Distinct evolutionary histories of the DNA-A and DNA-B components of bipartite begomoviruses

BMC Evolutionary Biology

Volumn 10, Issue 1, 2010, Pages

  Briddon, Rob W ^a   Patil, Basavaprabhu L ^b   Bagewadi, Basavaraj ^b   Nawaz Ul Rehman, Muhammad Shah ^c   Fauquet, Claude M ^b  

^a NATIONAL INSTITUTE FOR BIOTECHNOLOGY AND GENETIC ENGINEERING NIBGE   (Pakistan)

^b DONALD DANFORTH PLANT SCIENCE CENTER   (United States)

^c UNIVERSITY OF KENTUCKY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COEVOLUTION; CULTIVATION; DNA; EVOLUTIONARY THEORY; GENE EXPRESSION; GENETIC VARIATION; GENOME; HOST PLANT; HYPOTHESIS TESTING; INVASIVE SPECIES; MOLECULAR ANALYSIS; PHYLOGENETICS; PROTEIN; VIRUS;

BEGOMOVIRUS; GEMINIVIRIDAE; HEXAPODA;

VIRUS DNA;

ARTICLE; BEGOMOVIRUS; CLASSIFICATION; COMPARATIVE GENOMIC HYBRIDIZATION; DNA SEQUENCE; GENETICS; MOLECULAR EVOLUTION; PHYLOGENY; SEQUENCE ALIGNMENT; VIRUS GENOME;

BEGOMOVIRUS; COMPARATIVE GENOMIC HYBRIDIZATION; DNA, VIRAL; EVOLUTION, MOLECULAR; GENOME, VIRAL; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

EID: 77950645032     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-10-97     Document Type: Article

References (86)

