Complete genome sequence of a Chinese isolate of Potato virus X and analysis of genetic diversity

Journal of Phytopathology

Volumn 156, Issue 6, 2008, Pages 346-351

  Yu, X Q ^a,b   Wang, H Y ^a   Lan, Y F ^a   Zhu, X P ^a   Li, X D ^a,b   Fan, Z F ^a,c   Li, H F ^a,c   Wang, Y Y ^a,d  

^a SHANDONG AGRICULTURAL UNIVERSITY   (China)

^b State Key Laboratory of Crop Biology   (China)

^c CHINA AGRICULTURAL UNIVERSITY   (China)

^d INSTITUTE OF PLANT PROTECTION   (China)

Author keywords

China; Complete genomic sequence; Phylogenetic analysis; Potato; Potato virus X

Indexed keywords

BIOGEOGRAPHY; DNA; GENE EXPRESSION; GENETIC VARIATION; NUCLEIC ACID ANALYSIS; PHYLOGENETICS; POTATO; PROTEIN; VIRAL DISEASE;

ASIA; CHINA; EURASIA; FAR EAST;

DIOSCOREA POLYSTACHYA; POTATO VIRUS X; SOLANUM TUBEROSUM;

EID: 42649115769     PISSN: 09311785     EISSN: 14390434     Source Type: Journal    
DOI: 10.1111/j.1439-0434.2007.01365.x     Document Type: Article

References (36)

1. Adams MJ, Antoniw JF, Bar-Joseph M, Brunt AA, Candresse T, Foster GD, Martelli GP, Milne RG, Zavriev SK, Fauquet CM 2004) The new plant virus family Flexiviridae and assessment of molecular criteria for species demarcation. Arch Virol 149 : 1045 1060.
2. Brunt AA, Crabtree K, Dallwitz MJ, Gibbs AJ, Watson L, Zurcher EJ (eds 1996 onwards). Plant Viruses Online: Descriptions and Lists from the VIDE Database.
3. Drake JW, Holland JJ 1999) Mutation rates among RNA viruses. Proc Natl Acad Sci U S A 96 : 13910 13913.
4. Fan Z, Chen H, Cai S, Deng C, Wang W, Liang X, Li H 2003) Molecular characterization of a distinct potyvirus from whitegrass in China. Arch Virol 148 : 1219 1224.
5. García-Arenal F, Fraile A, Malpica JM 2001) Variability and genetic structure of plant virus populations. Annu Rev Phytopathol 39 : 157 186.
6. Guyader S, Ducray DG 2002) Sequence analysis of Potato leafroll virus isolates reveals genetic stability, major evolutionary events and differential selection pressure between overlapping reading frame products. J Gen Virol 83 : 1799 1807.
7. Huisman MJ, Linthorst HJM, Bol JF, Cornelissen BJC 1988) The complete nucleotide sequence of Potato virus X and its homologies at the amino acid level with various plus-stranded RNA viruses. J Gen Virol 69 : 1789 1798.
8. Kagiwada S, Yamaji Y, Nakabayashi H, Ugaki M, Namba S 2002) The complete nucleotide sequence of Potato virus X strain OS: the first complete sequence of a Japanese isolate. J Gen Plant Pathol 68 : 94 98.
9. Kavanagh T, Goulden M, Santa Cruz S, Chapman S, Barker I, Baulcombe D 1992) Molecular analysis of a resistance-breaking strain of Potato virus X. Virology 189 : 609 617.
10. Kimura M 1980) A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16 : 111 120.
11. Komatsu K, Kagiwada S, Takahashi S et al. (2005) Phylogenetic characteristics, genomic heterogenecity and symptomatic variation of five closely related Japanese strains of Potato virus X. Virus Genes 31 : 99 105.
12. Kumar S, Tamura K, Nei M 2004) MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5 : 150 163.
13. Li WH 1993) Unbiased estimation of the rates of synonymous and non-synonymous substitution. J Mol Evol 36 : 96 99.
14. Ling KS, Zhu HY, Petrovic N, Gonsalves D 2007) Serological detection of Grapevine leafroll virus 2 using an antiserum developed against the recombinant coat protein. J Phytopathol 155 : 65 69.
15. Malcuit I, Jong W, Baulcombe DC, Shields DC, Kavanagh TA 2000) Acquisition of multiple virulence/avirulence determinants by Potato virus X (PVX) has occurred through convergent evolution rather than through recombination. Virus Genes 20 : 165 172.
16. Marco CF, Aranda MA 2005) Genetic diversity of a natural population of Cucurbit yellow stunting disorder virus. J Gen Virol 86 : 815 822.
17. 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.
18. Morozov SY, Solovyev AG 2003) Triple gene block: modular design of a multifunctional machine for plant virus movement. J Gen Virol 84 : 1351 1366.
19. Nei M. Molecular Evolutionary Genetics. New York, NY, Columbia University Press, 1987.
20. Nei M, Gojobori T 1986) Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 3 : 418 426.
21. Nei M, Kumar S. Molecular Evolution and Phylogenetics. New York, NY, Oxford University Press, 2000.
22. 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.
23. Orman BE, Celnik RM, Mandel AM, Torres HN, Mentaberry AN 1990) Complete cDNA sequence of a South American isolate of Potato virus X. Virus Res 16 : 293 306.
24. Pamilo P, Bianchi NO 1993) Evolution of the Zfx and Zfy, genes: rates and interdependence between the genes. Mol Biol Evol 10 : 271 281.
25. Qu J, Zhu C, Wen F, Guo X, Song Y 2003) Coat protein gene analysis and identification of an isolate of Potato virus X. J Plant Prot 30 : 358 384.
26. Rochow WF, Ross AF 1955) Virus multiplication in plants doubly infected by Potato viruses X and Y. Virology 1 : 10 27.
27. Skryabin KG, Kraev AS, Morozov SY, Rozanov MN, Chernov BK, Lukasheva LI, Atabekov JG 1988) The nucleotide sequence of Potato virus X RNA. Nucleic Acids Res 16 : 10929 10930.
28. Thompson JD, Higgins DG, Gibson TJ 1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22 : 4673 4680.
29. Tian YP, Zhu XP, Liu JL, Yu XQ, Du J, Kreuze J, Li XD 2007) Molecular characterization of the 3′-terminal region of Turnip mosaic virus isolates from Eastern China. J Phytopathol 155 : 333 341.
30. Tomitaka Y, Ohshima K 2006) A phylogeographical study of the Turnip mosaic virus population in East Asia reveals an 'emergent' lineage in Japan. Mol Ecol 15 : 4437 4457.
31. Tsompana M, Abad J, Purgganan M, Moyer W 2005) The molecular population genetics of the Tomato spotted wilt virus (TSWV) genome. Mol Ecol 14 : 53 66.
32. Vance VB 1991) Replication of Potato virus X RNA is altered in coinfections with Potato virus Y. Virology 182 : 486 494.
33. Vance VB, Berger PH, Carrington JC, Hunt AG, Shi XM 1995) 5′ proximal potyviral sequences mediate Potato virus X/potyviral synergistic disease in transgenic tobacco. Virology 206 : 583 590.
34. Verchot-Lubicz J 2005) A new model for cell-to-cell movement of potexviruses. Mol Plant Microbe Interact 8 : 283 290.
35. Verchot-Lubicz J, Ye C-M, Bamunusinghe D 2007) Molecular biology of potexviruses: recent advances. J Gen Virol 88 : 1643 1655.
36. Yang Z, Bielawski JP 2000) Statistical methods for detecting molecular adaptation. Trends Ecol Evol 15 : 496 503.