Recombination in eukaryotic single stranded DNA viruses

Viruses

Volumn 3, Issue 9, 2011, Pages 1699-1738

  Martin, Darren P ^a   Biagini, Philippe ^b   Lefeuvre, Pierre ^c   Golden, Michael ^a   Roumagnac, Philippe ^d   Varsani, Arvind ^a,e  

^a UNIVERSITY OF CAPE TOWN   (South Africa)

^b CNRS   (France)

^c UNIVERSITÉ DE LA RÉUNION   (France)

^d CIRAD   (France)

^e UNIVERSITY OF CANTERBURY   (New Zealand)

Author keywords

Anellovirus; Circovirus; Geminivirus; Nanovirus; Parvovirus

Indexed keywords

SINGLE STRANDED DNA; VIRUS PROTEIN;

DNA REPLICATION; DNA REPLICATION ORIGIN; DNA STRUCTURE; DNA TRANSCRIPTION; DNA VIRUS; EUKARYOTE; EVOLUTIONARY ADAPTATION; EVOLUTIONARY HOMOLOGY; GENE INTERACTION; GENETIC EPIDEMIOLOGY; GENETIC RECOMBINATION; GENOME ANALYSIS; GEOGRAPHIC DISTRIBUTION; HOMOLOGOUS RECOMBINATION; HOST RANGE; METAGENOMICS; MINICHROMOSOME; NONHUMAN; OLIGOMERIZATION; PHYLOGENETIC TREE; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; REVIEW; SEQUENCE HOMOLOGY; VIRAL TROPISM; VIRUS GENE; VIRUS GENOME; VIRUS INFECTIVITY; VIRUS RECOMBINATION; VIRUS REPLICATION;

ANELLOVIRUS; CIRCOVIRUS; GEMINIVIRUS; NANOVIRUS; PARVOVIRUS;

ANIMALS; DNA VIRUSES; DNA, SINGLE-STRANDED; DNA, VIRAL; EUKARYOTA; EVOLUTION, MOLECULAR; GENETIC VARIATION; GENOME, VIRAL; HUMANS; PLANTS; RECOMBINATION, GENETIC; SELECTION, GENETIC;

ANELLOVIRUS; ANIMALIA; ARTHROPODA; CIRCOVIRUS; DNA VIRUSES; EUKARYOTA; GEMINIVIRIDAE; NANOVIRUS; PARVOVIRUS; SSDNA VIRUSES;

EID: 80053361715     PISSN: None     EISSN: 19994915     Source Type: Journal    
DOI: 10.3390/v3091699     Document Type: Review

References (257)

