The genetic structure of populations of Turnip mosaic virus in Kyushu and central Honshu, Japan

Journal of General Plant Pathology

Volumn 73, Issue 3, 2007, Pages 197-208

  Tomitaka, Yasuhiro ^a   Yamashita, Tohru ^b   Ohshima, Kazusato ^a  

^a SAGA UNIVERSITY   (Japan)

^b Nagano Agricultural Experiment Station   (Japan)

Author keywords

Evolution; Expansion; Genetic structure; Recombination; Turnip mosaic virus

Indexed keywords

BRASSICA; BRASSICA RAPA SUBSP. RAPA; RAPHANUS; RAPHANUS SATIVUS; TURNIP MOSAIC VIRUS;

EID: 34347374731     PISSN: 13452630     EISSN: 1610739X     Source Type: Journal    
DOI: 10.1007/s10327-007-0003-2     Document Type: Article

References (64)

1. Atreya PL, Atreya CD, Pirone TP (1991) Amino acid substitutions in the coat protein result in loss of insect transmissibility of a plant virus. Proc Natl Acad Sci USA 88:11919-11923
2. Bermingham E, Moritz C (1998) Comparative phylogeography: concepts and application. Mol Ecol 7:367-369
3. Briddon RW, Stanley J (2006) Subviral agents associated with plant single-stranded DNA viruses. Virology 344:198-210
4. Brown JK (2001) The molecular epidemiology of begomoviruses. In: Khan JA, Dykstra J (eds) Trends in plant pathology. Haworth Press, New York, pp 279-316
5. Chare ER, Holmes EC (2006) A phylogenetic survey of recombination frequency in plant RNA viruses. Arch Virol 151:933-946
6. Chen J, Chen JS (2000) Occurrence and control of mosaic disease [turnip mosaic virus] in saffron (Crocus sativus). Zhejiang Nongye Kexue 3:132-135
7. Chen J, Zheng HY, Chen JP, Adams MJ (2002) Characterisation of a potyvirus and a potexvirus from Chinese scallion. Arch Virol 147:683-693
8. Chen J, Chen JP, Langeveld SA, Derks AFLM, Adams MJ (2003) Molecular characterization of Carla- and Potyviruses from Narcissus in China. J Phytopathol 151:26-29
9. Dolja VV, Haldeman R, Robertson NL, Dougherty WG, Carrington JC (1994) Distinct functions of capsid protein in assembly and movement of tobacco etch potyvirus in plants. EMBO J 13:1482-1491
10. Excoffier L, Laval G, Schneider S (2005) Arlequin (Version 3.0): an integrated software package for population genetics data analysis. Evol Bioinform Online 1:47-50
11. Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (2005) Virus taxonomy. In: 8th Report of the international committee on taxonomy of Viruses. Elsevier Academic, San Diego
12. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791
13. Felsenstein J (1993) PHYLIP (Phylogeny interference package), Version 3.5. Department of Genetics, University of Washington, Seattle
14. Fu YX, Li WH (1993) Statistical tests of neutrality of mutations. Genetics 133:693-709
15. Fuji S, Nakamae H (1999) Complete nucleotide sequence of the genomic RNA of a Japanese yam mosaic virus, a new potyvirus in Japan. Arch Virol 144:231-240
16. Fuji S, Nakamae H (2000) Complete nucleotide sequence of the genomic RNA of a mild strain of Japanese yam mosaic potyvirus in Japan. Arch Virol 145:635-640
17. García-Arenal F, Escriu F, Aranda MA, Alonso-Prados JL, Malpica JM, Fraile A (2000) Molecular epidemiology of Cucumber mosaic virus and its satellite RNA. Virus Res 71:1-8
18. Gera A, Lesemann DE, Cohen J, Franck A, Levy S, Salomon R (1997) The natural occurrence of turnip mosaic potyvirus in Allium ampeloprasum. J Phytopathol 145:289-293
19. Gibbs MJ, Armstrong JS, Gibbs AJ (2000) Sister-scanning: a Monte Carlo procedure for assessing signals in recombinant sequences. Bioinformatics 16:573-582; http://www.anu.edu.au/BoZo/software/
20. 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
21. Hamlyn BMG (1953) Quantitative studies on the transmission of cabbage black ringspot virus by Myzus persicae (Sulz.). Ann Appl Biol 40:393-402
22. Hasegawa M, Kishino H, Yano T (1985) Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 22:160-174
23. Hey J, Harris E (1999) Population bottlenecks and patterns of human polymorphism. Mol Biol Evol 16:1423-1426
24. Hu WQ, Pu ZQ, Xu ZG, Fang ZD (1996) A viral disease of broad bean caused by a non-aphid-transmissible strain of turnip mosaic virus. Plant Pathol 45:843-847
25. Jeanmougin F, Thompson JD, Gouy M, Higgins DG, Gibson TJ (1998) Multiple sequence alignment with Clustal X. Trends Biochem Sci 23:403-405
26. 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
27. Klein PG, Klein RR, Rodríquez-Cerezo E, Hunt AG, Shaw JG (1994) Mutational analysis of the tobacco vein mottling virus genome. Virology 204:759-769
28. Martin D, Rybicki E (2000) RDP: detection of recombination amongst aligned sequences. Bioinformatics 16:562-563
29. Martin D, Williamson C, Posada D (2005) RDP2: recombination detection and analysis from sequence alignment. Bioinformatics 21:260-262
30. Maynard Smith J (1992) Analyzing the mosaic structure of genes. J Mol Evol 34:126-129
31. Moreno IM, Malpica JM, Díaz-Pendón 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
