Evolutionary trajectory of turnip mosaic virus populations adapting to a new host

Journal of General Virology

Volumn 91, Issue 3, 2010, Pages 788-801

  Ohshima, Kazusato ^a   Akaishi, Sadayuki ^a   Kajiyama, Hiromi ^a   Koga, Ryoko ^a   Gibbs, Adrian J ^b  

^a SAGA UNIVERSITY   (Japan)

^b NONE   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; NUCLEOTIDE;

ARTICLE; CONSENSUS SEQUENCE; MOLECULAR CLONING; MOLECULAR DYNAMICS; MOLECULAR EVOLUTION; MOSAIC VIRUS; NONHUMAN; PRIORITY JOURNAL; PROGENY; RADISH; TURNIP; TURNIP MOSAIC VIRUS; VIRAL GENETICS; VIRAL PLANT DISEASE; VIRUS CELL INTERACTION; VIRUS ISOLATION;

ADAPTATION, BIOLOGICAL; BRASSICA NAPUS; BRASSICA RAPA; EVOLUTION, MOLECULAR; GENETIC VARIATION; GENOME, VIRAL; GREAT BRITAIN; POTYVIRUS; RAPHANUS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, VIRAL; SEQUENCE ANALYSIS, DNA; TOBACCO;

BRASSICA; BRASSICA RAPA; NICOTIANA BENTHAMIANA; RAPHANUS; RAPHANUS SATIVUS; TURNIP MOSAIC VIRUS;

EID: 76849087848     PISSN: 00221317     EISSN: 14652099     Source Type: Journal    
DOI: 10.1099/vir.0.016055-0     Document Type: Article

References (58)