1. Geminiviridae. J Stanley DM Bisaro RW Briddon JK Brown CM Fauquet BD Harrison EP Rybicki DC Stenger, Virus Taxonomy. VIIIth Report of the International Committee on Taxonomy of Viruses London: Elsevier/Academic Press, Fauquet C, Mayo M, Maniloff J, Desselberger U, Ball L, 2005 301 326
2. Tomato yellow leaf curl virus: a whitefly-transmitted geminivirus with a single genomic component. N Navot E Pichersky M Zeidan D Zamir H Czosnek, Virology 1991 185 151 161 10.1016/0042-6822(91)90763-2 1926771
3. Tomato yellow leaf curl virus from Sardinia is a whitefly-transmitted monopartite geminivirus. A Kheyr-Pour M Bendahmane V Matzeit GP Accotto S Crespi B Gronenborn, Nucleic Acids Res 1991 19 6763 6769 10.1093/nar/19.24.6763 1840676 (Pubitemid 21913112)
4. Introduction of tomato yellow leaf curl virus in Florida and implications for the spread of this and other geminiviruses of tomato. J Polston R McGovern L Brown, Plant Dis 1999 83 984 988 10.1094/PDIS.1999.83.11.984 (Pubitemid 29514491)
5. Sub-viral agents associated with plant-infecting single-stranded DNA viruses. RW Briddon J Stanley, Virology 2006 344 198 210 10.1016/j.virol.2005. 09.042 16364750 (Pubitemid 41814462)
6. Nanoviruses: genome organisation and protein function. B Gronenborn, Vet Microbiol 2004 98 103 109 10.1016/j.vetmic.2003.10.015 14741122
7. Getting it together in plant virus movement: cooperative interactions between bipartite geminivirus movement proteins. AA Sanderfoot SG Lazarowitz, Trends Cell Biol 1996 6 353 358 10.1016/0962-8924(96)10031-3 15157433
8. Geminviruses: models for plant DNA replication, transcription, and cell cycle regulation. L Hanley-Bowdoin SB Settlage BM Orozco S Nagar D Robertson, Crit Rev Plant Sci 1999 18 71 106 10.1016/S0735-2689(99)00383-4 (Pubitemid 29079785)
9. 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. GR Argüello-Astorga R Ruiz-Medrano, Arch Virol 2001 146 1465 1485 10.1007/s007050170072 11676411
10. Genetic analysis of the tomato golden mosaic virus. II. The product of the AL1 coding sequence is required for replication. JS Elmer L Brand G Sunter WE Gardiner DM Bisaro SG Rogers, Nucleic Acids Res 1988 16 7043 7060 10.1093/nar/16.14.7043 3405758
11. Geminivirus replication origins have a group-specific organization of iterative elements: a model for replication. GR Argüello-Astorga RG Guevara-Gonzlez LR Herrera-Estrella RF Rivera-Bustamante, Virology 1994 203 90 100 10.1006/viro.1994.1458 8093156
12. Interaction between a geminivirus replication protein and origin DNA is essential for viral replication. EP Fontes PA Eagle PS Sipe VA Luckow L Hanley-Bowdoin, J Biol Chem 1994 269 8459 8465 8132573
13. Recombination, pseudorecombination and synergism of geminiviruses are determinant keys to the epidemic of severe cassava mosaic disease in Uganda. JS Pita VN Fondong A Sangare GW Otim-Nape S Ogwal CM Fauquet, J Gen Virol 2001 82 655 665 11172108
14. Genetic diversity and phylogeography of cassava mosaic viruses in Kenya. SE Bull RW Briddon WS Sserubombwe K Ngugi PG Markham J Stanley, J Gen Virol 2006 87 3053 3065 10.1099/vir.0.82013-0 16963765
15. Legume yellow mosaic viruses: genetically isolated begomoviruses. J Qazi M Ilyas S Mansoor R Briddon, Mol Plant Pathol 2007 8 343 348 10.1111/j.1364-3703.2007.00402.x (Pubitemid 46985623)
16. Cowpea golden mosaic disease in Gujarat is caused by a Mungbean yellow mosaic India virus isolate with a DNA B variant. P John PN Sivalingam QM Haq N Kumar A Mishra RW Briddon VG Malathi, Arch Virol 2008 153 1359 1365 10.1007/s00705-008-0116-8 18516489
17. Characterisation of Sri Lankan cassava mosaic virus and Indian cassava mosaic virus: evidence for acquisition of a DNA B component by a monopartite begomovirus. K Saunders N Salim VR Mali VG Malathi RW Briddon PG Markham J Stanley, Virology 2002 293 63 74 10.1006/viro.2001.1251 11853400