1. Blinkova, O.; Rosario, K.; Li, L.; Kapoor, A.; Slikas, B.; Bernardin, F.; Breitbart, M.; Delwart, E. Frequent detection of highly diverse variants of cardiovirus, cosavirus, bocavirus, and circovirus in sewage samples collected in the united states. J. Clin. Microbiol. 2009, 47, 3507-3513.
2. Blinkova, O.; Victoria, J.; Li, Y.Y.; Keele, B.F.; Sanz, C.; Ndjango, J.B.N.; Peeters, M.; Travis, D.; Lonsdorf, E.V.; Wilson, M.L., et al. Novel circular DNA viruses in stool samples of wild-living chimpanzees. J. Gen. Virol. 2010, 91, 74-86.
3. Kim, K.H.; Chang, H.W.; Nam, Y.D.; Roh, S.W.; Kim, M.S.; Sung, Y.; Jeon, C.O.; Oh, H.M.; Bae, J.W. Amplification of uncultured single-stranded DNA viruses from rice paddy soil. Appl. Environ. Microbiol. 2008, 74, 5975-5985.
4. Krupovic, M.; Ravantti, J.J.; Bamford, D.H. Geminiviruses: A tale of a plasmid becoming a virus. BMC Evol. Biol. 2009, 9, 112.
5. Lopez-Bueno, A.; Tamames, J.; Velazquez, D.; Moya, A.; Quesada, A.; Alcami, A. High diversity of the viral community from an antarctic lake. Science 2009, 326, 858-861.
6. Yu, X.; Li, B.; Fu, Y.P.; Jiang, D.H.; Ghabrial, S.A.; Li, G.Q.; Peng, Y.L.; Xie, J.T.; Cheng, J.S.; Huang, J.B., et al. A geminivirus-related DNA mycovirus that confers hypovirulence to a plant pathogenic fungus. Proc. Natl. Acad. Sci. U. S. A. 2010, 107, 8387-8392.
7. Rosario, K.; Duffy, S.; Breitbart, M. Diverse circovirus-like genome architectures revealed by environmental metagenomics. J. Gen. Virol. 2009, 90, 2418-2424.
8. Nishigawa, H.; Oshima, K.; Kakizawa, S.; Jung, H.; Kuboyama, T.; Miyata, S.; Ugaki, M.; Namba, S. Evidence of intermolecular recombination between extrachromosomal dnas in phytoplasma: A trigger for the biological diversity of phytoplasma? Microbiology 2002, 148, 1389-1396.
9. Campos-Olivas, R.; Louis, J.M.; Clerot, D.; Gronenborn, B.; Gronenborn, A.M. The structure of a replication initiator unites diverse aspects of nucleic acid metabolism. Proc. Natl. Acad. Sci. U. S. A. 2002, 99, 10310-10315.
10. Koonin, E.V.; Ilyina, T.V. Geminivirus replication proteins are related to prokaryotic plasmid rolling circle DNA-replication initiator proteins. J. Gen. Virol. 1992, 73, 2763-2766.
11. Ilyina, T.V.; Koonin, E.V. Conserved sequence motifs in the initiator proteins for rolling circle DNA replication encoded by diverse replicons from eubacteria, eucaryotes and archaebacteria. Nucleic Acids Res. 1992, 20, 3279-3285.
12. Londono, A.; Riego-Ruiz, L.; Arguello-Astorga, G.R. DNA-binding specificity determinants of replication proteins encoded by eukaryotic ssdna viruses are adjacent to widely separated rcr conserved motifs. Arch. Virol. 2010, 155, 1033-1046.
13. Koonin, E.V. On the origin of cells and viruses primordial virus world scenario. Ann. NY Acad. Sci. 2009, 1178, 47-64.
14. Koonin, E.V.; Senkevich, T.G.; Dolja, V.V. The ancient virus world and evolution of cells. Biol. Direct 2006, 1, 29.
15. Shackelton, L.A.; Holmes, E.C. Phylogenetic evidence for the rapid evolution of human b19 erythrovirus. J. Virol. 2006, 80, 3666-3669.
16. Duffy, S.; Holmes, E.C. Phylogenetic evidence for rapid rates of molecular evolution in the single-stranded DNA begomovirus tomato yellow leaf curl virus. J. Virol. 2008, 82, 957-965.
17. Gallian, P.; Biagini, P.; Attoui, H.; Cantaloube, J.F.; Dussol, B.; Berland, Y.; de Micco, P.; de Lamballerie, X. High genetic diversity revealed by the study of tlmv infection in french hemodialysis patients. J. Med. Virol. 2002, 67, 630-635.
18. Ge, L.M.; Zhang, J.T.; Zhou, X.P.; Li, H.Y. Genetic structure and population variability of tomato yellow leaf curl china virus. J. Virol. 2007, 81, 5902-5907.
19. Grigoras, I.; Timchenko, T.; Grande-Perez, A.; Katul, L.; Vetten, H.J.; Gronenborn, B. High variability and rapid evolution of a nanovirus. J. Virol. 2010, 84, 9105-9117.
20. Isnard, M.; Granier, M.; Frutos, R.; Reynaud, B.; Peterschmitt, M. Quasispecies nature of three maize streak virus isolates obtained through different modes of selection from a population used to assess response to infection of maize cultivars. J. Gen. Virol. 1998, 79, 3091-3099.
21. van der Walt, E.; Rybicki, E.P.; Varsani, A.; Polston, J.E.; Billharz, R.; Donaldson, L.; Monjane, A.L.; Martin, D.P. Rapid host adaptation by extensive recombination. J. Gen. Virol. 2009, 90, 734-746.
22. Raney, J.L.; Delongchamp, R.R.; Valentine, C.R. Spontaneous mutant frequency and mutation spectrum for gene a of phi x174 grown in E. coli. Environ. Mol. Mutagen. 2004, 44, 119-127.
23. Drake, J.W. A constant rate of spontaneous mutation in DNA-based microbes. Proc. Natl. Acad. Sci. U. S. A. 1991, 88, 7160-7164.
24. Shackelton, L.A.; Parrish, C.R.; Truyen, U.; Holmes, E.C. High rate of viral evolution associated with the emergence of carnivore parvovirus. Proc. Natl. Acad. Sci. U. S. A. 2005, 102, 379-384.
25. Gibbs, M.J.; Weiller, G.F. Evidence that a plant virus switched hosts to infect a vertebrate and then recombined with a vertebrate-infecting virus. Proc. Natl. Acad. Sci. U. S. A. 1999, 96, 8022-8027.
26. Suchard, M.A.R., B. D. Bali-phy: Simultaneous bayesian inference of alignment and phylogeny. Bioinformatics 2006, 22, 2047-2048.
27. Saccardo, F.; Cettul, E; Palmano, S; Noris, E; Firrao, G. On the alleged origin of geminiviruses from extrachromosomal DNAs of phytoplasmas. BMC Evol. Biol. 2011, 11, 185.
28. Gibbs, M.J.; Smeianov, V.V.; Steele, J.L.; Upcroft, P.; Efimov, B.A. Two families of rep-like genes that probably originated by interspecies recombination are represented in viral, plasmid, bacterial, and parasitic protozoan genomes. Mol. Biol. Evol. 2006, 23, 1097-1100.
29. Klute, K.A.; Nadler, S.A.; Stenger, D.C. Horseradish curly top virus is a distinct subgroup ii geminivirus species with rep and c4 genes derived from a subgroup iii ancestor. J. Gen. Virol. 1996, 77, 1369-1378.
30. Briddon, R.W.; Bedford, I.D.; Tsai, J.H.; Markham, P.G. Analysis of the nucleotide sequence of the treehopper-transmitted geminivirus, tomato pseudo-curly top virus, suggests a recombinant origin. Virology 1996, 219, 387-394.
31. Varsani, A.; Shepherd, D.N.; Dent, K.; Monjane, A.L.; Rybicki, E.P.; Martin, D.P. A highly divergent south african geminivirus species illuminates the ancient evolutionary history of this family. Virol. J. 2009, 6, 36.
32. Yazdi, H.R.B.; Heydarnejad, J.; Massumi, H. Genome characterization and genetic diversity of beet curly top iran virus: A geminivirus with a novel nonanucleotide. Virus Genes 2008, 36, 539-545.
33. Zhou, X.P.; Liu, Y.L.; Calvert, L.; Munoz, C.; OtimNape, G.W.; Robinson, D.J.; Harrison, B.D. Evidence that DNA-a of a geminivirus associated with severe cassava mosaic disease in uganda has arisen by interspecific recombination. J. Gen. Virol. 1997, 78, 2101-2111.
34. Zhou, X.P.; Liu, Y.L.; Robinson, D.J.; Harrison, B.D. Four DNA-a variants among pakistani isolates of cotton leaf curl virus and their affinities to DNA-a of geminivirus isolates from okra. J. Gen. Virol. 1998, 79, 915-923.
35. Fondong, V.N.; Pita, J.S.; Rey, M.E.C.; de Kochko, A.; Beachy, R.N.; Fauquet, C.M. Evidence of synergism between african cassava mosaic virus and a new double-recombinant geminivirus infecting cassava in cameroon. J. Gen. Virol. 2000, 81, 287-297.
36. Padidam, M.; Sawyer, S.; Fauquet, C.M. Possible emergence of new geminiviruses by frequent recombination. Virology 1999, 265, 218-225.
37. Varsani, A.; Regnard, G.L.; Bragg, R.; Hitzeroth, II; Rybicki, E.P. Global genetic diversity and geographical and host-species distribution of beak and feather disease virus isolates. J. Gen. Virol. 2011, 92, 752-767.