1. Ali, A., Li, H., Schneider, W. L., Sherman, D. J., Gray, S., Smith, D. & Roossinck, M. J. (2006). Analysis of genetic bottlenecks during horizontal transmission of Cucumber mosaic virus. J Virol 80, 8345-8350.
2. Badgett, M. R., Auer, A., Carmichael, L. E., Parrish, C. R. & Bull, J. J. (2002). Evolutionary dynamics of viral attenuation. J Virol 76, 10524-10529.
3. Berger, P. H., Adams, M. J., Brunt, A. A., Hammond, J., Hill, J. H., Jordan, R. L., Kashiwazalci, S., Rybicki, E., Spence, N. & Stenger, D. C. (2005). Family Potyviridae. In Virus Taxonomy: Classification and Nomenclature of Viruses. Eighth Report of the International Committee on Taxonomy of Viruses, pp. 819-841. Edited by C. M. Fauquet, M. A. Mayo, J. Maniloff, U. Desselberger & L. A. Ball. San Diego, CA: Elsevier Academic Press.
4. Bull, J. J., Badgett,M. R.,Wichman, H. A., Huelsenbeck, J. P., Hillis, D.M., Gulati, A., Ho, C. & Molineux, I. J. (1997). Exceptional convergent evolution in a virus. Genetics 147, 1497-1507.
5. Carrillo, C., Lu, Z., Borca, M. V., Vagnozzi, A., Kutish, G. F. & Rock, D. L. (2007). Genetic and phenotypic variation of foot-and-mouth disease virus during serial passages in a natural host. J Virol 81, 11341-11351.
6. Clark, M. F. & Adams, A. N. (1977). Characteristics of the microplate method of enzyme-linked immunosorbent assay for the detection of plant viruses. J Gen Virol 34, 475-485.
7. Clement, M., Posada, D. & Crandall, K. A. (2000). TCS: a computer program to estimate gene genealogies. Mol Ecol 9, 1657-1660.
8. Crill, W. D., Wichman, H. A. & Bull, J. J. (2000). Evolutionary reversals during viral adaptation to alternating hosts. Genetics 154, 27-37.
9. Domingo, E., Escarmís, C., Menéndez-Arias, L., Perales, C., Herrera, M., Novella, S. & Holland, J. J. (2008). Viral quasispecies: dynamics, interactions, and pathogenesis. In Origin and Evolution of Viruses, 2nd edn, pp. 87-118. Edited by E. Domingo, C. R. Parrish & J. J. Holland. Elsevier Academic Press.
10. Eigen, M. (1996). On the nature of virus quasispecies. Trends Microbiol 4, 216-218.
11. Eigen, M. & Biebricher, C. K. (1988). Sequence space and quasispecies distribution. In RNA Genetics, vol. 3, pp. 211-245. Edited by E. Domingo, P. Ahlquist & J. J. Holland. Boca Raton, FL: CRC Press.
12. Elena, S. F. & Sanjuán, R. (2007). Virus evolution: insights from experimental approach. Annu Rev Ecol Syst 38, 27-52.
13. Excoffier, L., Laval, G. & Schneider, S. (2005). Arlequin (version 3.0): an integrated software package for population genetics data analyses. Evol Bioinform Online 1, 47-50.
14. French, R. & Stenger, D. C. (2003). Evolution of wheat streak mosaic virus: dynamics of population growth within plants may explain limited variation. Annu Rev Phytopathol 41, 199-214.
15. French, R. & Stenger, D. C. (2005). Population structure within lineages of Wheat streak mosaic virus derived from a common founding event exhibits stochastic variation inconsistent with the deterministic quasi-species model. Virology 343, 179-189.
16. García-Arenal, F., Fraile, A. & Malpica, J. M. (2001). Variability and genetic structure of plant virus populations. Annu Rev Phytopathol 39, 157-186.
17. Gibbs, A. J., Ohshima, K., Gibbs, M. & Garciá-Arenal, F. (2008a). More about plant virus evolution; past, present and future. In Origin and Evolution of Viruses, 2nd edn, pp. 229-249. Edited E. Domingo, C. R. Parrish & J. J. Holland. Elsevier Academic Press.
18. Gibbs, A. J., Ohshima, K., Phillips, M. J. & Gibbs, M. (2008b). The prehistory of potyviruses: their initial radiation was during the dawn of agriculture. PLoS ONE 3, e2523.
19. Hall, T. A. (1999). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41, 95-98.
20. Hall, J. S., French, R., Hein, G. L., Morris, T. J. & Stenger, D. C. (2001). Three distinct mechanisms facilitate genetic isolation of sympatric wheat streak mosaic virus lineages. Virology 282, 230-236.
21. Hughes, A. L. (2009). Small effective population sizes and rare nonsynonymous variants in potyviruses. Virology 393, 127-134.
22. Iglesia, F. & Elena, S. F. (2007). Fitness declines in Tobacco etch virus upon serial bottleneck transfers. J Virol 81, 4941-4947.
23. Jenner, C. E., Sánchez, F., Nettleship, S. B., Foster, G. D., Ponz, F. Walsh, J. A. (2000). The cylindrical inclusion gene of Turnip mosaic virus encodes a pathogenic determinant to the Brassica resistance gene TuRB01. Mol Plant Microbe Interact 13, 1102-1108.
24. Jenner, C. E., Tomimura, K., Ohshima, K., Hughes, S. L. & Walsh, J. (2002). Mutations in Turnip mosaic virus P3 and cylindrical inclusion proteins are separately required to overcome two Brassica napus resistance genes. Virology 300, 50-59.
25. Jenner, C. E., Wang, X., Tomimura, K., Ohshima, K., Ponz, F. & Walsh, J. A. (2003). The dual role of the potyvirus P3 protein of Turnip mosaic virus as a symptom and avirulence determinant in brassicas. Mol Plant Microbe Interact 16, 777-784.
26. Ji, J. P. & Loeb, L. A. (1992). Fidelity of HIV-1 reverse transcriptase copying RNA in vitro. Biochemistry 31, 954-958.
27. Kimura, M. (1980). A simple method for estimating evolutionary rate of base substitution through comparative studies of nucleotide sequences. J Mol Evol 16, 111-120.
