Correction: The temporal evolution and global spread of Cauliflower mosaic virus, a plant pararetrovirus (PLoS ONE (2014) 9, 1, (e85641) DOI:10.1371/journal.pone.0085641);The temporal evolution and global spread of Cauliflower mosaic virus, a plant pararetrovirus

PLoS ONE

Volumn 9, Issue 1, 2014, Pages

  Yasaka, Ryosuke ^a   Nguyen, Huy D ^a,b   Ho, Simon Y W ^c   Duchêne, Sebastián ^c   Korkmaz, Savas ^d   Katis, Nikolaos ^e   Takahashi, Hideki ^f   Gibbs, Adrian J ^g   Ohshima, Kazusato ^a,b  

^a SAGA UNIVERSITY   (Japan)

^b KAGOSHIMA UNIVERSITY   (Japan)

^c UNIVERSITY OF SYDNEY   (Australia)

^d ÇANAKKALE ONSEKIZ MART UNIVERSITY   (Turkey)

^e ARISTOTLE UNIVERSITY OF THESSALONIKI   (Greece)

^f TOHOKU UNIVERSITY   (Japan)

^g AUSTRALIAN NATIONAL UNIVERSITY   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

SINGLE STRANDED DNA; VIRUS RNA;

ARTICLE; BRASSICA; BROCCOLI; CABBAGE; CAULIFLOWER; CAULIFLOWER MOSAIC VIRUS; CONTROLLED STUDY; EVOLUTION; GENE FLOW; GENE SEQUENCE; GENETIC RECOMBINATION; GENETIC VARIABILITY; GREECE; HAPLOTYPE; IRAN; JAPAN; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PHYLOGENY; POPULATION GENETICS; RADISH; RAPESEED; TURKEY (REPUBLIC); VIRUS GENOME; VIRUS ISOLATION; VIRUS TRANSMISSION;

ANIMALS; APHIDS; BIOLOGICAL EVOLUTION; BRASSICA; CAULIMOVIRUS; DNA, VIRAL; GENOME, VIRAL; INSECT VECTORS; JAPAN; MEDITERRANEAN REGION; OPEN READING FRAMES; PHYLOGENY; PHYLOGEOGRAPHY; PLANT DISEASES; SPATIO-TEMPORAL ANALYSIS;

EID: 84899549687     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0095410     Document Type: Erratum

References (74)