38. Heath, L.; Martin, D.P.; Warburton, L.; Perrin, M.; Horsfield, W.; Kingsley, C.; Rybicki, E.P.; Williamson, A.L. Evidence of unique genotypes of beak and feather disease virus in southern Africa. J. Virol. 2004, 78, 9277-9284.
39. Rosario, K.; Marinov, M.; Stainton, D.; Kraberger, S.; Wiltshire, E.J.; Collings, D.A.; Walters, M.; Martin, D.P.; Breitbart, M.; Varsani, A. Dragonfly cyclovirus, a novel single-stranded DNA virus discovered in dragonflies (odonata: Anisoptera). J. Gen. Virol. 92, 1302-1308.
40. Lefeuvre, P.; Lett, J.M.; Varsani, A.; Martin, D.P. Widely conserved recombination patterns among single-stranded DNA viruses. J. Virol. 2009, 83, 2697-2707.
41. Hesse, R.; Kerrigan, M.; Rowland, R.R. Evidence for recombination between PCV2a and PCV2b in the field. Virus Res. 2008, 132, 201-207.
42. Cheung, A.K. Homologous recombination within the capsid gene of porcine circovirus type 2 subgroup viruses via natural co-infection. Arch. Virol. 2009, 154, 531-534.
43. Ma, C.M.; Hon, C.C.; Lam, T.Y.; Li, V.Y.; Wong, C.K.; de Oliveira, T.; Leung, F.C. Evidence for recombination in natural populations of porcine circovirus type 2 in hong kong and mainland china. J. Gen. Virol. 2007, 88, 1733-1737.
44. He, C.Q.; Ding, N.Z.; Fan, W.; Wu, Y.H.; Li, J.P.; Li, Y.L. Identification of chicken anemia virus putative intergenotype recombinants. Virology 2007, 366, 1-7.
45. Lefebvre, D.J.; Van Doorsselaere, J.; Delputte, P.L.; Nauwynck, H.J. Recombination of two porcine circovirus type 2 strains. Arch. Virol. 2009, 154, 875-879.
46. Hughes, A.L. Birth-and-death evolution of protein-coding regions and concerted evolution of non-coding regions in the multi-component genomes of nanoviruses. Mol. Phylogenet. Evol. 2004, 30, 287-294.
47. Hu, J.M.; Fu, H.C.; Lin, C.H.; Su, H.J.; Yeh, H.H. Reassortment and concerted evolution in banana bunchy top virus genomes. J. Virol. 2007, 81, 1746-1761.
48. Manni, F.; Rotola, A.; Caselli, E.; Bertorelle, G.; Di Luca, D. Detecting recombination in tt virus: A phylogenetic approach. J. Mol. Evol. 2002, 55, 563-572.
49. Biagini, P.; Gallian, P.; Attoui, H.; Touinssi, M.; Cantaloube, J.; de Micco, P.; de Lamballerie, X. Genetic analysis of full-length genomes and subgenomic sequences of tt virus-like mini virus human isolates. J. Gen. Virol. 2001, 82, 379-383.
50. Worobey, M. Extensive homologous recombination among widely divergent tt viruses. J. Virol. 2000, 74, 7666-7670.
51. Lukashov, V.V.; Goudsmit, J. Evolutionary relationships among parvoviruses: Virus-host coevolution among autonomous primate parvoviruses and links between adeno-associated and avian parvoviruses. J. Virol. 2001, 75, 2729-2740.
52. Kapoor, A.; Simmonds, P.; Slikas, E.; Li, L.L.; Bodhidatta, L.; Sethabutr, O.; Triki, H.; Bahri, O.; Oderinde, B.S.; Baba, M.M., et al. Human bocaviruses are highly diverse, dispersed, recombination prone, and prevalent in enteric infections. J. Infect. Dis. 2010, 201, 1633-1643.
53. Fu, X.; Wang, X.; Ni, B.; Shen, H.; Wang, H.; Zhang, X.; Chen, S.; Shao, S.; Zhang, W. Recombination analysis based on the complete genome of bocavirus. Virol. J. 2011, 8, 182.
54. Shackelton, L.A.; Hoelzer, K.; Parrish, C.R.; Holmes, E.C. Comparative analysis reveals frequent recombination in the parvoviruses. J. Gen. Virol. 2007, 88, 3294-3301.
55. Kapoor, A.; Simmonds, P.; Slikas, E.; Li, L.; Bodhidatta, L.; Sethabutr, O.; Triki, H.; Bahri, O.; Oderinde, B.S.; Baba, M.M., et al. Human bocaviruses are highly diverse, dispersed, recombination prone, and prevalent in enteric infections. J. Infect. Dis. 2010, 201, 1633-1643.
56. Grigoras, I.; Timchenko, T.; Katul, L.; Grande-Perez, A.; Vetten, H.J.; Gronenborn, B. Reconstitution of authentic nanovirus from multiple cloned dnas. J. Virol. 2009, 83, 10778-10787.
57. Desai, M.; Pal, R.; Deshmukh, R.; Banker, D. Replication of tt virus in hepatocyte and leucocyte cell lines. J. Med. Virol. 2005, 77, 136-143.
58. Kakkola, L.; Tommiska, J.; Boele, L.C.; Miettinen, S.; Blom, T.; Kekarainen, T.; Qiu, J.; Pintel, D.; Hoeben, R.C.; Hedman, K., et al. Construction and biological activity of a full-length molecular clone of human torque teno virus (ttv) genotype 6. FEBS J. 2007, 274, 4719-4730.
59. Leppik, L.; Gunst, K.; Lehtinen, M.; Dillner, J.; Streker, K.; de Villiers, E.M. In vivo and in vitro intragenomic rearrangement of tt viruses. J. Virol. 2007, 81, 9346-9356.
60. Cheung, A.K. Palindrome regeneration by template strand-switching mechanism at the origin of DNA replication of porcine circovirus via the rolling-circle melting-pot replication model. J. Virol. 2004, 78, 9016-9029.
61. Timchenko, T.; de Kouchkovsky, F.; Katul, L.; David, C.; Vetten, H.J.; Gronenborn, B. A single rep protein initiates replication of multiple genome components of faba bean necrotic yellows virus, a single-stranded DNA virus of plants. J. Virol. 1999, 73, 10173-10182.
62. Saunders, K.; Lucy, A.; Stanley, J. DNA forms of the geminivirus african cassava mosaic-virus consistent with a rolling circle mechanism of replication. Nucleic Acids Res. 1991, 19, 2325-2330.
63. Cheung, A.K. Identification of an octanucleotide motif sequence essential for viral protein, DNA, and progeny virus biosynthesis at the origin of DNA replication of porcine circovirus type 2. Virology 2004, 324, 28-36.
64. Cheung, A.K. Identification of the essential and non-essential transcription units for protein synthesis, DNA replication and infectious virus production of porcine circovirus type 1. Arch. Virol. 2004, 149, 975-988.
65. Gutierrez, C.; Ramirez-Parra, E.; Castellano, M.M.; Sanz-Burgos, A.P.; Luque, A.; Missich, R. Geminivirus DNA replication and cell cycle interactions. Vet. Microbiol. 2004, 98, 111-119.
66. Tattersall, P.; Ward, D.C. Rolling hairpin model for replication of parvovirus and linear chromosomal DNA. Nature 1976, 263, 106-109.
67. Cotmore, S.F.; Tattersall, P. Resolution of parvovirus dimer junctions proceeds through a novel heterocruciform intermediate. J. Virol. 2003, 77, 6245-6254.
68. Cotmore, S.F.; Tattersall, P. Parvovirus DNA Replication. In DNA Replication in Eukaryotic Cells; DePamphilis, M.L., Ed.; Cold Spring Harbour Laboratory press: Cold Spring Harbor, NY, USA. 1996; pp. 199-813.
69. Abouzid, A.M.; Frischmuth, T.; Jeske, H. A putative replicative form of the abutilon mosaic-virus (gemini group) in a chromatin-like structure. Mol. Gen. Genet. 1988, 212, 252-258.
70. Pilartz, M.; Jeske, H. Abutilon mosaic geminivirus double-stranded DNA is packed into minichromosomes. Virology 1992, 189, 800-802.
71. Pilartz, M.; Jeske, H. Mapping of abutilon mosaic geminivirus minichromosomes. J. Virol. 2003, 77, 10808-10818.
72. Heyraud-Nitschke, F.; Schumacher, S.; Laufs, J.; Schaefer, S.; Schell, J.; Gronenborn, B. Determination of the origin cleavage and joining domain of geminivirus rep proteins. Nucleic Acids Res. 1995, 23, 910-916.
73. Cheung, A.K. Detection of template strand switching during initiation and termination of DNA replication of porcine circovirus. J. Virol. 2004, 78, 4268-4277.
74. Laufs, J.; Traut, W.; Heyraud, F.; Matzeit, V.; Rogers, S.G.; Schell, J.; Gronenborn, B. In-vitro cleavage and joining at the viral origin of replication by the replication initiator protein of tomato yellow leaf curl virus. Proc. Natl. Acad. Sci. U. S. A. 1995, 92, 3879-3883.
75. Orozco, B.M.; Hanley-Bowdoin, L. Conserved sequence and structural motifs contribute to the DNA binding and cleavage activities of a geminivirus replication protein. J. Biol. Chem. 1998, 273, 24448-24456.
