Application of Motif-Based Tools on Evolutionary Analysis of Multipartite Single-Stranded DNA Viruses

PLoS ONE

Volumn 8, Issue 8, 2013, Pages

  Wang, Hsiang Iu ^a   Chang, Chih Hung ^a   Lin, Po Heng ^a   Fu, Hui Chuan ^c   Tang, ChuanYi ^a,b   Yeh, Hsin Hung ^c  

^a NATIONAL TSING HUA UNIVERSITY   (Taiwan)

^b PROVIDENCE UNIVERSITY   (Taiwan)

^c NATIONAL TAIWAN UNIVERSITY   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

SINGLE STRANDED DNA;

ARTICLE; BABUVIRUS; BIPARTITE BEGOMOVIRUS; DNA RECOMBINATION; DNA VIRUS; FABA BEAN NECROTIC YELLOW VIRUS; GENE REARRANGEMENT; GENE SEQUENCE; GENE STRUCTURE; GOSSYPIUM PUNCTATUM MILD LEAF CURL VIRUS; MATHEMATICAL MODEL; MONOPARTITE BEGOMOVIRUS; MOTIF BASED TOOL; MULTIPARTITE SINGLE STRANDED DNA VIRUS; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; POTATO YELLOW MOSAIC PANAMA VIRUS; PROMOTER REGION; SEQUENCE ALIGNMENT; SWEET POTATO LEAF CURL VIRUS; TOMATO LEAF CURL CHINA VIRUS; TOMATO LEAF CURL HSINCHU VIRUS; TOMATO YELLOW LEAF CURL KANCHANABURI VIRUS; VIRUS GENOME; VIRUS IDENTIFICATION;

DNA VIRUSES; DNA, SINGLE-STRANDED; EVOLUTION, MOLECULAR; GENOMICS; NUCLEOTIDE MOTIFS; PLANTS; RECOMBINATION, GENETIC;

EID: 84881184571     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0071565     Document Type: Article

References (51)

