Long-term evolution of the Luteoviridae: Time scale and mode of virus speciation

Journal of Virology

Volumn 84, Issue 12, 2010, Pages 6177-6187

  Pagán, Israel ^a   Holmes, Edward C ^a,b  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

^b NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COAT PROTEIN;

ARTICLE; GENETIC ANALYSIS; GENETIC VARIABILITY; LUTEOVIRIDAE; MOLECULAR CLOCK; MOLECULAR EVOLUTION; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PRIORITY JOURNAL; VIRUS DETECTION; VIRUS RECOMBINATION;

CAPSID PROTEINS; EVOLUTION, MOLECULAR; GENETIC SPECIATION; GENETIC VARIATION; LUTEOVIRIDAE; MOLECULAR SEQUENCE DATA; PHYLOGENY;

ANIMALIA; LUTEOVIRIDAE; RNA VIRUSES;

EID: 77952709019     PISSN: 0022538X     EISSN: None     Source Type: Journal    
DOI: 10.1128/JVI.02160-09     Document Type: Article

References (78)

1. Barrell, B. G., G. M. Air, and C. A. Hutchison III. 1976. Overlapping genes in bacteriophage X174. Nature 264:34-41.
2. Belshaw, R., O. G. Pybus, and A. Rambaut. 2007. The evolution of genome compression and genomic novelty in RNA viruses. Genome Res. 17:1496-1504. (Pubitemid 47529434)
3. Beuve, M., M. Stevens, H.-Y. Liu, W. M. Witermantel, S. Hauser, and O. Lemaire. 2008. Biological and molecular characterization of an American sugar beet-infecting Beet western yellows virus isolate. Plant Dis. 92:51-60.
4. Blok, J., A. Mackenzie, P. Guy, and A. Gibbs. 1987. Nucleotide sequence comparisons of Turnip yellow mosaic virus isolates from Australia and Europe. Arch. Virol. 97:283-295.
5. Botstein, D. 1980. A theory of modular evolution for bacteriophages. Ann. N. Y. Acad. Sci. 354:484-491.
6. Brault, V., S. Périgon, C. Reinbold, M. Erdinger, D. Scheidecker, E. Herrbach, K. Richards, and V. Ziegler-Graff. 2005. The polerovirus minor capsid protein determines vector specificity and intestinal tropism in the aphid. J. Virol. 79:9685-9693. (Pubitemid 41022311)
7. Chay, C. A., U. B. Gunasinge, S. P. Dinesh-Kumar, W. A. Miller, and S. M. Gray. 1996. Aphid transmission and systemic plant infection determinants of Barley yellow dwarf Luteovirus-PAV are contained in the coat protein readthrough domain and 17-kDa protein, respectively. Virology 219:57-65.
8. Cornish, P. V., M. Hennig, and D. P. Giedroc. 2005. A loop 2 cytidine-stem 1 minor groove interaction as a positive determinant for pseudoknot-stimulated -1 ribosomal frameshifting. Proc. Natl. Acad. Sci. U. S. A. 102:12694-12699.
9. Dolja, V. V., and J. C. Carrington. 1992. Evolution of positive-strand RNA viruses. Semin. Virol. 3:315-326.
10. Drake, J. W., B. Charlesworth, D. Charlesworth, and J. F. Crow. 1998. Rates of spontaneous mutation. Genetics 148:1667-1686.
11. Drummond, A. J., and A. Rambaut. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7:214.
12. Drummond, A. J., S. Y. W. Ho, M. J. Phillips, and A. Rambaut. 2006. Relaxed phylogenetics and dating with confidence. PLoS Biol. 4:e88.
13. Duffy, S., L. A. Shackelton, and E. C. Holmes. 2008. Rates of evolutionary change in viruses: patterns and determinants. Nat. Rev. Genet. 9:267-276.
14. Edgar, R. C. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32:1792-1797. (Pubitemid 38832724)
15. Elena, S. F., P. Agudelo-Romero, P. Carrasco, F. M. Codoner, S. Martin, C. Torres-Barcelo, and R. Sanjuán. 2008. Experimental evolution of plant RNA viruses. Heredity 100:478-483.
16. Elena, S. F., and R. Sanjuán. 2005. Adaptive value of high mutation rates of RNA viruses: separating causes from consequences. J. Virol. 79:11555-11558.
17. Fargette, D., A. Pinel-Galzi, D. Sereme, S. Lacombe, E. Hebrard, O. Traore, and G. Konate. 2008. Diversification of Rice yellow mottle virus and related viruses spans the history of agriculture from the Neolithic to the present. PLoS Pathog. 4:e1000125.