76. Castellano, M.M.; Sanz-Burgos, A.P.; Gutierrez, C. Initiation of DNA replication in a eukaryotic rolling-circle replicon: Identification of multiple rna-protein complexes at the geminivirus origin. J. Mol. Biol. 1999, 290, 639-652.
77. Hafner, G.J.; Stafford, M.R.; Wolter, L.C.; Harding, R.M.; Dale, J.L. Nicking and joining activity of banana bunchy top virus replication protein in vitro. J. Gen. Virol. 1997, 78, 1795-1799.
78. Jeske, H.; Lutgemeier, M.; Preiss, W. DNA forms indicate rolling circle and recombination-dependent replication of abutilon mosaic virus. EMBO J. 2001, 20, 6158-6167.
79. Okamoto, H.; Ukita, M.; Nishizawa, T.; Kishimoto, J.; Hoshi, Y.; Mizuo, H.; Tanaka, T.; Miyakawa, Y.; Mayumi, M. Circular double-stranded forms of tt virus DNA in the liver. J. Virol. 2000, 74, 5161-5167.
80. Okamoto, H.; Takahashi, M.; Nishizawa, T.; Tawara, A.; Sugai, Y.; Sai, T.; Tanaka, T.; Tsuda, F. Replicative forms of tt virus DNA in bone marrow cells. Biochem. Biophys. Res. Commun. 2000, 270, 657-662.
81. de Villiers, E.M.; Borkosky, S.S.; Kimmel, R.; Gunst, K.; Fei, J.W. The diversity of torque teno viruses: In vitro replication leads to the formation of additional replication-competent subviral molecules. J. Virol. 2011, 85, 7284-7295.
82. Heyraud, F.; Matzeit, V.; Schaefer, S.; Schell, J.; Gronenborn, B. The conserved nonanucleotide motif of the geminivirus stem-loop sequence promotes replicational release of virus molecules from redundant copies. Biochimie 1993, 75, 605-615.
83. Owor, B.E.; Martin, D.P.; Shepherd, D.N.; Edema, R.; Monjane, A.L.; Rybicki, E.P.; Thomson, J.A.; Varsani, A. Genetic analysis of maize streak virus isolates from uganda reveals widespread distribution of a recombinant variant. J. Gen. Virol. 2007, 88, 3154-3165.
84. Xu, Y.; Price, B.D. Chromatin dynamics and the repair of DNA double strand breaks. Cell Cycle 2011, 10, 261-267.
85. Alberter, B.; Rezaian, M.A.; Jeske, H. Replicative intermediates of tomato leaf curl virus and its satellite dnas. Virology 2005, 331, 441-448.
86. Jovel, J.; Preiss, W.; Jeske, H. Characterization of DNA intermediates of an arising geminivirus. Virus Res. 2007, 130, 63-70.
87. Erdmann, J.B.; Shepherd, D.N.; Martin, D.P.; Varsani, A.; Rybicki, E.P.; Jeske, H. Replicative intermediates of maize streak virus found during leaf development. J. Gen. Virol. 2010, 91, 1077-1081.
88. Preiss, W.; Jeske, H. Multitasking in replication is common among geminiviruses. J. Virol. 2003, 77, 2972-2980.
89. Varsani, A.; Shepherd, D.N.; Monjane, A.L.; Owor, B.E.; Erdmann, J.B.; Rybicki, E.P.; Peterschmitt, M.; Briddon, R.W.; Markham, P.G.; Oluwafemi, S., et al. Recombination, decreased host specificity and increased mobility may have driven the emergence of maize streak virus as an agricultural pathogen. J. Gen. Virol. 2008, 89, 2063-2074.
90. Stenger, D.C.; Revington, G.N.; Stevenson, M.C.; Bisaro, D.M. Replicational release of geminivirus genomes from tandemly repeated copies-Evidence for rolling-circle replication of a plant viral-DNA. Proc. Natl. Acad. Sci. U. S. A. 1991, 88, 8029-8033.
91. Fenaux, M.; Halbur, P.G.; Haqshenas, G.; Royer, R.; Thomas, P.; Nawagitgul, P.; Gill, M.; Toth, T.E.; Meng, X.J. Cloned genomic DNA of type 2 porcine circovirus is infectious when injected directly into the liver and lymph nodes of pigs: Characterization of clinical disease, virus distribution, and pathologic lesions. J. Virol. 2002, 76, 541-551.
92. Burns, T.M.; Harding, R.M.; Dale, J.L. The genome organization of banana bunchy top virus- analysis of 6 ssdna components. J. Gen. Virol. 1995, 76, 1471-1482.
93. Katul, L.; Timchenko, T.; Gronenborn, B.; Vetten, H.J. Ten distinct circular ssdna components, four of which encode putative replication-associated proteins, are associated with the faba bean necrotic yellows virus genome. J. Gen. Virol. 1998, 79, 3101-3109.
94. Boevink, P.; Chu, P.W.; Keese, P. Sequence of subterranean clover stunt virus DNA: Affinities with the geminiviruses. Virology 1995, 207, 354-361.
95. Sano, Y.; Wada, M.; Hashimoto, Y.; Matsumoto, T.; Kojima, M. Sequences of ten circular ssdna components associated with the milk vetch dwarf virus genome. J. Gen. Virol. 1998, 79, 3111-3118.
96. Hill, J.E.; Strandberg, J.O.; Hiebert, E.; Lazarowitz, S.G. Asymmetric infectivity of pseudorecombinants of cabbage leaf curl virus and squash leaf curl virus: Implications for bipartite geminivirus evolution and movement. Virology 1998, 250, 283-292.
97. Chakraborty, S.; Vanitharani, R.; Chattopadhyay, B.; Fauquet, C.M. Supervirulent pseudorecombination and asymmetric synergism between genomic components of two distinct species of begomovirus associated with severe tomato leaf curl disease in india. J. Gen. Virol. 2008, 89, 818-828.
98. Gilbertson, R.L.; Hidayat, S.H.; Paplomatas, E.J.; Rojas, M.R.; Hou, Y.M.; Maxwell, D.P. Pseudorecombination between infectious cloned DNA-components of tomato mottle and bean dwarf mosaic geminiviruses. J. Gen. Virol. 1993, 74, 23-31.
99. von Arnim, A.; Stanley, J. Determinants of tomato golden mosaic-virus symptom development located on DNA-b. Virology 1992, 186, 286-293.
100. Pita, J.S.; Fondong, V.N.; Sangare, A.; Otim-Nape, G.W.; Ogwal, S.; Fauquet, C.M. Recombination, pseudorecombination and synergism of geminiviruses are determinant keys to the epidemic of severe cassava mosaic disease in uganda. J. Gen. Virol. 2001, 82, 655-665.
101. Unseld, S.; Ringel, M.; Hofer, P.; Hohnle, M.; Jeske, H.; Bedford, I.D.; Markham, P.G.; Frischmuth, T. Host range and symptom variation of pseudorecombinant virus produced by two distinct bipartite geminiviruses. Arch. Virol. 2000, 145, 1449-1454.
102. Unseld, S.; Ringel, M.; Konrad, A.; Lauster, S.; Frischmuth, T. Virus-specific adaptations for the production of a pseudorecombinant virus formed by two distinct bipartite geminiviruses from central america. Virology 2000, 274, 179-188.
103. Briddon, R.W.; Patil, B.L.; Bagewadi, B.; Nawaz-ul-Rehman, M.S.; Fauquet, C.M. Distinct evolutionary histories of the DNA-A and DNA-B components of bipartite begomoviruses. BMC Evol. Biol. 2010, 10, 97.
104. Saunders, K.; Salim, N.; Mali, V.R.; Malathi, V.G.; Briddon, R.; Markham, P.G.; Stanley, J. Characterisation of sri lankan cassava mosaic virus and indian cassava mosaic virus: Evidence for acquisition of a DNA b component by a monopartite begomovirus. Virology 2002, 293, 63-74.
105. Saunders, K.; Stanley, J. A nanovirus-like DNA component associated with yellow vein disease of ageratum conyzoides: Evidence for interfamilial recombination between plant DNA viruses. Virology 1999, 264, 142-152.
106. Chen, L.F.; Rojas, M.; Kon, T.; Gamby, K.; Xoconostle-Cazares, B.; Gilbertson, R.L. A severe symptom phenotype in tomato in mali is caused by a reassortant between a novel recombinant begomovirus (tomato yellow leaf curl mali virus) and a betasatellite. Mol. Plant. Pathol. 2009, 10, 415-430.
107. Lefeuvre, P.; Martin, D.P.; Hoareau, M.; Naze, F.; Delatte, H.; Thierry, M.; Varsani, A.; Becker, N.; Reynaud, B.; Lett, J.M. Begomovirus 'melting pot' in the south-west indian ocean islands: Molecular diversity and evolution through recombination. J. Gen. Virol. 2007, 88, 3458-3468.
108. Bell, K.E.; Dale, J.L.; Ha, C.V.; Vu, M.T.; Revill, P.A. Characterisation of rep-encoding components associated with banana bunchy top nanovirus in vietnam. Arch. Virol. 2002, 147, 695-707.