1. Nee S, (1987) The Evolution of Multicompartmental Genomes in Viruses. Journal of Molecular Evolution 25: 277-281.
2. Chao L, (1991) Levels of Selection, Evolution of Sex in Rna Viruses, and the Origin of Life. Journal of Theoretical Biology 153: 229-246.
3. Fu HC, Hu JM, Hung TH, Su HJ, Yeh HH, (2009) Unusual Events Involved in Banana bunchy top virus Strain Evolution. Phytopathology 99: 812-822.
4. Hyder MZ, Shah SH, Hameed S, Naqvi SM, (2011) Evidence of recombination in the Banana bunchy top virus genome. Infect Genet Evol 11: 1293-1300.
5. Stainton D, Kraberger S, Walters M, Wiltshire EJ, Rosario K, et al. (2012) Evidence of inter-component recombination, intra-component recombination and reassortment in banana bunchy top virus. J Gen Virol 93: 1103-1119.
6. Orlich M, Gottwald H, Rott R, (1994) Nonhomologous recombination between the hemagglutinin gene and the nucleoprotein gene of an influenza virus. Virology 204: 462-465.
7. Martin DP, Biagini P, Lefeuvre P, Golden M, Roumagnac P, et al. (2011) Recombination in eukaryotic single stranded DNA viruses. Viruses 3: 1699-1738.
8. Sztuba-Solinska J, Urbanowicz A, Figlerowicz M, Bujarski JJ, (2011) RNA-RNA recombination in plant virus replication and evolution. Annu Rev Phytopathol 49: 415-443.
9. Bruyere A, Wantroba M, Flasinski S, Dzianott A, Bujarski JJ, (2000) Frequent homologous recombination events between molecules of one RNA component in a multipartite RNA virus. J Virol 74: 4214-4219.
10. Lefeuvre P, Lett JM, Varsani A, Martin DP, (2009) Widely conserved recombination patterns among single-stranded DNA viruses. J Virol 83: 2697-2707.
11. Duffy S, Holmes EC, (2008) Phylogenetic evidence for rapid rates of molecular evolution in the single-stranded DNA begomovirus Tomato yellow leaf curl virus. Journal of Virology 82: 957-965.
12. Harkins GW, Martin DP, Duffy S, Monjane AL, Shepherd DN, et al. (2009) Dating the origins of the maize-adapted strain of maize streak virus, MSV-A. J Gen Virol 90: 3066-3074.
13. Grigoras I, Timchenko T, Grande-Perez A, Katul L, Vetten HJ, et al. (2010) High variability and rapid evolution of a nanovirus. J Virol 84: 9105-9117.
14. Roossinck MJ, (1997) Mechanisms of plant virus evolution. Annu Rev Phytopathol 35: 191-209.
15. Posada D, (2002) Evaluation of methods for detecting recombination from DNA sequences: Empirical data. Molecular Biology and Evolution 19: 708-717.
16. Posada D, Crandall KA, (2002) The effect of recombination on the accuracy of phylogeny estimation. Journal of Molecular Evolution 54: 396-402.
17. Sankoff D, Cedergren R, Abel Y, (1990) Genomic Divergence through Gene Rearrangement. Methods in Enzymology 183: 428-438.
18. Sankoff D, (1992) Edit Distance for Genome Comparison Based on Nonlocal Operations. Lecture Notes in Computer Science 644: 121-135.
19. Lin YC, Lu CL, Chang HY, Tang CY, (2005) An efficient algorithm for sorting by block-interchanges and its application to the evolution of vibrio species. J Comput Biol 12: 102-112.
20. Das MK, Dai HK, (2007) A survey of DNA motif finding algorithms. BMC Bioinformatics 8 Suppl 7: S21.
21. Albuquerque LC, Inoue-Nagata AK, Pinheiro B, Resende RO, Moriones E, et al. (2012) Genetic diversity and recombination analysis of sweepoviruses from Brazil. Virol J 9: 241.
22. Martin DP, Posada D, Crandall KA, Williamson C, (2005) A modified bootscan algorithm for automated identification of recombinant sequences and recombination breakpoints. AIDS Res Hum Retroviruses 21: 98-102.
23. Posada D, Crandall KA, (2001) Evaluation of methods for detecting recombination from DNA sequences: computer simulations. Proc Natl Acad Sci U S A 98: 13757-13762.
24. Padidam M, Sawyer S, Fauquet CM, (1999) Possible emergence of new geminiviruses by frequent recombination. Virology 265: 218-225.
25. Smith JM, (1992) Analyzing the mosaic structure of genes. J Mol Evol 34: 126-129.
26. Martin D, Rybicki E, (2000) RDP: detection of recombination amongst aligned sequences. Bioinformatics 16: 562-563.
27. Gibbs MJ, Armstrong JS, Gibbs AJ, (2000) Sister-scanning: a Monte Carlo procedure for assessing signals in recombinant sequences. Bioinformatics 16: 573-582.
28. Boni MF, Posada D, Feldman MW, (2007) An exact nonparametric method for inferring mosaic structure in sequence triplets. Genetics 176: 1035-1047.
29. 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.
30. Bailey TL, Williams N, Misleh C, Li WW, (2006) MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Research 34: W369-W373.
31. Bailey TL, Boden M, Buske FA, Frith M, Grant CE, et al. (2009) MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res 37: W202-208.
32. Tao X, Zhou X, (2008) Pathogenicity of a naturally occurring recombinant DNA satellite associated with tomato yellow leaf curl China virus. J Gen Virol 89: 306-311.
33. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL, (2008) GenBank. Nucleic Acids Research 36: D25-D30.
34. Gronenborn B, (2004) Nanoviruses: genome organisation and protein function. Vet Microbiol 98: 103-109.
35. Burns TM, Harding RM, Dale JL, (1995) The Genome Organization of Banana Bunchy Top Virus- Analysis of 6 Ssdna Components. Journal of General Virology 76: 1471-1482.
36. Harding RM, Burns TM, Hafner G, Dietzgen RG, Dale JL, (1993) Nucleotide sequence of one component of the banana bunchy top virus genome contains a putative replicase gene. J Gen Virol 74 (Pt 3) (): 323-328.
37. Niu S, Wang B, Guo X, Yu J, Wang X, et al. (2009) Identification of two RNA silencing suppressors from banana bunchy top virus. Arch Virol 154: 1775-1783.
38. Horser C, Harding R, Dale J, (2001) Banana bunchy top nanovirus DNA-1 encodes the 'master' replication initiation protein. J Gen Virol 82: 459-464.
39. Hafner GJ, Stafford MR, Wolter LC, Harding RM, Dale JL, (1997) Nicking and joining activity of banana bunchy top virus replication protein in vitro. J Gen Virol 78 (Pt 7) (): 1795-1799.
40. Hanley-Bowdoin L, Settlage SB, Orozco BM, Nagar S, Robertson D, (2000) Geminiviruses: models for plant DNA replication, transcription, and cell cycle regulation. Crit Rev Biochem Mol Biol 35: 105-140.
41. Karan M, Harding RM, Dale JL, (1994) Evidence for two groups of banana bunchy top virus isolates. J Gen Virol 75 (Pt 12) (): 3541-3546.
42. Hu JM, Fu HC, Lin CH, Su HJ, Yeh HH, (2007) Reassortment and concerted evolution in Banana bunchy top virus genomes. Journal of Virology 81: 1746-1761.
43. Lin YC, Lu CL, Liu YC, Tang CY, (2006) SPRING: a tool for the analysis of genome rearrangement using reversals and block-interchanges. Nucleic Acids Research 34: W696-W699.
44. 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.
45. Tamura K, Dudley J, Nei M, Kumar S, (2007) MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Molecular Biology and Evolution 24: 1596-1599.
46. 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.
47. Swofford DL, (1993) Paup- a Computer-Program for Phylogenetic Inference Using Maximum Parsimony. Journal of General Physiology 102: A9-A9.
48. Bailey TL, Elkan C, (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 2: 28-36.
49. Bailey TL, Gribskov M, (1998) Methods and statistics for combining motif match scores. Journal of Computational Biology 5: 211-221.
50. Bailey TL, Gribskov M, (1998) Combining evidence using p-values: application to sequence homology searches. Bioinformatics 14: 48-54.
51. Hamming RW, (1950) Error Detecting and Error Correcting Codes. Bell System Technical Journal 29: 147-160.