1. Gibbs AJ, Ohshima K, Phillips MJ, Gibbs MJ (2008) The prehistory of potyviruses: their initial radiation was during the dawn of agriculture. PLoS One 3: e2523.
2. Sacristán S, García-Arenal F (2008) The evolution of virulence and pathogenicity in plant. Mol Plant Pathoz.
3. Gibbs AJ, Ohshima K (2010) Potyviruses and the digital revolution. Annu Rev Phytopathol 48: 205-223.
4. García-Arenal F, Frail A, Malpica JM (2001) Variability and genetic structure of plant virus populations. Annu Rev Phytopathol 39: 157-186. (Pubitemid 32965183)
5. Ohshima K, Akaishi S, Kajiyama H, Koga R, Gibbs AJ (2010) Evolutionary trajectory of turnip mosaic virus populations adapting to a new host. J Gen Virol 91: 788-801.
6. Gibbs AJ, Fargette D, García-Arenal F, Gibbs MJ (2010) Time-the emerging dimension of plant virus studies. J Gen Virol 91: 13-22.
7. Roossinck MJ (1997) Mechanisms of plant virus evolution. Annu Rev Phytopathol 35: 191-209.
8. García-Arenal F, Frail A, Malpica JM (2003) Variation and evolution of plant virus populations. Int Microbiol 6: 225-232. (Pubitemid 37524234)
9. Nguyen HD, Tomitaka Y, Ho SYW, Duchêne S, Vetten H-J, et al. (2013) Turnip mosaic potyvirus probably first spread to Eurasian brassica crops from wild orchids about 1000 years ago. PLoS One 8: e55336.
10. Duffy S, Holmes EC (2008) Phylogenetic evidence for rapid rates of molecular evolution in the single-stranded DNA begomovirus Tomato yellow leaf curl virus. J Virol 82: 957-965.
11. Harkins G, Delport W, Duffy S, Wood N, Monjane A, et al. (2009) Experimental evidence indicating that mastreviruses probably did not codiverge with their hosts. Virol J 6: 104.
12. Lefeuvre P, Martin DP, Harkins G, Lemey P, Gray AJA, et al. (2010) The spread of tomato yellow leaf curl virus from the Middle East to the world. PLoS Pathog 6: e1001164.
13. Monjane AL, Harkins GW, Martin DP, Lemey P, Lefeuvre P, et al. (2011) Reconstructing the history of maize streak virus strain a dispersal to reveal diversification hot spots and its origin in southern Africa. J Virol 85: 9623-9636.
14. Rocha CS, Castillo-Urquiza GP, Lima ATM, Silva FN, Xavier CAD, et al. (2013) Brazilian begomovirus populations are highly recombinant, rapidly evolving, and segregated based on geographical location. J Virol 87: 5784-5799.
15. Rodelo-Urrego M, Pagán I, González-Jara P, Betancourt M, Moreno-Letelier A, et al. (2013) Landscape heterogeneity shapes host-parasite interactions and results in apparent plant-virus codivergence. Mol Ecol 22: 2325-2340.
16. King AMQ, Adams MJ, Carstens EB, Lefkowitz EJ (2012) Virus Taxonomy: Classification and nomenclature of viruses. Ninth report of the International Committee on Taxonomy of Viruses. San Diego: Elsevier/Academic Press. pp. 432-433.
17. Shepherd RJ (1981) CMI/AAB descriptions of plant viruses, no. 243. Commonwealth Mycological Institute, Kew, Surrey, United Kingdom.
18. Franck A, Guilley H, Jonard G, Richards K, Hirth L (1980) Nucleotide sequence of Cauliflower mosaic virus DNA. Cell 21: 285-294.
19. Shockey MW, Gardner CO Jr, Melcher U, Essenberg RC (1980) Polypeptides associated with inclusion bodies from leaves of turnip infected with cauliflower mosaic virus. Virology 105: 575-581. (Pubitemid 10047167)
20. Haas M, Bureau M, Geldreich A, Yot P, Keller M (2002) Cauliflower mosaic virus: still in the news. Mol Plant Pathol 3: 419-429. (Pubitemid 35374662)
21. Harlan JR (1998) Distributions of agricultural origins: A global perspective. In: Damania AB, Valkoun J, Willcox G, Qualset CO, editors. Origins of Agriculture and Crop Domestication. ICARDA, Aleppo, Syria. pp. 1-2.
22. Crisp P (1995) Radish, Raphanus sativus (Cruciferae). In: Smartt J, Simmonds NW, editors. Evolution of Crop Plants. 2nd ed. UK, Harlow: Longman scientific & technical. pp. 86-89.
23. Hemingway JS (1995) Mustards, Brassica spp. and Sinapis alba (Cruciferae). In: Smartt J, Simmonds NW, editors. Evolution of Crop Plants. 2nd ed. UK, Harlow: Longman scientific & technical. pp. 82-86.