109. Horser, C.L.; Karan, M.; Harding, R.M.; Dale, J.L. Additional rep-encoding dnas associated with banana bunchy top virus. Arch. Virol. 2001, 146, 71-86.
110. Sung, Y.K.; Coutts, R.H.A. Pseudorecombination and complementation between potato yellow mosaic geminivirus and tomato golden mosaic geminivirus. J. Gen. Virol. 1995, 76, 2809-2815.
111. Lazarowitz, S.G.; Wu, L.C.; Rogers, S.G.; Elmer, J.S. Sequence-specific interaction with the viral al1 protein identifies a geminivirus DNA-replication origin. Plant Cell 1992, 4, 799-809.
112. Fontes, E.P.B.; Gladfelter, H.J.; Schaffer, R.L.; Petty, I.T.D.; Hanleybowdoin, L. Geminivirus replication origins have a modular organization. Plant Cell 1994, 6, 405-416.
113. Hou, Y.M.; Gilbertson, R.L. Increased pathogenicity in a pseudorecombinant bipartite geminivirus correlates with intermolecular recombination. J. Virol. 1996, 70, 5430-5436.
114. Stenger, D.C. Strain-specific mobilization and amplification of a transgenic defective-interfering DNA of the geminivirus beet curly top virus. Virology 1994, 203, 397-402.
115. Arguello-Astorga, G.R.; Ruiz-Medrano, R. An iteron-related domain is associated to motif 1 in the replication proteins of geminiviruses: Identification of potential interacting amino acid-base pairs by a comparative approach. Arch. Virol. 2001, 146, 1465-1485.
116. Timchenko, T.; Katul, L.; Sano, Y.; de Kouchkovsky, F.; Vetten, H.J.; Gronenborn, B. The master rep concept in nanovirus replication: Identification of missing genome components and potential for natural genetic reassortment. Virology 2000, 274, 189-195.
117. Dry, I.B.; Krake, L.R.; Rigden, J.E.; Rezaian, M.A. A novel subviral agent associated with a geminivirus: The first report of a DNA satellite. Proc. Natl. Acad. Sci. U. S. A. 1997, 94, 7088-7093.
118. Lin, B.C.; Behjatnia, S.A.A.; Dry, I.B.; Randles, J.W.; Ali Rezaian, M. High-affinity rep-binding is not required for the replication of a geminivirus DNA and its satellite. Virology 2003, 305, 353-363.
119. Briddon, R.W.; Bull, S.E.; Amin, I.; Idris, A.M.; Mansoor, S.; Bedford, I.D.; Dhawan, P.; Rishi, N.; Siwatch, S.S.; Abdel-Salam, A.M.; et al. Diversity of DNA beta, a satellite molecule associated with some monopartite begomoviruses. Virology 2003, 312, 106-121.
120. Roberts, S.; Stanley, J. Lethal mutations within the conserved stem-loop of african cassava mosaic-virus DNA are rapidly corrected by genomic recombination. J. Gen. Virol. 1994, 75, 3203-3209.
121. Hyder, M.Z.; Shah, S.H.; Hameed, S.; Naqvi, S.M. Evidence of recombination in the banana bunchy top virus genome. Infect Genet Evol. 2011, 11, 1293-1300.
122. Jovel, J.; Reski, G.; Rothenstein, D.; Ringel, M.; Frischmuth, T.; Jeske, H. Sida micrantha mosaic is associated with a complex infection of begomoviruses different from abutilon mosaic virus. Arch. Virol. 2004, 149, 829-841.
123. Stanley, J.; Saunders, K.; Pinner, M.S.; Wong, S.M. Novel defective interfering dnas associated with ageratum yellow vein geminivirus infection of ageratum conyzoides. Virology 1997, 239, 87-96.
124. Tao, X.R.; Zhou, X.P. Pathogenicity of a naturally occurring recombinant DNA satellite associated with tomato yellow leaf curl china virus. J. Gen. Virol. 2008, 89, 306-311.
125. Gafni, Y.; Epel, B.L. The role of host and viral proteins in intra- and inter-cellular trafficking of geminiviruses. Physiol. Mol. Plant Pathol. 2002, 60, 231-241.
126. Saunders, K.; Norman, A.; Gucciardo, S.; Stanley, J. The DNA beta satellite component associated with ageratum yellow vein disease encodes an essential pathogenicity protein (beta c1). Virology 2004, 324, 37-47.
127. Duan, Y.P.; Powell, C.A.; Webb, S.E.; Purcifull, D.E.; Hiebert, E. Geminivirus resistance in transgenic tobacco expressing mutated bc1 protein. Mol. Plant Microbe Interact. 1997, 10, 617-623.
128. Briddon, R.W.; Mansoor, S.; Bedford, I.D.; Pinner, M.S.; Saunders, K.; Stanley, J.; Zafar, Y.; Malik, K.A.; Markham, P.G. Identification of DNA components required for induction of cotton leaf curl disease. Virology 2001, 285, 234-243.
129. Cui, X.F.; Tao, X.R.; Xie, Y.; Fauquet, C.M.; Zhou, X.P. A DNA beta associated with tomato yellow leaf curl china virus is required for symptom induction. J. Virol. 2004, 78, 13966-13974.
130. Briddon, R.W.; Stanley, J. Subviral agents associated with plant single-stranded DNA viruses. Virology 2006, 344, 198-210.
131. Saeed, M.; Zafar, Y.; Randles, J.W.; Rezaian, M.A. A monopartite begomovirus-associated DNA beta satellite substitutes for the DNA b of a bipartite begomovirus to permit systemic infection. J. Gen. Virol. 2007, 88, 2881-2889.
132. Kikuno, R.; Toh, H.; Hayashida, H.; Miyata, T. Sequence similarity between putative gene-products of geminiviral dnas. Nature 1984, 308, 562-562.
133. de Villiers, E.M.; Kimmel, R.; Leppik, L.; Gunst, K. Intragenomic rearrangement in tt viruses: A possible role in the pathogenesis of disease. In TT Viruses. The Still Elusive Human Pathogens; de Villiers, E.M., zur Hausen, H., Eds.; Springer: Berlin, Germany, 2009; Volume 331, pp. 91-107.
134. Roberts, E.J.F.; Buck, K.W.; Coutts, R.H.A. Characterization of potato yellow mosaic-virus as a geminivirus with a bipartite genome. Intervirology 1988, 29, 162-169.
135. Faust, E.A.; Ward, D.C. Incomplete genomes of the parvovirus minute virus of mice-Selective conservation of genome termini, including the origin for DNA-replication. J. Virol. 1979, 32, 276-292.
136. Hogan, A.; Faust, E.A. Nonhomologous recombination in the parvovirus chromosome: Role for a ctatttct motif. Mol. Cell. Biol. 1986, 6, 3005-3009.
137. Clement, N.; Avalosse, B.; El Bakkouri, K.; Velu, T.; Brandenburger, A. Cloning and sequencing of defective particles derived from the autonomous parvovirus minute virus of mice for the construction of vectors with minimal cis-acting sequences. J. Virol. 2001, 75, 1284-1293.
138. Allen, J.M.; Debelak, D.J.; Reynolds, T.C.; Miller, A.D. Identification and elimination of replication-competent adeno-associated virus (aav) that can arise by nonhomologous recombination during aav vector production. J. Virol. 1997, 71, 6816-6822.
139. Rhode, S.L., 3rd. Defective interfering particles of parvovirus h-1. J. Virol. 1978, 27, 347-356.
140. Hoelzer, K.; Shackelton, L.A.; Holmes, E.C.; Parrish, C.R. Within-host genetic diversity of endemic and emerging parvoviruses of dogs and cats. J. Virol. 2008, 82, 11096-11105.
141. MacDowell, S.W.; Coutts, R.H.; Buck, K.W. Molecular characterisation of subgenomic single-stranded and double-stranded DNA forms isolated from plants infected with tomato golden mosaic virus. Nucleic Acids Res. 1986, 14, 7967-7984.
142. Liu, Y.L.; Robinson, D.J.; Harrison, B.D. Defective forms of cotton leaf curl virus DNA-a that have different combinations of sequence deletion, duplication, inversion and rearrangement. J. Gen. Virol. 1998, 79, 1501-1508.
143. Stanley, J.; Townsend, R. Characterisation of DNA forms associated with cassava latent virus infection. Nucleic Acids Res. 1985, 13, 2189-2206.
144. Macdonald, H.; Coutts, R.H.A.; Buck, K.W. Characterization of a subgenomic DNA isolated from triticum-aestivum plants infected with wheat dwarf virus. J. Gen. Virol. 1988, 69, 1339-1344.
145. Casado, C.G.; Javier Ortiz, G.; Padron, E.; Bean, S.J.; McKenna, R.; Agbandje-McKenna, M.; Boulton, M.I. Isolation and characterization of subgenomic dnas encapsidated in single t=1 isometric particles of maize streak virus. Virology 2004, 323, 164-171.
146. Ndunguru, J.; Legg, J.P.; Fofana, I.B.F.; Aveling, T.A.S.; Thompson, G.; Fauquet, C.M. Identification of a defective molecule derived from DNA-a of the bipartite begomovirus of east african cassava mosaic virus. Plant Pathol. 2006, 55, 2-10.