18. Fauquet, C. M., M. A. Mayo, J. Maniloff, U. Desselberger, and B. A. Ball. 2005. Virus taxonomy: classification and nomenclature of viruses. 8th report of the International Committee on the Taxonomy of Viruses. Elsevier-Academic Press, San Diego, CA.
19. Fitch, W. N. 1971. Toward defining the course of evolution: minimal change for a specific tree topology. Syst. Zool. 20:406-416.
20. García-Arenal, F., and B. A. McDonald. 2003. An analysis of the durability of resistance to plant viruses. Phytopathology 93:941-952. (Pubitemid 36953347)
21. Gibbs, A. J. 1980. How ancient are the tobamoviruses? Intervirology 14:101-108.
22. Gibbs, A. J., D. Fargette, F. Garcia-Arenal, and M. J. Gibbs. 2010. Time - the emerging dimension of plant virus studies. J. Gen. Virol. 91:13-22.
23. Gibbs, A. J., J. Blok, D. J. Coates, P. L. Guy, A. Mackenzie, and N. Pigram. 1986. Turnip yellow mosaic virus in an endemic Australian alpine Cardamine, p. 289-300. In B. A. Barlow (ed.), Flora and fauna of alpine Australasia; ages and origins. CSIRO, Collingwood, Victoria, Australia.
24. Gibbs, A. J., K. Ohshima, M. J. Phillips, and M. J. Gibbs. 2008. The prehistory of potyviruses: their initial radiation was during the dawn of agriculture. PLoS One 3:e2523.
25. Gibbs, A. J., M. J. Gibbs, K. Ohshima, and F. Garcia-Arenal. 2008. More plant virus evolution; past present and future, p. 229-250. In E. Domingo, C. R. Parrish and J. J. Holland (ed.), Origin and evolution of viruses, 2nd ed. Academic Press, London, United Kingdom.
26. Gibbs, M. J. 1995. The luteovirus supergroup: rampant recombination and persistent partnerships, p. 351-368. In A. Gibbs, C. H. Calisher, and F. García-Arenal (ed.), Molecular basis of virus evolution. Cambridge University Press, Cambridge, United Kingdom.
27. Gray, S., and F. E. Gildow. 2003. Luteovirus-aphid interactions. Annu. Rev. Phytopathol. 41:539-566.
28. Guyader, S., and D. G. Ducray. 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.
29. Hanada, K., Y. Suzuki, and T. Gojobori. 2004. A large variation in the rates of synonymous substitution for RNA viruses and its relationship to a diversity of viral infection and transmission modes. Mol. Biol. Evol. 21:1074-1080.
30. Hasegawa, M., H. Kishino, and T. Yano. 1985. Dating the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22:160-174.
31. Holmes, E. C. 2003. Patterns of intra- and inter-host nonsynonymous variation reveal strong purifying selection in dengue virus. J. Virol. 77:11296-11298.
32. Holmes, E. C. 2003. Molecular clocks and the puzzle of RNA virus origins. J. Virol. 77:3893-3897. (Pubitemid 36350930)
33. Holmes, E. C. 2003. Error thresholds and the constraints to RNA virus evolution. Trends Microbiol. 11:543-546. (Pubitemid 37500904)
34. Holmes, E. C. 2009. The evolution and emergence of RNA viruses. Oxford University Press, Oxford, United Kingdom.
35. Hughes, A. L., K. Westover, J. da Silva, D. H. O'Connor, and D. I. Watkins. 2001. Simultaneous positive and purifying selection on overlapping reading frames of the tat and vpr genes of simian immunodeficiency virus. J. Virol. 75:7966-7972.
36. Hughes, A. L., and M. A. Hughes. 2005. Patterns of nucleotide difference in overlapping and non-overlapping reading frames of papillomavirus genomes. Virus Res. 113:81-88.
37. Jenkins, G. M., A. Rambaut, O. G. Pybus, and E. C. Holmes. 2002. Rates of molecular evolution in RNA viruses: a quantitative phylogenetic analysis. J. Mol. Evol. 54:156-165.
