Characterization, genetic diversity, and evolutionary link of cucumber mosaic virus strain New Delhi from India

Biochemical Genetics

Volumn 49, Issue 1-2, 2011, Pages 25-38

  Koundal, Vikas ^a   Haq , Qazi Mohd Rizwanul ^b   Praveen, Shelly ^a  

^a INDIAN AGRICULTURAL RESEARCH INSTITUTE   (India)

^b JAMIA MILLIA ISLAMIA CENTRAL UNIVERSITY   (India)

Author keywords

2b; CMV ND; Cucumovirus; Genome diversity

Indexed keywords

COAT PROTEIN; HELICASE; METHYLTRANSFERASE; RNA POLYMERASE; SINGLE STRANDED RNA; VIRUS RNA;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ARTICLE; CUCUMBER MOSAIC VIRUS; GENETIC ANALYSIS; GENETIC CONSERVATION; GENETIC RECOMBINATION; GENETIC VARIABILITY; INDIA; NONHUMAN; NUCLEOTIDE SEQUENCE; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; STRAIN DIFFERENCE; TAIWAN; TOMATO; VIRUS GENOME;

AMINO ACID SEQUENCE; BASE SEQUENCE; BIOLOGICAL EVOLUTION; CUCUMOVIRUS; GENES, VIRAL; GENETIC VARIATION; INDIA; LYCOPERSICON ESCULENTUM; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PHYLOGEOGRAPHY; RECOMBINATION, GENETIC; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; VIRAL PROTEINS;

CUCUMBER MOSAIC VIRUS; CUCUMOVIRUS; LYCOPERSICON ESCULENTUM;

EID: 79151475884     PISSN: 00062928     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10528-010-9382-8     Document Type: Article

References (46)