32. Moyer JW (1999) Tospoviruses (Bunyaviridae). In: Webster R, Granoff A (eds) Encyclopedia of virology. Academic, London, pp 1803-1807
33. Ohshima K, Tanaka M, Sako N (1996) The complete nucleotide sequence of turnip mosaic virus RNA Japanese strain. Arch Virol 141:1991-1997
34. Ohshima K, Yamaguchi Y, Hirota R, Hamamoto T, Tomimura K, Tan Z, Sano T, Azuhata F, Walsh JA, Fletcher J, Chen J, Gera A, Gibbs A. (2002) Molecular evolution of Turnip mosaic virus; evidence of host adaptation, genetic recombination and geographical spread. J Gen Virol 83:1511-1521
35. Pagán I, Córdoba-Sellés MC, Martínez-Priego L, Fraile A, Malpica JM, Jordá C, García-Arenal F (2006) Genetic structure of the population of Pepino mosaic virus infecting tomato crops in Spain. Phytopathology 96:274-279
36. Page RDM (1996) TreeView: an application to display phylogenetic trees on personal computer. Comput Appl Biosci 12:357-358
37. Page RDM, Holmes EC (1998) Molecular evolution: a phylogenetic approach. Blackwell Science, Oxford, pp 89-134
38. Parks TD, Howard ED, Wolpert TJ, Arp DJ, Dougherty WG (1995) Expression and purification of a recombinant tobacco etch virus NIa proteinase: biochemical analyses of the full-length and a naturally occurring truncated proteinase form. Virology 210:194-201
39. Posada D, Crandall KA (2001) Evaluation of methods for detecting recombination from DNA sequences: computer simulations. Proc Natl Acad Sci USA 98:13757-13762
40. Provvidenti R (1996) Turnip mosaic potyvirus. In: Brunt AA, Crabtree K, Dallwitz MJ, Gibbs AJ, Watson L (eds) Viruses of plants. CABI, Wallingford, pp 1340-1343
41. Restrepo-Hartwig MA, Carrington JC (1994) The tobacco etch potyvirus 6-kilodalton protein is membrane associated and involved in viral replication. J Virol 68:2388-2397
42. Rogers AR (1995) Genetic evidence for a Pleistocene population explosion. Evolution 49:608-615
43. Rogers AR, Harpending H (1992) Population growth makes waves in the distribution of pairwise genetic differences. Mol Biol Evol 9:552-569
44. Rozas J, Sánchez-DeI, Barrio JC, Messeguer X, Rozas R (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19:2496-2497
45. Rubio L, Angeles M, Ayllón A, Kong P, Fernándes A, Polek M, Guerri J, Moreno P, Falk BW (2001) Genetic variation of Citrus tristeza virus isolates from California and Spain: evidence for mixed infections and recombination. J Virol 75:8054-8062
46. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425
47. 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
48. Sawyer SA (1999) GENECONV: a computer package for the statistical detection of gene conversion. Distributed by the author. Department of Mathematics, Washington University in St. Louis, available at http://www.math.wustl.edu/∼sawyer
49. Schaad MC, Lellis AD, Carrington JC (1997) VPg of tobacco etch potyvirus is a host genotype-specific determinant for long-distance movement. J Virol 71:8624-8631
50. Strimmer K, von Haeseler A (1996) Quartet puzzling: a quartet maximum likelihood method for reconstructing tree topologies. Mol Biol Evol 13:964-969
51. Strimmer K, Goldman N, von Haeseler A (1997) Bayesian probabilities and quartet puzzling. Mol Biol Evol 14:210-211
52. Swofford DL (1998) PAUP*: Phylogenetic analysis using parsimony (*and other methods), Version 4. Sinauer, Sunderland, Massachusetts
53. Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585-595
54. Tan Z, Wada Y, Chen J, Ohshima K (2004) Inter- and intra-lineage recombinants are common in natural populations of Turnip mosaic virus. J Gen Virol 85:2683-2696
55. Tomimura K, Gibbs AJ, Jenner CE, Walsh JA, Ohshima K (2003) The phylogeny of Turnip mosaic virus; comparisons of thirty-eight genomic sequences reveal a Eurasian origin and a recent 'emergence' in east Asia. Mol Ecol 12:2099-2111
56. Tomimura K, Špak 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
57. 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
58. Tomlinson JA (1987) Epidemiology and control of virus diseases of vegetables. Ann Appl Biol 110:661-681
59. Tsompana M, Abad J, Purugganan M, Moyer JW (2005) The molecular population genetics of the Tomato spotted wilt virus (TSWV) genome. Mol Ecol 14:53-66
60. Urcuqui-Inchima S, Haenni A-L, Bernardi F (2001) Potyvirus proteins: a wealth of functions. Virus Res 74:157-175
61. Verchot J, Herndon KL, Carrington JC (1992) Mutational analysis of the tobacco etch potyviral 35-kDa proteinase: identification of essential residues and requirements for autoproteolysis. Virology 190:298-306
62. Walsh JA, Jenner CE (2002) Turnip mosaic virus and the quest for durable resistance. Mol Plant Pathol 3:289-300
63. Weiller GF (1998) Phylogenetic profiles: a graphical method for detecting genetic recombinations in homologous sequences. Mol Biol Evol 15:326-335
64. Yang Z (1997) PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 13:555-556; http://abacus.gene.ucl.ac.uk/ software/paml.html