147. Patil, B.L.; Dutt, N.; Briddon, R.W.; Bull, S.E.; Rothenstein, D.; Borah, B.K.; Dasgupta, I.; Stanley, J.; Jeske, H. Deletion and recombination events between the DNA-a and DNA-b components of indian cassava-infecting geminiviruses generate defective molecules in nicotiana benthamiana. Virus Res. 2007, 124, 59-67.
148. Frischmuth, T.; Stanley, J. Strategies for the control of geminivirus diseases. Semin. Virol. 1993, 4, 329-337.
149. Horn, J.; Lauster, S.; Krenz, B.; Kraus, J.; Frischmuth, T.; Jeske, H. Ambivalent effects of defective DNA in beet curly top virus-infected transgenic sugarbeet plants. Virus Res. 2011, 158, 169-178.
150. Stanley, J.; Frischmuth, T.; Ellwood, S. Defective viral-DNA ameliorates symptoms of geminivirus infection in transgenic plants. Proc. Natl. Acad. Sci. U. S. A. 1990, 87, 6291-6295.
151. Frischmuth, T.; Stanley, J. Beet curly top virus symptom amelioration in nicotiana benthamiana transformed with a naturally occurring viral subgenomic DNA. Virology 1994, 200, 826-830.
152. Frischmuth, T.; Engel, M.; Jeske, H. Beet curly top virus di DNA-mediated resistance is linked to its size. Mol. Breed. 1997, 3, 213-217.
153. Etessami, P.; Watts, J.; Stanley, J. Size reversion of african cassava mosaic-virus coat protein gene deletion mutants during infection of nicotiana-benthamiana. J. Gen. Virol. 1989, 70, 277-289.
154. Shen, W.H.; Hohn, B. Mutational analysis of the small intergenic region of maize streak virus. Virology 1991, 183, 721-730.
155. Bisaro, D.M. Recombination in the geminiviruses: Mechanisms for maintaining genome size and generating genomic diversity. In Homologous Recombination and Gene Silencing in Plants; Paszkowski, J., Ed.; Kluwer Academic Publishers: Dordrecht, The Netherlands, 1994; pp. 39-60.
156. Frischmuth, T.; Ringel, M.; Kocher, C. The size of encapsidated single-stranded DNA determines the multiplicity of african cassava mosaic virus particles. J. Gen. Virol. 2001, 82, 673-676.
157. Qian, Y.J.; Tan, Z.; Liu, Y.; Briddon, R.W.; Zhou, X.P. Size reversion of a truncated DNA beta associated with tobacco curly shoot virus. Virus Res. 2008, 131, 288-292.
158. Cheung, A.K. Mutational analysis of the direct tandem repeat sequences at the origin of DNA replication of porcine circovirus type 1. Virology 2005, 339, 192-199.
159. Frischmuth, T.; Stanley, J. Recombination between viral DNA and the transgenic coat protein gene of african cassava mosaic geminivirus. J. Gen. Virol. 1998, 79, 1265-1271.
160. Belyi, V.A.; Levine, A.J.; Skalka, A.M. Sequences from ancestral single-stranded DNA viruses in vertebrate genomes: The parvoviridae and circoviridae are more than 40 to 50 million years old. J. Virol. 2010, 84, 12458-12462.
161. Krupovic, M.; Forterre, P. Microviridae goes temperate: Microvirus-related proviruses reside in the genomes of bacteroidetes. PLoSONE 2011, 6, e19893.
162. Liu, H.; Fu, Y.; Xie, J.; Cheng, J.; Ghabrial, S.A.; Li, G.; Peng, Y.; Yi, X.; Jiang, D. Widespread endogenization of densoviruses and parvoviruses in animal and human genomes. J. Virol. 2011, doi:10.1128/JVI.00828-11.
163. Dutheil, N.; Shi, F.; Dupressoir, T.; Linden, R.M. Adeno-associated virus site-specifically integrates into a muscle-specific DNA region. Proc. Natl. Acad. Sci. U. S. A. 2000, 97, 4862-4866.
164. Ashby, M.K.; Warry, A.; Bejarano, E.R.; Khashoggi, A.; Burrell, M.; Lichtenstein, C.P. Analysis of multiple copies of geminiviral DNA in the genome of four closely related nicotiana species suggest a unique integration event. PlantMol. Biol. 1997, 35, 313-321.
165. Bejarano, E.R.; Khashoggi, A.; Witty, M.; Lichtenstein, C. Integration of multiple repeats of geminiviral DNA into the nuclear genome of tobacco during evolution. Proc. Natl. Acad. Sci. U. S. A. 1996, 93, 759-764.
166. Murad, L.; Bielawski, J.P.; Matyasek, R.; Kovarik, A.; Nichols, R.A.; Leitch, A.R.; Lichtenstein, P. The origin and evolution of geminivirus-related DNA sequences in nicotiana. Heredity 2004, 92, 352-358.
167. Kenton, A.; Khashoggi, A.; Parokonny, A.; Bennett, M.D.; Lichtenstein, C. Chromosomal location of endogenous geminivirus-related DNA-sequences in nicotiana-tabacum-l. Chromosome Res. 1995, 3, 346-350.
168. Gibbs, A.J.; Fargette, D.; Garcia-Arenal, F.; Gibbs, M.J. Time-The emerging dimension of plant virus studies. J. Gen. Virol. 91, 13-22.
169. Lefeuvre, P.; Harkins, G.W.; Lett, J.-M.; Briddon, R.W.; Leitch, A.R.; Chase, M.W.; Moury, B.; Martin, D.P. Evolutionary time-scale of begomoviruses: Evidence from integrated sequences in nicotiana genome. PLoS ONE 2011, 6, e19193.
170. Rojas, M.R.; Hagen, C.; Lucas, W.J.; Gilbertson, R.L. Exploiting chinks in the plant's armor: Evolution and emergence of geminiviruses. Ann. Rev. Phytopathol. 2005, 43, 361-394.
171. Varsani, A.; Monjane, A.L.; Donaldson, L.; Oluwafemi, S.; Zinga, I.; Komba, E.K.; Plakoutene, D.; Mandakombo, N.; Mboukoulida, J.; Semballa, S., et al. Comparative analysis of panicum streak virus and maize streak virus diversity, recombination patterns and phylogeography. Virol. J. 2009, 6, 194.
172. Varsani, A.; Regnard, G.L.; Bragg, R.; Hitzeroth, I.I.; Rybicki, E.P. Global genetic diversity and geographical and host-species distribution of beak and feather disease virus isolates. J. Gen. Virol. 2011, 92, 752-767.
173. Karan, M.; Harding, R.M.; Dale, J.L. Evidence for two groups of banana bunchy top virus isolates. J. Gen. Virol. 1994, 75, 3541-3546.
174. Prasanna, H.C.; Sinha, D.P.; Verma, A.; Singh, M.; Singh, B.; Rai, M.; Martin, D.P. The population genomics of begomoviruses: Global scale population structure and gene flow. Virol. J. 2010, 7, 220.
175. Briddon, R.W.; Bull, S.E.; Amin, I.; Mansoor, S.; Bedford, I.D.; Rishi, N.; Siwatch, S.S.; Zafar, Y.; Abdel-Salam, A.M.; Markham, P.G. Diversity of DNA 1: A satellite-like molecule associated with monopartite begomovirus-DNA beta complexes. Virology 2004, 324, 462-474.
176. Hoelzer, K.; Shackelton, L.A.; Parrish, C.R.; Holmes, E.C. Phylogenetic analysis reveals the emergence, evolution and dispersal of carnivore parvoviruses. J. Gen. Virol. 2008, 89, 2280-2289.
177. Saback, F.L.; Gomes, S.A.; Niel, C. High frequency of mixed tt virus infections in healthy adults and children detected by a simplified heteroduplex mobility assay. J. Virol. Meth. 2002, 101, 117-125.
178. Bigarre, L.; Beven, V.; de Boisseson, C.; Grasland, B.; Rose, N.; Biagini, P.; Jestin, A. Pig anelloviruses are highly prevalent in swine herds in france. J. Gen. Virol. 2005, 86, 631-635.
179. Morales, F.J. History and current distribution of begomoviruses in latin america. Plant Virus Epidemiol. 2006, 67, 127-162.
180. Ribeiro, S.G.; de Ãvila, A.C.; Bezerra, I.C.; Fernandes, J.J.; Faria, J.C.; Lima, M.F.; Gilbertson, R.L.; Maciel-Zambolim, E.; Zerbini, F.M. Widespread occurrence of tomato geminiviruses in brazil, associated with the new biotype of the whitefly vector. Plant Dis. 1998, 82, 830-830.
181. França, F.H.; Villas Bôas, G.L.; Branco, M.C. Occurrence of bemisia argentifolii bellows & perring (homoptera: Aleyrodidae) in the federal district. Anais da Sociedade Entomoldgica do Brasil 1996, 25, 369-372.
182. Albuquerque, L.C.; Martin, D.P.; Avila, A.C.; Inoue-Nagata, A.K. Characterization of tomato yellow vein streak virus, a begomovirus from brazil. Virus Genes 2010, 40, 140-147.