1. MF Boni D Posada MW Feldman 2007 An exact nonparametric method for inferring mosaic structure in sequence triplets Genetics 176 1035 1047 1:CAS:528:DC%2BD2sXovVOqsrw%3D 10.1534/genetics.106.068874 17409078 (Pubitemid 46961105)
2. J Bonneta A Fraile S Sacristan JM Malpica F Garcia-Arenal 2005 Role of recombination in the evolution of natural populations of Cucumber mosaic virus, a tripartite RNA plant virus Virology 332 359 368 10.1016/j.virol.2004.11.017 (Pubitemid 40127255)
3. A Bruyere M Wantroba S Flasinski A Dzianott JJ Bujarski 2000 Frequent homologous recombination events between molecules of one RNA component in a multipartite RNA virus J Virol 74 4214 4219 1:CAS:528:DC%2BD3cXislGru7w%3D 10.1128/JVI.74.9.4214-4219.2000 10756034 (Pubitemid 30214427)
4. ER Chare EC Holmes 2006 A phylogenetic survey of recombination frequency in plant RNA viruses Arch Virol 151 933 946 1:CAS:528:DC%2BD28Xjs1Klurw%3D 10.1007/s00705-005-0675-x 16292597
5. ER Chare EA Gould EC Holmes 2003 Phylogenetic analysis reveals a low rate of homologous recombination in negative sense RNA viruses J Gen Virol 84 2691 2703 1:CAS:528:DC%2BD3sXotF2gtLg%3D 10.1099/vir.0.19277-0 13679603 (Pubitemid 37321311)
6. Y Chen J Chen H Zhang X Tang Z Du 2007 Molecular evidence and sequence analysis of a natural reassortant between Cucumber mosaic virus subgroup IA and II strains Virus Genes 35 405 413 1:CAS:528:DC%2BD2sXnvFeitro%3D 10.1007/s11262-007-0094-z 17417698 (Pubitemid 47087548)
7. JW Drake JJ Holland 1999 Mutation rates among RNA viruses Proc Natl Acad Sci USA 96 13910 13913 1:CAS:528:DyaK1MXns1Oqtb0%3D 10.1073/pnas.96.24.13910 10570172
8. J Felsenstein 1985 Confidence limits on phylogenies: an approach using the bootstrap Evolution 39 783 791 10.2307/2408678
9. MM Finetti Sialer F Cillo L Barbarossa D Gallitelli 1999 Differentiation of Cucumber mosaic virus subgroups by RT-PCR RFLP J Plant Pathol 81 145 148
10. A Fraile JL Alonso-Prados MA Aranda JJ Bernal JM Malpica F Garcia-Arenal 1997 Genetic exchange by recombination or reassortment is infrequent in natural population of a tripartite RNA plant virus J Virol 71 934 940 1:CAS:528:DyaK2sXls1ejtA%3D%3D 8995610
11. R Galetto M Negroni 2005 Mechanistic features of recombination in HIV AIDS Rev 7 92 102 16092503
12. L Galipienso L Rubio C Lopez S Soler J Aramburu 2009 Complete nucleotide sequence of a Spanish isolate of Parietaria mottle virus infecting tomato Virus Genes 39 256 260 1:CAS:528:DC%2BD1MXhsVamsbfF 10.1007/s11262-009-0388-4
13. MJ Gibbs JS Armstrong AJ Gibbs 2000 Sister-scanning: a Monte Carlo procedure for assessing signals in recombinant sequences Bioinformatics 16 573 582 1:CAS:528:DC%2BD3cXosFSqs7g%3D 10.1093/bioinformatics/16.7.573 11038328
14. MV Graves MJ Roossinck 1995 Characterization of defective RNAs derived from RNA 3 of the Fny strain of cucumber mosaic cucumovirus J Virol 69 4746 4751 1:CAS:528:DyaK2MXmvFWgsrw%3D 7609040
15. TA Hall 1999 BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT Nucl Acids Symp Ser 41 95 98 1:CAS:528:DC%2BD3cXhtVyjs7Y%3D
16. EC Holmes M Worobey A Rambaut 1999 Phylogenetic evidence for recombination in dengue virus Mol Biol Evol 16 405 409 1:CAS:528: DyaK1MXhvVOqtLY%3D 10331266
17. JS Hu HP Li K Barry M Wang R Jordan 1995 Comparison of dot-blot, Elisa, and RT-PCR assays for detection of two Cucumber mosaic virus isolates infecting banana in Hawaii Plant Dis 79 902 906 1:CAS:528:DyaK2MXos1Gmt78%3D 10.1094/PD-79-0902
18. V Ilardi M Mazzei S Loreti L Tomassoli M Barba 1995 Biomolecular and serological methods to identify strains of Cucumber mosaic cucumovirus on tomato EPPO Bull 25 321 327 10.1111/j.1365-2338.1995.tb01473.x
19. IB Jakobsen S Easteal 1996 A program for calculating and displaying compatibility matrices as an aid in determining reticulate evolution in molecular sequences Comput Appl Biosci 12 291 295 1:CAS:528:DyaK28XmvFWrtr0%3D 8902355
20. MMC Lai 1992 RNA recombination in animal and plant viruses Microbiol Rev 56 61 79 1:CAS:528:DyaK38XitlWgt7Y%3D 1579113
21. SK Mangrauthia B Parameswari RK Jain S Praveen 2008 Role of genetic recombination in the molecular architecture of Papaya ringspot virus Biochem Genet 46 835 846 1:CAS:528:DC%2BD1cXhtlalsLjM 10.1007/s10528-008-9198-y 18807167
22. T Maoka YS Hayano M Iwasaki K Yoshida C Masuta 2010 Mixed infection in tomato to ensure frequent generation of a natural reassortant between two subgroups of Cucumber mosaic virus Virus Genes 40 148 150 1:CAS:528: DC%2BC3cXitlyqug%3D%3D 10.1007/s11262-009-0414-6 19866353
23. DP Martin C Williamson D Posada 2005 RDP2: recombination detection and analysis from sequence alignments Bioinformatics 21 260 262 1:CAS:528: DC%2BD2MXkt1Whug%3D%3D 10.1093/bioinformatics/bth490 15377507 (Pubitemid 40202028)
24. J Maynard Smith 1992 Analyzing the mosaic structure of genes J Mol Evol 34 126 129