38. Jin, Z., X. Wang, S. Chang, and G. Zhou. 2004. The complete nucleotide sequence and its organization of the genome of Barley yellow dwarf virus-GAV. Sci. China C Life Sci. 47:175-182.
39. Jordan, I. K., B. A. Sutter IV, and M. A. McClure. 2000. Molecular evolution of the Paramyxoviridae and Rhabdoviridae multiple-protein-encoding P gene. Mol. Biol. Evol. 17:75-86.
40. Kosakovsky Pond, S. L., and S. D. W. Frost. 2005. Datamonkey: rapid detection of selective pressure on individual sites of codon alignments. Bioinformatics 21:2531-2533.
41. Krakauer, D. C. 2000. Stability and evolution of overlapping genes. Evolution 54:731-739.
42. Krakauer, D. C., and J. B. Plotkin. 2002. Redundancy, antiredundancy, and the robustness of genomes. Proc. Natl. Acad. Sci. U. S. A. 99:1405-1409.
43. Malmstrom, C., R. Shu, E. W. Linton, L. A. Newton, and M. Cook. 2007. Barley yellow dwarf viruses (BYDVs) preserved in herbarium specimens illuminate historical disease ecology of invasive and native grasses. J. Ecol. 95:1153-1166. (Pubitemid 47620390)
44. Mangwende, T., M.-L. Wang, W. Borth, J. Hu, P. H. Moore, E. T. Mirkov, and H. H. Albert. 2009. The P0 gene of Sugarcane yellow leaf virus encodes an RNA silencing suppressor with unique activities. Virology 384:38-50.
45. Martin, D. P., C. Williamson, and D. Posada. 2005. RDP2: recombination detection and analysis from sequence alignments. Bioinformatics 21:260-262. (Pubitemid 40202028)
46. Martin, R. R., P. K. Keese, M. J. Young, P. M. Waterhouse, and W. L. Gerlach. 1990. Evolution and molecular biology of luteoviruses. Annu. Rev. Phytopathol. 28:341-363.
47. McDonald, B. A., and C. Linde. 2002. The population genetics of plant pathogens and breeding strategies for durable resistance. Euphytica 124:163-180. (Pubitemid 34623075)
48. Miller, W. A., and L. Rasochova. 1997. Barley yellow dwarf viruses. Annu. Rev. Phytopathol. 35:167-190.
49. Miller, W. A., S. Liu, and R. Beckett. 2002. Barley yellow dwarf virus: Luteoviridae or Tombusviridae? Mol. Plant Pathol. 3:177-183.
50. Miyata, T., and T. Yasunaga. 1978. Evolution of overlapping genes. Nature 272:532-535.
51. Moonan, F., J. Molina, and T. E. Mirkov. 2000. Sugarcane yellow leaf virus: an emerging virus that has evolved by recombination between luteoviral and poleroviral ancestors. Virology 269:156-171.
52. Moonan, F., and T. E. Mirkov. 2002. Analyses of genotypic diversity among North, South, and Central American isolates of Sugarcane yellow leaf virus: evidence for Colombian origins and for intraspecific spatial phylogenetic variation. J. Virol. 76:1339-1348.
53. Moya, A., E. C. Holmes, and F. González-Candelas. 2004. The population genetics and evolutionary epidemiology of RNA viruses. Nat. Rev. Microbiol. 2:279-288.
54. Parker, J., A. Rambaut, and O. G. Pybus. 2008. Correlating viral phenotypes with phylogeny: accounting for phylogenetic uncertainty. Infect. Genet. Evol. 8:239-246.
55. Pavesi, A. 2006. Origin and evolution of overlapping genes in the family Microviridae. J. Gen. Virol. 87:1013-1017.
56. Pazhouhandeh, M., M. Dieterle, K. Marrocco, E. Lechner, B. Berry, V. Brault, O. Hemmer, T. Kretsch, K. E. Richards, P. Genschik, and V. Zieger-Graff. 2006. F-box-like domain in the Polerovirus protein P0 is required for silencing suppressor function. Proc. Natl. Acad. Sci. U. S. A. 103:1994-1999.
57. Peter, K. A., D. Liang, P. Palukaitis, and S. M. Gray. 2008. Small deletions in the Potato leafroll virus readthrough protein affect particle morphology, aphid transmission, virus movement and accumulation. J. Gen. Virol. 89(Pt. 8):2037-2045.
58. Peter, K. A., F. Gildow, P. Palukaitis, and S. M. Gray. 2009. The C terminus of the polerovirus P5 readthrough domain limits virus infection to the phloem. J. Virol. 83:5419-5429.
