characterization and strain identification of a Potato virus Y isolate non-reactive with monoclonal antibodies specific to the ordinary and necrotic strains. Intervirology 37:12-19.
19. Hataya T, Uchino K, Arimoto R, Suda N, Sano T, Shikata E, Uyeda I. (2000) Molecular characterization of Hop latent virus and phylogenetic relationships among viruses closely related to carlaviruses. Arch Virol 145:2503-2524.
20. Hu X, Karasev AV, Brown CJ, Lorenzen JH. (2009a) Sequence characteristics of potato virus Y recombinants. J Gen Virol 90:3033-3041.
21. Hu X, Meacham T, Ewing L, Gray SM, Karasev AV. (2009b) A novel recombinant strain of Potato virus Y suggests a new viral genetic determinant of vein necrosis in tobacco. Virus Res 143:68-76.
22. Jones RAC. (1990) Strain group specific and virus specific hypersensitive reactions to infection with potyviruses in potato cultivars. Ann Appl Biol 117:93-105.
23. Karasev AV, Hu X, Brown CJ, Kerlan C, Nikolaeva OV, Crosslin JM, Gray SM. (2011) Genetic diversity of the ordinary strain of Potato virus Y (PVY) and origin of recombinant PVY strains. Phytopathology 101:778-785.
24. Kerlan C, Tribodet M, Glais L, Guillet M. (1999) Variability of potato virus Y in potato crops in France. J Phytopathol 147:643-651.
25. Kimura M. (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111-120.
26. King AMQ, Adams MJ, Carstens EB, Lefkowitz EJ. (2012) Virus Taxonomy, Ninth Report of the International Committee on Taxonomy of Viruses. San Diego, CA, USA: Elsevier Academic Press, pp 1327.
27. Larkin MA, Blackshields G, Brown NP et al. (2007) CLUSTAL W and CLUSTAL X version 2.0. Bioinformatics 23:2947-2948.
28. Librado P, Rozas J. (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451-1452.
29. Lorenzen JH, Meacham T, Berger PH, Shiel PJ, Crosslin JM, Hamm PB, Kopp H. (2006) Whole genome characterization of Potato virus Y isolates collected in the western USA and their comparison to isolates from Europe and Canada. Arch Virol 151:1055-1074.
30. Martin D, Rybicki E. (2000) RDP: detection of recombination amongst aligned sequences. Bioinformatics 16:562-563.
31. Martin DP, Lemey P, Lott M, Moulton V, Posada D, Lefeuvre P. (2010) RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics 26:2462-2463.
32. Maynard-Smith J. (1992) Analyzing the mosaic structure of genes. J Mol Evol 34:126-129.
33. Moreno IM, Malpica JM, Diaz-Pendon JA, Moriones E, Fraile A, García-Arenal F. (2004) Variability and genetic structure of the population of watermelon mosaic virus infecting melon in Spain. Virology 318:451-460.
34. NTN. J Virol Methods 103:145-156.
35. Nie X, Singh RP, Singh M. (2004) Molecular and pathological characterization of N:O isolates of the Potato virus Y from Monitoba, Canada. Can J Plant Pathol 26:573-583.
36. Ogawa T, Tomitaka Y, Nakagawa A, Ohshima K. (2008) Genetic structure of a population of Potato virus Y inducing potato tuber necrotic ringspot disease in Japan; comparison with North American and European populations. Virus Res 131:199-212.
37. Ohshima K, Inoue AK, Ishikawa Y, Shikata E, Hagita T. (1990) Production and application of monoclonal antibodies specific to ordinary strain and necrotic strain of potato virus Y. Ann Phytopath Soc Japan 56:508-514 (in Japanese).
38. Ohshima K, Hataya T, Sano T, Inoue AK, Shikata E, Hagita T. (1991) Comparison of biological properties, serological characteristics and amino acid sequences of coat protein between potato virus Y ordinary strain and necrotic strain. Ann Phytopath Soc Japan 57:615-622 (in Japanese).
39. Ohshima K, Sako K, Hiraishi C, Nakagawa A, Matsuo K, Ogawa T, Shikata E, Sako N. (2000) Potato tuber necrotic ringspot disease occurring in Japan: its association with Potato virus Y necrotic strain. Plant Dis 10:1109-1115.
40. Ohshima K, Yamaguchi Y, Hirota R et al. (2002) Molecular evolution of Turnip mosaic virus: evidence of host adaptation, genetic recombination and geographical spread. J Gen Virol 83:1511-1521.
41. Page RDM. (1996) Treeview: an application to display phylogenetic trees on personal computer. Comput Appl Biosci 12:357-358.
42. Posada D. (2008) jModelTest: phylogenetic model averaging. Mol Biol Evol 25:1253-1256.
43. Posada D, Crandall KA. (2001) Evaluation of methods for detecting recombination from DNA sequences: computer simulations. Proc Natl Acad Sci USA 98:13757-13762.
44. Revers F, Le Gall O, Candresse T, Le Romancer M, Dunez J. (1996) Frequent occurrence of recombinant potyvirus isolates. J Gen Virol 77:1953-1965.
45. Saitou N, Nei M. (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425.
46. Salminen MO, Carr JK, Burke DS, McCutchan FE. (1995) Identification of breakpoints in intergenotypic recombinants of HIV type 1 by Bootscanning. AIDS Res Hum Retroviruses 11:1423-1425.
47. Sawyer SA. (1999) GENECONV: A Computer Package for the Statistical Detection of Gene Conversion. Distributed by the Author. St Louis, MO, USA, Department of Mathematics, Washington University, available at http://www.math.wustl.edu/~sawyer.
48. Schubert J, Fomitcheva V, Sztangret-Wisniewska J. (2007) Differentiation of Potato virus Y strains using improved sets of diagnostic PCR-primers. J Virol Methods 140:66-74.
49. Seo JK, Ohshima K, Lee HG, So M, Choi HS, Lee SH, Sohn SH, Kim KH. (2009) Molecular variability and genetic structure of the population of Soybean mosaic virus based on the analysis of complete genome sequences. Virology 393:91-103.
50. Singh RP, Valkonen JPT, Gray SM, Boonham N, Jones RAC, Kerlan C, Schubert J. (2008) Discussion paper: the naming of Potato virus Y strains infecting potato. Arch Virol 153:1-13.
51. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731-2739.
52. Tomimura K, Spǎk J, Katis N, Jenner CE, Walsh JA, Gibbs AJ, Ohshima K. (2004) Comparisons of the genetic structure of populations of Turnip mosaic virus in West and East Eurasia. Virology 330:408-423.
53. Tomitaka Y, Ohshima K. (2006) A phylogeographic study of the Turnip mosaic virus population in east Asia reveals an 'emergent' lineage in Japan. Mol Ecol 15:4437-4457.
54. Wang B, Jia JL, Wang XQ, Wang ZY, Yang BH, Li XD, Zhu XP. (2012) Molecular characterization of two recombinant potato virus Y isolates from China. Arch Virol 157:401-403.
55. Weiller GF. (1998) Phylogenetic profiles: a graphical method for detecting genetic recombinations in homologous sequences. Mol Biol Evol 15:326-355.