28. Kurath, G. & Palukaitis, P. (1989). RNA sequence heterogeneity natural populations of three satellite RNAs of cucumber mosaic virus. Virology 173, 231-240.
29. Larkin, M. A., Blackshields, G., Brown, N. P., Chenna, R., McGettigan, P. A., McWilliam, H., Valentin, F., Wallace, I. M., Wilm, A. & other authors (2007). CLUSTAL W and CLUSTAL_X version 2.0. Bioinformatics 23, 2947-2948.
30. Li, W.-H. (1997). Molecular Evolution. Sunderland, MA: Sinauer Associates.
31. Li, H. & Roossinck, M. J. (2004). Genetic bottlenecks reduce population variation in an experimental RNA virus population. J Virol 78, 10582-10587.
32. Liang, X.-Z., Lee, B. T. K. & Wong, S.-M. (2002). Covariation in the capsid protein of hibiscus chlorotic ringspot virus induced by serial passaging in a host that restricts movement leads to avirulence in its systemic host. J Virol 76, 12320-12324.
33. Librado, P. & Rozas, J. (2009). DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25, 1451-1452.
34. Moreno, I. M., Malpica, J.M., Díaz-Pendón, J. A., 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.
35. Novella, I. S. (2004). Negative effect of genetic bottlenecks on the adaptability of vesicular stomatitis virus. J Mol Biol 336, 61-67.
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., Yamaguchi, Y., Hirota, R., Hamamoto, T., Tomimura, K., Tan, Z., Sano, T., Azuhata, F., Walsh, J. A. & other authors (2002). Molecular evolution of Turnip mosaic virus: evidence of host adaptation, genetic recombination and geographical spread. J Gen Virol 83, 1511-1521.
38. Ohshima, K., Tomitaka, Y., Wood, J. T., Minematsu, Y., Kajiyama, H., Tomimura, K. & Gibbs, A. J. (2007). Patterns of recombination in turnip mosaic virus genomic sequences indicate hotspots of recombination. J Gen Virol 88, 298-315.
39. Sacristán, S., Malpica, J. M., Fraile, A. & García-Arenal, F. (2003). Estimation of population bottlenecks during systemic movement of tobacco mosaic virus in tobacco plants. J Virol 77, 9906-9911.
40. Sacristán, S., Fraile, A., Malpica, J. M. & García-Arenal, F. (2005). An analysis of host adaptation and its relationship with virulence in Cucumber mosaic virus. Phytopathology 95, 827-833.
41. Sánchez, F., Martínez-Herrera, D., Aguilar, I. & Ponz, F. (1998). Infectivity of turnip mosaic potyvirus cDNA clones and transcripts on the systemic host Arabidopisis thaliana and local lesion hosts. Virus Res 55, 207-219.
42. Sanjuán, R., Moya, A. & Elena, S. F. (2004). The contribution of epistasis to the architecture of fitness in an RNA virus. Proc Natl Acad Sci U S A 101, 15376-15379.
43. Sanjuán, R., Agudelo-Romero, P. & Elena, S. F. (2009). Upper-limit mutation rate estimation for a plant RNA virus. Biol Lett 5, 394-396.
44. Schneider, W. L. & Roossinck, M. J. (2000). Evolutionarily related Sindbis-like plant viruses maintain different levels of population diversity in a common host. J Virol 74, 3130-3134.
45. Schneider, W. L. & Roossinck, M. J. (2001). Genetic diversity in RNA virus quasispecies is controlled by host-virus interactions. J Virol 75, 6566-6571.
46. Seo, J.-K., Ohshima, K., Lee, H.-G., So, M., Choi, H.-S., Lee, S.-H., Sohn, S.-H. & Kim, K.-H. (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.
47. Smith, D. B., McAllister, J., Casino, C. & Simmonds, P. (1997). Virus quasispecies: making a mountain out of a molehill? J Gen Virol 78, 1511-1519.
48. Tan, Z., Wada, Y., Chen, J. & Ohshima, K. (2004). Inter- and intralineage recombinants are common in natural populations of Turnip mosaic virus. J Gen Virol 85, 2683-2696.
49. Tan, Z., Gibbs, A. J., Tomitaka, Y., Sánchez, F., Ponz, F. & Ohshima, K. (2005). Mutations in Turnip mosaic virus genomes that have adapted to Raphanus sativus. J Gen Virol 86, 501-510.
50. Tomimura, K., Gibbs, A. J., Jenner, C. E., Walsh, J. A. & Ohshima, K. (2003). The phylogeny of Turnip mosaic virus; comparisons of 38 genomic sequences reveal a Eurasian origin and a recent 'emergence' in east Asia. Mol Ecol 12, 2099-2111.
51. Tomimura, K., Špak, J., Katis, N., Jenner, C. E., Walsh, J. A., Gibbs, A. J. & Ohshima, K. (2004). Comparisons of the genetic structure of populations of Turnip mosaic virus in West and East Eurasia. Virology 330, 408-423.
52. 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.
53. Tomitaka, Y., Yamashita, T. & Ohshima, K. (2007). The genetic structure of populations of Turnip mosaic virus in Kyushu and central Honshu, Japan. J Gen Plant Pathol 73, 197-208.
54. Urcuqui-Inchima, S., Haenni, A.-L. & Bernardi, F. (2001). Potyvirus proteins: a wealth of functions. Virus Res 74, 157-175.
55. Wallis, C. M., Stone, A. L., Sherman, D. J., Damsteegt, V. D., Gildow, F. E. & Schneider, W. L. (2007). Adaptation of plum pox virus to a herbaceous host (Pisum sativum) following serial passages. J Gen Virol 88, 2839-2845.
56. Walsh, J. A. & Jenner, C. E. (2002). Turnip mosaic virus and the quest for durable resistance. Mol Plant Pathol 3, 289-300.
57. Wichman, H. A., Badgett, M. R., Scott, L. A., Boulianne, C. M. & Bull, J. J. (1999). Different trajectories of parallel evolution during viral adaptation. Science 285, 422-424.
58. Wichman, H. A., Millstein, J. & Bull, J. J. (2005). Adaptive molecular evolution for 13,000 phage generations: a possible arms race. Genetics 170, 19-31.