59. Pfeffer, S., P. Dunoyer, F. Heim, K. E. Richards, G. Jonard, and V. Ziegler-Graff. 2002. P0 of Beet western yellow virus is a suppressor of posttranscriptional gene silencing. J. Virol. 76:6815-6824.
60. Posada, D., and K. A. Crandall. 1998. Modeltest: testing the model of DNA substitution. Bioinformatics 14:817-818. (Pubitemid 28552116)
61. Ranjith-Kumar, C. T., K. Gopinath, A. N. K. Jacob, V. Svrividhya, P. Elango, and S. H. Savithri. 1998. Genomic sequence of Physalis mottle virus and its evolutionary relationship with other tymoviruses. Arch. Virol. 143:1489-1500.
62. Robertson, N. L., and R. French. 2007. Genetic structure in natural populations of barley/cereal yellow dwarf virus isolates from Alaska. Arch. Virol. 152:891-902.
63. Roossinck, M., and A. Ali. 2007. Mechanisms of plant virus evolution and identification of genetic bottlenecks: impact on disease management, p. 109-124. In Z. K. Punja, S. H. De Boer, and S. Sanfaçon (ed.), Biotechnology and plant disease management. CABI Publishing, Wallingford, United Kingdom.
64. Sadowy, E., M. Juszczuk, C. David, B. Gronenborn, and M. D. Hulanicka. 2001. Mutational analysis of the proteinase function of Potato leafroll virus. J. Gen. Virol. 82:1517-1527.
65. Sanjuán, R., P. Agudelo-Romero, and S. F. Elena. 2009. Upper-limit mutation rate estimation for plant RNA virus. Biol. Lett. 5:394-396.
66. Schierup, M. H., and J. Hein. 2000. Recombination and the molecular clock. Mol. Biol. Evol. 17:1578-1579.
67. Schluter, D. 2001. Ecology and the origin of species. Trends Ecol. Evol. 16:372-380.
68. Simmonds, P., and D. B. Smith. 1999. Structural constraints on RNA virus evolution. J. Virol. 73:5787-5794. (Pubitemid 29274865)
69. Simmons, H. E., E. C. Holmes, and A. G. Stephenson. 2008. Rapid evolutionary dynamics of Zucchini yellow mosaic virus. J. Gen. Virol. 89:1081-1085.
70. Smith, H. G., and H. Barker. 1999. The Luteoviridae. CABI Publishing, Wallingford, United Kingdom.
71. Stevens, M., B. Freeman, H.-Y. Liu, E. Herrbach, and O. Lemaire. 2005. Beet polerovirus: close friends or distant relatives? Mol. Plant Pathol. 6:1-9. (Pubitemid 40256951)
72. Terauchi, H., K. Honda, N. Yamagishi, S. Kanematsu, K. Ishiguro, and S. Hidaka. 2003. The N-terminal region of the readthrough domain is closely related to aphid vector specificity of Soybean dwarf virus. Phytopathology 93:1560-1564. (Pubitemid 37481672)
73. van der Wilk, F., M. Verbeek, A. M. Dullemans, and J. F. van den Heuvel. 1997. The genome-linked protein of Potato leafroll virus is located downstream of the putative protease domain of the ORF1 product. Virology 234:300-303.
74. Viswanathan, R., M. Balamuralikrishnan, and R. Karuppaiah. 2008. Identification of three genotypes of Sugarcane yellow leaf virus causing yellow leaf disease from India and their molecular characterization. Virus Genes 37:368-379.
75. Wang, T. H., Y. K. Donaldson, R. P. Brettle, J. E. Bell, and P. Simmonds. 2001. Identification of shared populations of human immunodeficiency virus type 1 infecting microglia and tissue macrophages outside the central nervous system. J. Virol. 75:11686-11699.
76. Whelan, S., and N. Goldman. 2001. A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol. Biol. Evol. 18:691-699.
77. Zaaijer, H. L., F. J. van Hemert, M. H. Koppelman, and V. V. Lukashov. 2007. Independent evolution of overlapping polymerase and surface protein genes of hepatitis B virus. J. Gen. Virol. 88:2137-2143.
78. Zhao, X., K. M. McGirr, and G. C. Buehring. 2007. Potential evolutionary influences on overlapping reading frames in the bovine leukemia virus pXBL region. Genomics 89:502-511. (Pubitemid 46413670)