18. Pathogenicity of a natural recombinant associated with ageratum yellow vein disease: implications for geminivirus evolution and disease aetiology. K Saunders ID Bedford J Stanley, Virology 2001 282 38 47 10.1006/viro.2000.0832 11259188
19. Systemic movement and symptom production following agroinoculation with a single DNA of tomato yellow leaf curl geminivirus (Thailand). DE Rochester W Kositratana RN Beachy, Virology 1990 178 520 526 10.1016/0042-6822(90)90349-V 2219706
20. Molecular characterization of tomato-infecting begomoviruses in Yunnan, China. ZH Li XP Zhou X Zhang Y Xie, Arch Virol 2004 149 1721 1732 15593415 (Pubitemid 39225264)
21. Molecular characterization of tomato-infecting begomoviruses in Thailand. S Sawangjit O Chatchawankanphanich P Chiemsombat T Attathom J Dale S Attathom, Virus Res 2005 109 1 8 10.1016/j.virusres.2004.10.001 15826907 (Pubitemid 40249352)
22. Defective Interfering DNAs of Plant Viruses. BL Patil I Dasgupta, Crit Rev Plant Sci 2006 25 47 64 10.1080/07352680500391295 (Pubitemid 43068154)
23. Deletion and recombination events between the DNA-A and DNA-B components of Indian cassava-infecting geminiviruses generate defective molecules in Nicotiana benthamiana. BL Patil N Dutt RW Briddon SE Bull D Rothenstein BK Borah I Dasgupta J Stanley H Jeske, Virus Res 2007 124 59 67 10.1016/j.virusres.2006. 10.003 17109983
24. S1-sensitive sites in the supercoiled double-stranded form of tomato golden mosaic virus DNA component B: identification of regions of potential alternative secondary structure and regulatory function. G Sunter KW Buck RH Coutts, Nucleic Acids Res 1985 13 4645 4659 10.1093/nar/13.13.4645 2991843
25. Multiple cis elements contribute to geminivirus origin function. BM Orozco HJ Gladfelter SB Settlage PA Eagle RN Gentry L Hanley-Bowdoin, Virology 1998 242 346 356 10.1006/viro.1997.9013 9514968 (Pubitemid 28414740)
26. Identification of a defective molecule derived from DNA-A of the bipartite begomovirus of East African cassava mosaic virus. J Ndunguru JP Legg IBF Fofana TAS Aveling G Thompson CM Fauquet, Plant Pathol 2006 55 2 10 10.1111/j.1365-3059.2005.01289.x
27. Determinants of tomato golden mosaic virus symptom development located on DNA B. Av Arnim J Stanley, Virology 1992 186 286 293 10.1016/0042-6822(92) 90083-2 1727604
28. Transgenic plants expressing geminivirus movement proteins: abnormal phenotypes and delayed infection by Tomato mottle virus in transgenic tomatoes expressing the Bean dwarf mosaic virus BV1 or BC1 proteins. YM Hou R Sanders VM Ursin RL Gilbertson, Mol Plant Microbe Interact 2000 13 297 308 10.1094/MPMI.2000.13.3.297 10707355 (Pubitemid 30118875)
29. The nuclear shuttle protein of Tomato leaf curl New Delhi virus is a pathogenicity determinant. M Hussain S Mansoor S Iram AN Fatima Y Zafar, J Virol 2005 79 4434 4439 10.1128/JVI.79.7.4434-4439.2005 15767443 (Pubitemid 40388380)
30. Functional analysis of proteins involved in movement of the monopartite begomovirus, Tomato yellow leaf curl virus. MR Rojas H Jiang R Salati B Xoconostle-Cazares MR Sudarshana WJ Lucas RL Gilbertson, Virology 2001 291 110 125 10.1006/viro.2001.1194 11878881
31. Classification and identification of geminiviruses using sequence comparisons. M Padidam RN Beachy CM Fauquet, J Gen Virol 1995 76 249 263 10.1099/0022-1317-76-2-249 7844548
32. Geminivirus strain demarcation and nomenclature. CM Fauquet RW Briddon JK Brown E Moriones J Stanley M Zerbini X Zhou, Arch Virol 2008 153 783 821 10.1007/s00705-008-0037-6 18256781