183. Calegario, R.F.; Ferreira, S.D.S.; de Andrade, E.C.; Zerbini, F.M. Characterization of tomato yellow spot virus, a novel tomato-infecting begomovirus in brazil. Pesquisa Agropecuaria Brasileira 2007, 42, 1335-1343.
184. Castillo-Urquiza, G.P.; Beserra, J.E.A.; Bruckner, F.P.; Lima, A.T.M.; Varsani, A.; Alfenas-Zerbini, P.; Zerbini, F.M. Six novel begomoviruses infecting tomato and associated weeds in southeastern brazil. Arch. Virol. 2008, 153, 1985-1989.
185. Fernandes, F.R.; de Albuquerque, L.C.; Giordano, L.D.B.; Boiteux, L.S.; de Avila, A.C.; Inoue-Nagata, A.K. Diversity and prevalence of brazilian bipartite begomovirus species associated to tomatoes. Virus Genes 2008, 36, 251-258.
186. Ribeiro, S.G.; Martin, D.P.; Lacorte, C.; Simoes, I.C.; Orlandini, D.R.S.; Inoue-Nagata, A.K. Molecular and biological characterization of tomato chlorotic mottle virus suggests that recombination underlies the evolution and diversity of brazilian tomato begomoviruses. Phytopathology 2007, 97, 702-711.
187. Ribeiro, S.G.; Ambrozevicius, L.P.; Avila, A.C.; Bezerra, I.C.; Calegario, R.F.; Fernandes, J.J.; Lima, M.F.; de Mello, R.N.; Rocha, H.; Zerbini, F.M. Distribution and genetic diversity of tomato-infecting begomoviruses in brazil. Arch. Virol. 2003, 148, 281-295.
188. Prasanna, H.C.; Rai, M. Detection and frequency of recombination in tomato-infecting begomoviruses of south and southeast asia. Virol. J. 2007, 4, 111.
189. Martin, D.P.; Lefeuvre, P.; Varsani, A.; Hoareau, M.; Semegni, J.Y.; Dijoux, B.; Vincent, C.; Lett, J.M. Complex recombination patterns arising during geminivirus coinfections both preserve and demarcate biologically important intra-genome interaction networks. PLoS Pathog. 2011, in press.
190. Worobey, M. Extensive homologous recombination among widely divergent tt viruses. J. Virol. 2000, 74, 7666-7670.
191. Mankertz, A.; Persson, F.; Mankertz, J.; Blaess, G.; Buhk, H.J. Mapping and characterization of the origin of DNA replication of porcine circovirus. J. Virol. 1997, 71, 2562-2566.
192. Stenger, D.C.; Davis, K.R.; Bisaro, D.M. Recombinant beet curly top virus genomes exhibit both parental and novel pathogenic phenotypes. Virology 1994, 200, 677-685.
193. Cheung, A.K. Homologous recombination plays minor role in excision of unit-length viral genomes from head-to-tail direct tandem repeats of porcine circovirus during DNA replication in escherichia coli. Arch. Virol. 2007, 152, 1531-1539.
194. Garcia-Andres, S.; Tomas, D.M.; Sanchez-Campos, S.; Navas-Castillo, J.; Moriones, E. Frequent occurrence of recombinants in mixed infections of tomato yellow leaf curl disease-associated begomoviruses. Virology 2007, 365, 210-219.
195. Rowe, C.L.; Fleming, J.O.; Nathan, M.J.; Sgro, J.Y.; Palmenberg, A.C.; Baker, S.C. Generation of coronavirus spike deletion variants by high-frequency recombination at regions of predicted rna secondary structure. J. Virol. 1997, 71, 6183-6190.
196. Koev, G.; Mohan, B.R.; Miller, W.A. Primary and secondary structural elements required for synthesis of barley yellow dwarf virus subgenomic RNA1. J. Virol. 1999, 73, 2876-2885.
197. Shen, W.; Gao, L.; Balakrishnan, M.; Bambara, R.A. A recombination hot spot in HIV-1 contains guanosine runs that can form a g-quartet structure and promote strand transfer in vitro. J. Biol. Chem. 2009, 284, 33883-33893.
198. Duch, M.; Carrasco, M.L.; Jespersen, T.; Aagaard, L.; Pedersen, F.S. An rna secondary structure bias for non-homologous reverse transcriptase-mediated deletions in vivo. Nucleic Acids Res.2004, 32, 2039-2048.
199. Draghici, H.K.; Varrelmann, M. Evidence for similarity-assisted recombination and predicted stem-loop structure determinant in potato virus x RNA recombination. J. Gen. Virol. 2010, 91, 552-562.
200. Simon-Loriere, E.; Martin, D.P.; Weeks, K.M.; Negroni, M. Rna structures facilitate recombination-mediated gene swapping in HIV-1. J. Virol. 2010, 84, 12675-12682.
201. Shepherd, D.N.; Martin, D.P.; Varsani, A.; Thomson, J.A.; Rybicki, E.P.; Klump, H.H. Restoration of native folding of single-stranded DNA sequences through reverse mutations: An indication of a new epigenetic mechanism. Arch. Biochem. Biophys. 2006, 453, 108-122.
202. Brewer, B.J. When polymerases collide-Replication and the transcriptional organization of the escherichia-coli chromosome. Cell 1988, 53, 679-686.
203. Lett, J.M.; Lefeuvre, P.; Couston, L.; Hoareau, M.; Thierry, M.; Reynaud, B.; Martin, D.P.; Varsani, A. Complete genomic sequences of tomato yellow leaf curl mali virus isolates infecting tomato and pepper from the north province of cameroon. Arch. Virol. 2009, 154, 535-540.
204. Ben Asher, E.; Bratosin, S.; Aloni, Y. Intracellular DNA of the parvovirus minute virus of mice is organized in a minichromosome structure. J. Virol. 1982, 41, 1044-1054.
205. Felsenstein, J. The evolutionary advantage of recombination. Genetics 1974, 78, 737-756.
206. Keightley, P.D.; Otto, S.P. Interference among deleterious mutations favours sex and recombination in finite populations. Nature 2006, 443, 89-92.
207. Martin, G.; Otto, S.P.; Lenormand, T. Selection for recombination in structured populations. Genetics 2006, 172, 593-609.
208. Gagnon, C.A.; Music, N.; Fontaine, G.; Tremblay, D.; Harel, J. Emergence of a new type of porcine circovirus in swine (pcv): A type 1 and type 2 pcv recombinant. Vet. Microbiol. 2010, 144, 18-23.
209. Kim, H.K.; Luo, Y.; Moon, H.J.; Park, S.J.; Keum, H.O.; Rho, S.; Park, B.K. Phylogenetic and recombination analysis of genomic sequences of pcv2 isolated in korea. Virus Genes 2009, 39, 352-358.
210. Amin, I.; Mansoor, S.; Amrao, L.; Hussain, M.; Irum, S.; Zafar, Y.; Bull, S.E.; Briddon, R.W. Mobilisation into cotton and spread of a recombinant cotton leaf curl disease satellite-Brief report. Arch. Virol. 2006, 151, 2055-2065.
211. Martin, D.P.; Willment, J.A.; Billharz, R.; Velders, R.; Odhiambo, B.; Njuguna, J.; James, D.; Rybicki, E.P. Sequence diversity and virulence in zea mays of maize streak virus isolates. Virology 2001, 288, 247-255.
212. Harkins, G.W.; Martin, D.P.; Duffy, S.; Monjane, A.L.; Shepherd, D.N.; Windram, O.P.; Owor, B.E.; Donaldson, L.; van Antwerpen, T.; Sayed, R.A., et al. Dating the origins of the maize-adapted strain of maize streak virus, msv-a. J. Gen. Virol. 2009, 90, 3066-3074.
213. Zhou, X.P.; Robinson, D.J.; Harrison, B.D. Types of variation in DNA-a among isolates of east african cassava mosaic virus from kenya, malawi and tanzania. J. Gen. Virol. 1998, 79, 2835-2840.
214. Pita, J.S.; Fondong, V.N.; Sangare, A.; Kokora, R.N.N.; Fauquet, C.M. Genomic and biological diversity of the african cassava geminiviruses. Euphytica 2001, 120, 115-125.
215. Sanz, A.I.; Fraile, A.; Garcia-Arenal, F.; Zhou, X.P.; Robinson, D.J.; Khalid, S.; Butt, T.; Harrison, B.D. Multiple infection, recombination and genome relationships among begomovirus isolates found in cotton and other plants in pakistan. J. Gen. Virol. 2000, 81, 1839-1849.
216. Monci, F.; Sanchez-Campos, S.; Navas-Castillo, J.; Moriones, E. A natural recombinant between the geminiviruses tomato yellow leaf curl sardinia virus and tomato yellow leaf curl virus exhibits a novel pathogenic phenotype and is becoming prevalent in spanish populations. Virology 2002, 303, 317-326.
217. Garcia-Andres, S.; Accotto, G.P.; Navas-Castillo, J.; Moriones, E. Founder effect, plant host, and recombination shape the emergent population of begomoviruses that cause the tomato yellow leaf curl disease in the mediterranean basin. Virology 2007, 359, 302-312.