25. G McGuire F Wright 2000 TOPAL 2.0: improved detection of mosaic sequences within multiple alignments Bioinformatics 16 130 134 1:CAS:528: DC%2BD3cXktVyisbc%3D 10.1093/bioinformatics/16.2.130 10842734
26. GAT McVean SR Myers S Hunt P Deloukas DR Bentley P Donnelly 2004 The fine-scale structure of recombination rate variation in the human genome Science 304 581 584 1:CAS:528:DC%2BD2cXjt1Cku7c%3D 10.1126/science.1092500 15105499 (Pubitemid 38541915)
27. PD Nagy AE Simon 1997 New insight into the mechanisms of RNA recombination Virology 235 1 9 1:CAS:528:DyaK2sXlsFGjtrs%3D 10.1006/viro.1997. 8681 9300032 (Pubitemid 27380801)
28. PD Nagy J Pogany AE Simon 1999 RNA elements required for RNA recombination function as replication enhancers in vitro and in vivo in a plus-strand RNA virus EMBO J 18 5653 5665 1:CAS:528:DyaK1MXntFCmsL0%3D 10.1093/emboj/18.20.5653 10523308 (Pubitemid 29486383)
29. J Owen P Palukaitis 1988 Characterization of Cucumber mosaic virus I: molecular heterogeneity mapping of RNA 3 in eight CMV strains Virology 166 495 502 1:CAS:528:DyaL1MXhvVag 10.1016/0042-6822(88)90520-X 3176343
30. J Owen M Shintaku P Aeschleman SF Tahar P Palukaitis 1990 Nucleotide sequence and evolutionary relationships of Cucumber mosaic virus (CMV) strains, CMV RNA 3 J Gen Virol 71 2243 2249 1:CAS:528:DyaK3MXhsFOrt7s%3D 10.1099/0022-1317-71-10-2243 2230731
31. M Padidam S Sawyer CM Fauquet 1999 Possible emergence of new geminiviruses by frequent recombination Virology 265 218 225 1:CAS:528:DyaK1MXnvFertbs%3D 10.1006/viro.1999.0056 10600594 (Pubitemid 30022217)
32. P Palukaitis M Zaitlin 1997 Replicase-mediated resistance to plant virus diseases Adv Virus Res 48 349 377 1:CAS:528:DyaK2sXntVeis7k%3D 10.1016/S0065-3527(08)60292-4 9233437
33. P Palukaitis MJ Roossinck RG Dietgen RIB Francki 1992 Cucumber mosaic virus Adv Virus Res 41 281 348 1:CAS:528:DyaK3sXjsVGn 10.1016/S0065-3527(08) 60039-1 1575085
34. D Posada KA Crandall 2001 Evaluation of methods for detecting recombination from DNA sequences: computer simulations Proc Natl Acad Sci USA 98 13757 13762 1:CAS:528:DC%2BD3MXovVyntrc%3D 10.1073/pnas.241370698 11717435 (Pubitemid 33115971)
35. D Posada KA Crandall 2002 The effect of recombination on accuracy of phylogeny estimation J Mol Evol 54 396 402 1:CAS:528:DC%2BD38XhsFKks78%3D 11847565
36. H Rizos LV Gunn RD Pares MR Gillings 1992 Differentiation of Cucumber mosaic virus isolates using the polymerase chain reaction J Gen Virol 73 2099 2103 1:CAS:528:DyaK38XlsVCntbs%3D 10.1099/0022-1317-73-8-2099 1645146
37. MJ Roossinck 1997 Mechanisms of plant virus evolution Ann Rev Phytopathol 35 191 209 1:CAS:528:DyaK2sXmtVGhsro%3D 10.1146/annurev.phyto.35.1.191 (Pubitemid 27422576)
38. MJ Roossinck 2001 Cucumber mosaic virus, a model for RNA virus evolution Mol Plant Pathol 2 59 63 1:CAS:528:DC%2BD3MXltVKksrs%3D 10.1046/j.1364-3703. 2001.00058.x 20572992 (Pubitemid 32532922)
39. MJ Roossinck 2002 Evolutionary history of Cucumber mosaic virus deduced by phylogenetic analyses J Virol 76 3382 3387 1:CAS:528:DC%2BD38Xit1Kjsrg%3D 10.1128/JVI.76.7.3382-3387.2002 11884564 (Pubitemid 34224541)
40. MO Salminen JK Carr DS Burke FE McCutchan 1995 Identification of breakpoints in intergenic recombinants of HIV type I by bootscanning AIDS Res Hum Retroviruses 11 1423 1425 1:CAS:528:DyaK28XitlKlsg%3D%3D 10.1089/aid.1995.11.1423 8573403
41. Seal S, Coates D (1998) Detection and quantification of plant viruses by PCR. In: Foster GD, Taylor SC (eds) Plant virology protocols, from virus isolation to transgenic resistance. Humana Press, Totowa, pp 469-485
42. BJ Shi P Palukaitis RH Symons 2002 Differential virulence by strains of Cucumber mosaic virus is mediated by the 2b gene Mol Plant Microbe Interact 15 947 955 1:CAS:528:DC%2BD38XntVSgsro%3D 10.1094/MPMI.2002.15.9.947 12236601
43. D Szilassy K Salanki E Balazs 1999 Molecular evidence for the existence of two distinct subgroups in Cucumber mosaic cucumovirus Virus Genes 18 221 227 1:CAS:528:DyaK1MXltVKrs7g%3D 10.1023/A:1008016202128 10456790 (Pubitemid 29353711)
44. JD Thompson TJ Gibson F Plewniak F Jeanmougin DG Higgins 1997 The Clustal X Windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools Nucleic Acids Res 24 4876 4882 10.1093/nar/25.24.4876 (Pubitemid 28022245)
45. Z Weng R Barthelson S Gowda ME Hilf WO Dawson DW Galbraith Z Xiong 2007 Persistent infection and promiscuous recombination of multiple genotypes of an RNA virus within a single host generate extensive diversity PLoS One 2 e917 10.1371/journal.pone.0000917 17878952 (Pubitemid 351445305)
46. V Wilson P Taylor U Desselberger 1988 Crossover regions in foot-and-mouth disease virus (FMDV) recombinants corresponds to regions of high local secondary structure Arch Virol 102 131 139 1:CAS:528:DyaL1MXlt1SmtQ%3D%3D 10.1007/BF01315570 2848475