33. Corchorus yellow vein virus, a New World geminivirus from the Old World. C Ha S Coombs P Revill R Harding M Vu J Dale, J Gen Virol 2006 87 997 1003 10.1099/vir.0.81631-0 16528050
34. Molecular characterization of begomoviruses and DNA satellites from Vietnam: additional evidence that the New World geminiviruses were present in the Old World prior to continental separation. C Ha S Coombs P Revill R Harding M Vu J Dale, J Gen Virol 2008 89 312 326 10.1099/vir.0.83236-0 18089756
35. Typing of human enteroviruses by partial sequencing of VP1. MS Oberste K Maher DR Kilpatrick MR Flemister BA Brown MA Pallansch, J Clin Microbiol 1999 37 1288 1293 10203472
36. Molecular criteria for genus and species discrimination within the family Potyviridae. MJ Adams JF Antoniw CM Fauquet, Arch Virol 2004 150 459 479 10.1007/s00705-004-0440-6 15592889
37. Revision of taxonomic criteria for species demarcation in the family Geminiviridae, and an updated list of begomovirus species. CM Fauquet DM Bisaro RW Briddon JK Brown BD Harrison EP Rybicki DC Stenger J Stanley, Arch Virol 2003 148 405 421 10.1007/s00705-002-0957-5 12557003
38. Molecular evolution of the human enteroviruses: correlation of serotype with VP1 sequence and application to picornavirus classification. MS Oberste K Maher DR Kilpatrick MA Pallansch, J Virol 1999 73 1941 1948 9971773
39. Classification of papillomaviruses. EM de Villiers CM Fauquet TR Broker HU Bernard H zur Hausen, Virology 2004 324 17 27 10.1016/j.virol.2004.03.033 15183049
40. Analysis of an isolate of Mungbean yellow mosaic virus (MYMV) with a highly variable DNA B component. AS Karthikeyan R Vanitharani V Balaji S Anuradha P Thillaichidambaram PV Shivaprasad C Parameswari V Balamani M Saminathan K Veluthambi, Arch Virol 2004 149 1643 1652 10.1007/s00705-004-0313-z 15290387 (Pubitemid 39059515)
41. Genetic and Phenotypic Variation of the Pepper golden mosaic virus Complex. JK Brown AM Idris KM Ostrow N Goldberg R French DC Stenger, Phytopathology 2005 95 1217 1224 10.1094/PHYTO-95-1217 18943475
42. Cassava mosaic geminiviruses: actual knowledge and perspectives. BL Patil CM Fauquet, Mol Plant Pathol 2009 10 685 701 10.1111/j.1364-3703.2009.00559.x 19694957
43. Both bipartite geminivirus movement proteins define viral host range, but only BL1 determines viral pathogenicity. DJ Ingham E Pascal SG Lazarowitz, Virology 1995 207 191 204 10.1006/viro.1995.1066 7871727
44. The fine structure of chloris striate mosaic virus. T Hatta RI Francki, Virology 1979 92 428 435 10.1016/0042-6822(79)90147-8 425323
45. Structure of the Maize streak virus geminate particle. W Zhang NH Olson TS Baker L Faulkner M Agbandje-McKenna MI Boulton JW Davies R McKenna, Virology 2001 279 471 477 10.1006/viro.2000.0739 11162803
46. The size of encapsidated single-stranded DNA determines the multiplicity of African cassava mosaic virus particles. T Frischmuth M Ringel C Kocher, J Gen Virol 2001 82 673 676 11172110
47. The evolutionary value of recombination is constrained by genome modularity. DP Martin E van der Walt D Posada EP Rybicki, PLoS Genet 2005 1 51 10.1371/journal.pgen.0010051 16244707
48. Viable chimaeric viruses confirm the biological importance of sequence specific maize streak virus movement protein and coat protein interactions. Evd Walt KE Palmer DP Martin EP Rybicki, Virol J 2008 5 61 72 10.1186/1743-422X-5-61 18489800
49. Two domains of the AL1 protein mediate geminivirus origin recognition. HJ Gladfelter PA Eagle EP Fontes L Batts L Hanley-Bowdoin, Virology 1997 239 186 197 10.1006/viro.1997.8869 9426458
50. Sequence parameters that determine specificity of binding of the replication-associated protein to its cognate in two strains of Tomato leaf curl virus-New Delhi. A Chatterji U Chatterji RN Beachy CM Fauquet, Virology 2000 273 341 350 10.1006/viro.2000.0434 10915605