24. Hodgkin T (1995) Cabbages, kales, etc. Brassica oleracea (Cruciferae). In: Smartt J, Simmonds NW, editors. Evolution of Crop Plants. 2nd ed. UK, Harlow: Longman scientific & technical. pp. 76-82.
25. MacNaughton IH (1995) Turnip and relatives, Brassica campestris (Cruciferae). In: Smartt J, Simmonds NW, editors. Evolution of Crop Plants. 2nd ed. UK, Harlow: Longman scientific & technical. pp. 62-68.
26. MacNaughton IH (1995) Swedes and rapes, Brassica napus (Cruciferae). In: Smartt J, Simmonds NW, editors. Evolution of Crop Plants. 2nd ed. UK, Harlow: Longman scientific & technical. pp. 68-75.
27. Ohshima K, Yamaguchi Y, Hirota R, Hamamoto T, Tomimura K, et al. (2002) Molecular evolution of Turnip mosaic virus: evidence of host adaptation, genetic recombination and geographical spread. J Gen Virol 83: 1511-1521. (Pubitemid 34591346)
28. Tomimura K, Špak J, Katis N, Jenner CE, Walsh JA, et al. (2004) Comparisons of the genetic structure of populations of Turnip mosaic virus in West and East Eurasia. Virology 330: 408-423. (Pubitemid 39572847)
29. 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. (Pubitemid 44749561)
30. Chenault KD, Melcher U (1994) Phylogenetic relationships reveal recombination among isolates of cauliflower mosaic virus. J Mol Evol 1994: 496-505. (Pubitemid 24346779)
31. Clark MF, Adams AN (1977) Characteristics of the microplate method of enzyme-linked immunosorbent assay for the detection of plant viruses. J Gen Virol 34: 475-483. (Pubitemid 8051946)
32. 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.
33. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947-2948. (Pubitemid 350162903)
34. Martin D, Rybicki E (2000) RDP: detection of recombination amongst aligned sequences. Bioinformatics 16: 562-563.
35. 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. Sawyer website. Available: http://www.math.wustl.edu/sawyer. Accessed 2013 Dec 6.
36. 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.
37. Maynard Smith J (1992) Analyzing the mosaic structure of genes. J Mol Evol 34: 126-129.
38. Posada D, Crandall KA (2001) Evaluation of methods for detecting recombination from DNA sequences: computer simulations. Proc Natl Acad Sci USA 98: 13757-13762. (Pubitemid 33115971)
39. Gibbs MJ, Armstrong JS, Gibbs AJ (2000) Sister-scanning: a Monte Carlo procedure for assessing signals in recombinant sequences. Bioinformatics 16: 573-582.
40. Martin DP, Lemey P, Lott M, Moulton V, Posada D, et al. (2010) RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics 26: 2462-2463.
41. Weiller GF (1998) Phylogenetic profiles: a graphical method for detecting genetic recombinations in homologous sequences. Mol Biol Evol 15: 326-335.
42. Etherington GJ, Dicks J, Roberts IN (2005) Recombination Analysis Tool (RAT): a program for the high-throughput detection of recombination. Bioinformatics 21: 278-281. (Pubitemid 40246598)
43. Huson DH, Bryant D (2006) Application of phylogenetic networks in evolutionary studies. Mol Biol Evol 23: 254-267. (Pubitemid 43100040)
44. Guindon S, Gascuel O (2003) A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood. Syst Biol 52: 696-704. (Pubitemid 37365050)
45. Schliep KP (2011) Phangorn: phylogenetic analysis in R. Bioinformatics 27: 592-593.
46. Luo A, Qiao H, Zhang Y, Shi W, Ho SY, et al. (2010) Performance of criteria for selecting evolutionary models in phylogenetics: a comprehensive study based on simulated datasets. BMC Evol Biol 10: 242.
47. Fourment M, Gibbs MJ (2006) PATRISTIC: a program for calculating patristic distances and graphically comparing the components of genetic change. BMC Evol Biol 6: 1.
48. Lemey P, Rambaut A, Drummond AJ, Suchard MA (2009) Bayesian phylogeography finds its roots. PLoS Comput Biol 5: e1000520.
49. Drummond AJ, Ho SYW, Phillips MJ, Rambaut A (2006) Relaxed phylogenetics and dating with confidence. PLoS Biol 4: e88.
50. Drummond AJ, Pybus OG, Rambaut A, Forsberg R, Rodrigo AG (2003) Measurably evolving populations. Trends Ecol Evol 18: 481-488. (Pubitemid 37007509)