218. Lefeuvre, P.; Martin, D.P.; Harkins, G.; Lemey, P.; Gray, A.J.A.; Meredith, S.; Lakay, F.; Monjane, A.; Lett, J.M.; Varsani, A., et al. The spread of tomato yellow leaf curl virus from the middle east to the world. PLoSPathog. 2010, 6, e1001164.
219. Briddon, R.W.; Pinner, M.S.; Stanley, J.; Markham, P.G. Geminivirus coat protein gene replacement alters insect specificity. Virology 1990, 177, 85-94.
220. Hofer, P.; Bedford, I.D.; Markham, P.G.; Jeske, H.; Frischmuth, T. Coat protein gene replacement results in whitefly transmission of an insect nontransmissible geminivirus isolate. Virology 1997, 236, 288-295.
221. Qin, Y.; Petty, I.T.D. Genetic analysis of bipartite geminivirus tissue tropism. Virology 2001, 291, 311-323.
222. Martin, D.P.; Rybicki, E.P. Investigation of maize streak virus pathogenicity determinants using chimaeric genomes. Virology 2002, 300, 180-188.
223. Schnippenkoetter, W.H.; Martin, D.P.; Hughes, F.L.; Fyvie, M.; Willment, J.A.; James, D.; von Wechmar, M.B.; Rybicki, E.P. The relative infectivities and genomic characterisation of three distinct mastreviruses from south africa. Arch. Virol. 2001, 146, 1075-1088.
224. Koerber, J.T.; Jang, J.H.; Schaffer, D.V. DNA shuffling of adeno-associated virus yields functionally diverse viral progeny. Mol. Ther. 2008, 16, 1703-1709.
225. Maheshri, N.; Koerber, J.T.; Kaspar, B.K.; Schaffer, D.V. Directed evolution of adeno-associated virus yields enhanced gene delivery vectors. Nat. Biotechnol. 2006, 24, 198-204.
226. Grimm, D.; Lee, J.S.; Wang, L.; Desai, T.; Akache, B.; Storm, T.A.; Kay, M.A. In vitro and in vivo gene therapy vector evolution via multispecies interbreeding and retargeting of adeno- associated viruses. J. Virol. 2008, 82, 5887-5911.
227. Morra, M.R.; Petty, I.T.D. Tissue specificity of geminivirus infection is genetically determined. Plant Cell 2000, 12, 2259-2270.
228. Li, W.; Asokan, A.; Wu, Z.; Van Dyke, T.; DiPrimio, N.; Johnson, J.S.; Govindaswamy, L.; Agbandje-McKenna, M.; Leichtle, S.; Redmond, D.E., Jr.; et al. Engineering and selection of shuffled aav genomes: A new strategy for producing targeted biological nanoparticles. Mol. Ther. 2008, 16, 1252-1260.
229. Yang, L.; Jiang, J.; Drouin, L.M.; Agbandje-McKenna, M.; Chen, C.; Qiao, C.; Pu, D.; Hu, X.; Wang, D.Z.; Li, J., et al. A myocardium tropic adeno-associated virus (aav) evolved by DNA shuffling and in vivo selection. Proc. Natl. Acad. Sci. U. S. A. 2009, 106, 3946-3951.
230. Koerber, J.T.; Schaffer, D.V. Transposon-based mutagenesis generates diverse adeno-associated viral libraries with novel gene delivery properties. Meth. Mol. Biol. 2008, 434, 161-170.
231. Evans, D.; Jeske, H. DNA b facilitates, but is not essential for, the spread of abutilon mosaic-virus in agroinoculated nicotiana-benthamiana. Virology 1993, 194, 752-757.
232. Vuillaume, F.; Thebaud, G.; Urbino, C.; Forfert, N.; Granier, M.; Froissart, R.; Blanc, S.; Peterschmitt, M. Distribution of the phenotypic effects of random homologous recombination between two virus species. PLoS Pathog. 2011, 7, e1002028.
233. Davino, S.; Napoli, C.; Dellacroce, C.; Miozzi, L.; Noris, E.; Davino, M.; Accotto, G.P. Two new natural begomovirus recombinants associated with the tomato yellow leaf curl disease co-exist with parental viruses in tomato epidemics in italy. Virus Res. 2009, 143, 15-23.
234. van der Walt, E.; Palmer, K.E.; Martin, D.P.; Rybicki, E.P. Viable chimaeric viruses confirm the biological importance of sequence specific maize streak virus movement protein and coat protein interactions. Virol. J. 2008, 5, 61.
235. Garcia-Andres, S.; Monci, F.; Navas-Castillo, J.; Moriones, E. Begomovirus genetic diversity in the native plant reservoir solanum nigrum: Evidence for the presence of a new virus species of recombinant nature. Virology 2006, 350, 433-442.
236. Garcia-Andres, S.; Tomas, D.M.; Navas-Castillo, J.; Moriones, E. Resistance-driven selection of begomoviruses associated with the tomato yellow leaf curl disease. Virus Res. 2009, 146, 66-72.
237. Accotto, G.-P. Istituto di Virologia Vegetale, C.N.R., Torino, Italy. Unpublished work, 2010.
238. Rokyta, D.R.; Wichman, H.A. Genic incompatibilities in two hybrid bacteriophages. Mol. Biol. Evol. 2009, 26, 2831-2839.
239. Lefeuvre, P.; Lett, J.M.; Reynaud, B.; Martin, D.P. Avoidance of protein fold disruption in natural virus recombinants. PLoSPathog. 2007, 3, 1782-1789.
240. Martin, D.P.; van der Walt, E.; Posada, D.; Rybicki, E.P. The evolutionary value of recombination is constrained by genome modularity. PLoS Genet. 2005, 1, 475-479.
241. Choi, I.R.; Stenger, D.C. Strain-specific determinants of beet curly top geminivirus DNA-replication. Virology 1995, 206, 904-912.
242. Choi, I.R.; Stenger, D.C. The strain-specific cis-acting element of beet curly top geminivirus DNA replication maps to the directly repeated motif of the ori. Virology 1996, 226, 122-126.
243. Willment, J.A.; Martin, D.P.; Palmer, K.E.; Schnippenkoetter, W.H.; Shepherd, D.N.; Rybicki, E.P. Identification of long intergenic region sequences involved in maize streak virus replication. J. Gen. Virol. 2007, 88, 1831-1841.
244. Voigt, C.A.; Martinez, C.; Wang, Z.G.; Mayo, S.L.; Arnold, F.H. Protein building blocks preserved by recombination. Nat. Struct. Biol. 2002, 9, 553-558.
245. Hauck, B.; Xiao, W.D. Characterization of tissue tropism determinants of adeno-associated virus type 1. J. Virol. 2003, 77, 2768-2774.
246. Orozco, B.M.; HanleyBowdoin, L. A DNA structure is required for geminivirus replication origin function. J. Virol. 1996, 70, 148-158.
247. Chen, K.C.; Tyson, J.J.; Lederman, M.; Stout, E.R.; Bates, R.C. A kinetic hairpin transfer model for parvoviral DNA replication. J. Mol. Biol. 1989, 208, 283-296.
248. Cotmore, S.F.; Tattersall, P. High-mobility group 1/2 proteins are essential for initiating rolling-circle-type DNA replication at a parvovirus hairpin origin. J. Virol. 1998, 72, 8477-8484.
249. Costello, E.; Sahli, R.; Hirt, B.; Beard, P. The mismatched nucleotides in the 5'-terminal hairpin of minute virus of mice are required for efficient viral-DNA replication. J. Virol. 1995, 69, 7489-7496.
250. Perros, M.; Spegelaere, P.; Dupont, F.; Vanacker, J.M.; Rommelaere, J. Cruciform structure of a DNA motif of parvovirus minute virus of mice (prototype strain) involved in the attenuation of gene-expression. J. Gen. Virol. 1994, 75, 2645-2653.
251. Taylor, J.E.; Korber, B.T. HIV-1 intra-subtype superinfection rates: Estimates using a structured coalescent with recombination. Infect. Genet. Evol. 2005, 5, 85-95.
252. Lemey, P.; Rambaut, A.; Drummond, A.J.; Suchard, M.A. Bayesian phylogeography finds its roots. PLoS Comput. Biol. 2009, 5, e1000520.
253. Lemey, P.; Rambaut, A.; Welch, J.J.; Suchard, M.A. Phylogeography takes a relaxed random walk in continuous space and time. Mol. Biol. Evol. 2010, 27, 1877-1885.
254. Currie, T.E.; Greenhill, S.J.; Gray, R.D.; Hasegawa, T.; Mace, R. Rise and fall of political complexity in island south-east asia and the pacific. Nature 2010, 467, 801-804.
255. van Bocxlaer, I.; Loader, S.P.; Roelants, K.; Biju, S.D.; Menegon, M.; Bossuyt, F. Gradual adaptation toward a range-expansion phenotype initiated the global radiation of toads. Science 2010, 327, 679-682.
256. Arenas, M.; Posada, D. The effect of recombination on the reconstruction of ancestral sequences. Genetics 2010, 184, 1133-1429.
257. Gullberg, M.; Tolf, C.; Jonsson, N.; Mulders, M.N.; Savolainen-Kopra, C.; Hovi, T.; Van Ranst, M.; Lemey, P.; Hafenstein, S.; Lindberg, A.M. Characterization of a putative ancestor of coxsackievirus b5. J. Virol. 2010, 84, 9695-9708.