51. Identification of replication specificity determinance in tomato leaf curl virus from New Delhi. A Chatterji M Padidam RN Beachy CM Fauquet, J Virol 1999 73 5481 5489 10364296
52. Bean golden yellow mosaic virus from Chiapas, Mexico: Characterization, Pseudorecombination with Other Bean-Infecting Geminiviruses and Germ Plasm Screening. ER Garrido-Ramirez MR Sudarshana RL Gilbertson, Phytopathology 2000 90 1224 1232 10.1094/PHYTO.2000.90.11.1224 18944424
53. Melon chlorotic leaf curl virus: characterization and differential reassortment with closest relatives reveal adaptive virulence in the squash leaf curl virus clade and host shifting by the host-restricted bean calico mosaic virus. AM Idris K Mills-Lujan K Martin JK Brown, J Virol 2008 82 1959 1967 10.1128/JVI.01992-07 18057231
54. Specificity of bipartite geminivirus movement proteins. T Frischmuth S Roberts A von Arnim J Stanley, Virology 1993 196 666 673 10.1006/viro.1993.1523 8372440
55. Natural Genomic and Antigenic Variation in Whitefly-Transmitted Geminiviruses (Begomoviruses). B Harrison D Robinson, Annu Rev Phytopathol 1999 37 369 398 10.1146/annurev.phyto.37.1.369 11701828
56. Molecular evidence for existence of a New World begomovirus associated with yellow mosaic disease of Corchorus capsularis in India. R Ghosh S Paul S Das P Palit S Acharyya A Das JI Mir SK Ghosh A Roy, Australasian Plant Dis Notes 2008 3 59 62
57. The role of AV2 ("precoat") and coat protein in viral replication and movement in tomato leaf curl geminivirus. M Padidam RN Beachy CM Fauquet, Virology 1996 224 390 404 10.1006/viro.1996.0546 8874500
58. Interaction with host SGS3 is required for suppression of RNA silencing by tomato yellow leaf curl virus V2 protein. E Glick A Zrachya Y Levy A Mett D Gidoni E Belausov V Citovsky Y Gafni, Proc Natl Acad Sci USA 2008 105 157 161 10.1073/pnas.0709036105 18165314
59. Advances in Geminivirus Research. B Harrison, Annu Rev Phytopathol 1985 23 55 82 10.1146/annurev.py.23.090185.000415
60. Analysis of the nucleotide sequence of the treehopper-transmitted geminivirus, tomato pseudo-curly top virus, suggests a recombinant origin. RW Briddon ID Bedford JH Tsai PG Markham, Virology 1996 219 387 394 10.1006/viro.1996.0264 8638404
61. Size reversion of African cassava mosaic virus coat protein gene deletion mutants during infection of Nicotiana benthamiana. P Etessami J Watts J Stanley, J Gen Virol 1989 70 277 289 10.1099/0022-1317-70-2-277 2732690
62. Possible emergence of new geminiviruses by frequent recombination. M Padidam S Sawyer CM Fauquet, Virology 1999 265 218 225 10.1006/viro.1999.0056 10600594
63. Lethal mutations within the conserved stem-loop of African cassava mosaic virus DNA are rapidly corrected by genomic recombination. S Roberts J Stanley, J Gen Virol 1994 75 3203 3209 10.1099/0022-1317-75-11-3203 7964630
64. The nucleotide sequence of an infectious clone of the geminivirus beet curly top virus. J Stanley PG Markham RJ Callis MS Pinner, EMBO J 1986 5 1761 1767 16453696
65. A nanovirus-like DNA component associated with yellow vein disease of Ageratum conyzoides: evidence for interfamilial recombination between plant DNA viruses. K Saunders J Stanley, Virology 1999 264 142 152 10.1006/viro.1999.9948 10544139
66. Pathogenicity of a naturally occurring recombinant DNA satellite associated with tomato yellow leaf curl China virus. X Tao X Zhou, J Gen Virol 2008 89 306 311 10.1099/vir.0.83388-0 18089755
67. Characterization of DNAbeta associated with begomoviruses in China and evidence for co-evolution with their cognate viral DNA-A. X Zhou Y Xie X Tao Z Zhang Z Li CM Fauquet, J Gen Virol 2003 84 237 247 10.1099/vir.0.18608-0 12533720