51. Ramsden C, Holmes EC, Charleston MA (2009) Hantavirus evolution in relation to its rodent and insectivore hosts: no evidence for codivergence. Mol Biol Evol 26: 143-153.
52. Firth C, Kitchen A, Shapiro B, Suchard MA, Holmes EC, et al. (2010) Using time-structured data to estimate evolutionary rates of double-stranded DNA viruses. Mol Biol Evol 27: 2038-2051.
53. Suchard MA, Weiss RE, Sinsheimer JS (2001) Bayesian selection of continuous-time Markov chain evolutionary models. Mol Biol Evol 18: 1001-1013. (Pubitemid 32520473)
54. Bielejec F, Rambaut A, Suchard MA, Lemey P (2011) SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics. Bioinformatics 27: 2910-2912.
55. Librado P, Rozas J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451-1452.
56. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731-2739.
57. Hubisz MJ, Falush D, Stephens M, Pritchard JK (2009) Inferring weak population structure with the assistance of sample group information. Mol Ecol Resour 9: 1322-1332.
58. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14: 2611-2620. (Pubitemid 40886055)
59. Hohn T (2013) Plant pararetroviruses: interactions of cauliflower mosaic virus with plants and insects. Curr. Opin. Virol 3: 1-10.
60. Froissart R, Roze D, Uzest M, Galibert L, Blanc S, et al. (2005) Recombination every day: abundant recombination in a virus during a single multi-cellular host infection. PLoS Biol 3: e89.
61. Padidam M, Sawyer S, Fauquet CM (1999) Possible emergence of new geminiviruses by frequent recombination. Virology 265: 218-225. (Pubitemid 30022217)
62. Lefeuvre P, Martin DP, Hoareau M, Naze F, Delatte H, et al. (2007) Begomovirus "melting pot" in the south-west Indian Ocean islands: molecular diversity and evolution through recombination. J Gen Virol 88: 3458-3468. (Pubitemid 350201858)
63. Ohshima K, Tomitaka Y, Wood JT, Minematsu Y, Kajiyama H, et al. (2007) Patterns of recombination in turnip mosaic virus genomic sequences indicate hotspots of recombination. J Gen Virol 88: 298-315. (Pubitemid 46085141)
64. Farzadfar S, Pourrahim R (2013) Biological and molecular variation of Iranian Cauliflower mosaic virus (CaMV) isolates. Virus Genes 47: 347-356.
65. Kobayashi K, Hohn T (2004) The avirulence domain of Cauliflower mosaic virus transactivator/viroplasmin is a determinant of viral virulence in susceptible hosts. Mol Plant-Microbe Interact 17: 475-483. (Pubitemid 38522256)
66. Hapiak M, Li Y, Agama K, Swade S, Okenka G,et al. (2008) Cauliflower mosaic virus gene VI product N-terminus contains regions involved in resistance-breakage, self-association and interactions with movement protein. Virus Res 138: 119-129.
67. Traore O, Sorho F, Pinel A, Abubakar Z, Banwo O, et al. (2005) Processes of diversification and dispersion of Rice yellow mottle virus inferred from large-scale and high-resolution phylogeographical studies. Mol Ecol 14: 2097-2110. (Pubitemid 40772426)
68. Zhang C-L, Gao R, Wang J, Zhang G-M, Li X-D, et al. (2011) Molecular variability of Tobacco vein banding mosaic virus populations. Virus Res 158: 188-198.
69. Katz SH, Weaver WW (2003) Encyclopedia of food and culture 2. Scribner. p. 284.
70. Buck PA (1956) Origin and taxonomy of broccoli. Econ Bot 10: 250-253.
71. Gray AR (1982) Taxonomy and evolution of broccoli (Brassica oleracea var. italica). Econ Bot 36: 397-410.
72. Monsion B, Froissant R, Michalakis Y, Blanc S (2008) Large bottleneck size in Cauliflower mosaic virus populations during host plan colonization. PLoS Pathog 4: e1000174.
73. Gayral P, Blondin L, Guidolin O, Carreel F, Hippolyte I, et al. (2010) Evolution of Endogenous Sequences of Banana Streak Virus: What Can We Learn from Banana (Musa sp.) Evolution? J Virol 84: 7346-7359.
74. Podevin N, du Jardin P (2012) Possible consequences of the overlap between the CaMV 35S promoter regions in plant transformation vectors used and the viral gene VI in transgenic plants. GM Crops and Food: Biotechnology in Agriculture and the Food Chain 3: 296-300.