68. Tobacco curly shoot virus DNAbeta Is Not Necessary for Infection but Intensifies Symptoms in a Host-Dependent Manner. Z Li Y Xie X Zhou, Phytopathology 2005 95 902 908 10.1094/PHYTO-95-0902 18944412
69. Severe leaf curl disease of cowpea - a new disease of cowpea in northern India caused by Mungbean yellow mosaic India virus and a satellite DNA A Rouhibakhsh VG Malathi, Plant Pathol 2004 54 259 10.1111/j.1365-3059.2005.01139. x
70. Infectivity, pseudorecombination and mutagenesis of Kenyan cassava mosaic begomoviruses. SE Bull RW Briddon WS Sserubombwe K Ngugi PG Markham J Stanley, J Gen Virol 2007 88 1624 1633 10.1099/vir.0.82662-0 17412996
71. A novel subviral agent associated with a geminivirus: the first report of a DNA satellite. IB Dry LR Krake JE Rigden MA Rezaian, Proc Natl Acad Sci USA 1997 94 7088 7093 10.1073/pnas.94.13.7088 9192696
72. Satellites of plant viruses. AF Murant MA Mayo, Ann Rev Phytopathol 1982 20 49 70 10.1146/annurev.py.20.090182.000405
73. Sequence similarity between putative gene products of geminiviral DNAs. R Kikuno H Toh H Hayashida T Miyata, Nature 1984 308 562 10.1038/308562a0 6709065
74. A unique virus complex causes Ageratum yellow vein disease. K Saunders ID Bedford RW Briddon PG Markham SM Wong J Stanley, Proc Natl Acad Sci USA 2000 97 6890 6895 10.1073/pnas.97.12.6890 10841581
75. Identification of DNA components required for induction of cotton leaf curl disease. RW Briddon S Mansoor ID Bedford MS Pinner K Saunders J Stanley Y Zafar KA Malik PG Markham, Virology 2001 285 234 243 10.1006/viro.2001.0949 11437658
76. A begomovirus DNA -encoded protein binds DNA, functions as a suppressor of RNA silencing, and targets the cell nucleus. X Cui G Li D Wang D Hu X Zhou, J Virol 2005 79 10764 10775 10.1128/JVI.79.16.10764-10775.2005 16051868
77. A monopartite begomovirus-associated DNA beta satellite substitutes for the DNA B of a bipartite begomovirus to permit systemic infection. M Saeed Y Zafar JW Randles MA Rezaian, J Gen Virol 2007 88 2881 2889 10.1099/vir.0.83049-0 17872543
78. Limitations on geminivirus genome size imposed by plasmodesmata and virus-encoded movement protein: insights into DNA trafficking. RL Gilbertson M Sudarshana H Jiang MR Rojas WJ Lucas, Plant Cell 2003 15 2578 2591 10.1105/tpc.015057 14555695
79. Identification of a novel circular single-stranded DNA associated with cotton leaf curl disease in Pakistan. S Mansoor SH Khan A Bashir M Saeed Y Zafar KA Malik RW Briddon J Stanley PG Markham, Virology 1999 259 190 199 10.1006/viro.1999.9766 10364503
80. Transactivation of geminivirus AR1 and BR1 gene expression by the viral AL2 gene product occurs at the level of transcription. G Sunter DM Bisaro, Plant Cell 1992 4 1321 1331 10.1105/tpc.4.10.1321 1446172
81. Phloem specific promoter from a satellite associated with a DNA virus. C Guan X Zhou, Virus Res 2006 115 150 157 10.1016/j.virusres.2005.08.002 16169625
82. Identification of sequence elements regulating promoter activity and replication of a monopartite begomovirus-associated DNA satellite. O Eini SAA Behjatnia S Dogra IB Dry JW Randles MA Rezaian, J Gen Virol 2009 90 253 260 10.1099/vir.0.002980-0 19088296
83. National center for biotechnology information viral genomes project. Y Bao S Federhen D Leipe V Pham S Resenchuk M Rozanov R Tatusov T Tatusova, J Virol 2004 78 7291 7298 10.1128/JVI.78.14.7291-7298.2004 15220402
84. PAUP User's Manual. D Swofford, Champaign: Illinois Natural History Survey 1991
85. Numerical Taxonomy. PH Sneath RR Sokal, San Francisco: W. H. Freeman 1973
86. The neighbor-joining method: a new method for reconstructing phylogenetic trees. N Saitou M Nei, Mol Biol Evol 1987 4 406 425 3447015