Recombination analysis of Soybean mosaic virus sequences reveals evidence of RNA recombination between distinct pathotypes

Virology Journal

Volumn 5, Issue , 2008, Pages

  Gagarinova, Alla G ^a,b,d   Babu, Mohan ^a   Strömvik, Martina V ^c   Wang, Aiming ^a,b  

^a AGRICULTURE AND AGRI FOOD CANADA   (Canada)

^b UNIVERSITY OF WESTERN ONTARIO   (Canada)

^c MCGILL UNIVERSITY   (Canada)

^d UNIVERSITY OF TORONTO   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

CAPSID PROTEIN; VIRUS RNA;

AMINO TERMINAL SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; CONTROLLED STUDY; GENE SEQUENCE; MOSAIC VIRUS; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; RNA RECOMBINATION; SEQUENCE ALIGNMENT; SOYBEAN; CLASSIFICATION; DNA SEQUENCE; GENETIC RECOMBINATION; GENETICS; MOLECULAR EVOLUTION; MOLECULAR GENETICS; PHYLOGENY; PLANT DISEASE; POTYVIRUS; VIROLOGY;

APHIDIDAE; GLYCINE MAX; MIRIDAE; RNA VIRUSES; SOYBEAN MOSAIC VIRUS;

EVOLUTION, MOLECULAR; MOLECULAR SEQUENCE DATA; PHYLOGENY; PLANT DISEASES; POTYVIRUS; RECOMBINATION, GENETIC; RNA, VIRAL; SEQUENCE ANALYSIS, DNA; SOYBEANS;

EID: 58449106533     PISSN: None     EISSN: 1743422X     Source Type: Journal    
DOI: 10.1186/1743-422X-5-143     Document Type: Article

References (38)

1. Evaluation of resistance in soybean germplasm to Soybean mosaic potyvirus under field conditions. M Arif S Hassan, J Biol Sci 2002 2 601 604
2. Genetic and phenotypic analysis of Soybean mosaic virus resistance in PI 88788 soybean. I Gunduz GR Buss P Chen SA Tolin, Phytopathology 2004 94 687 692 10.1094/PHYTO.2004.94.7.687 18943900
3. Inheritance and allelism of resistance to Soybean mosaic virus in Zao18 soybean from China. L Liao P Chen GR Buss Q Yang SA Tolin, J Hered 2002 93 447 452 10.1093/jhered/93.6.447 12642647
4. Association of the transcriptional response of soybean plants with soybean mosaic virus systemic infection. M Babu AG Gagarinova JE Brandle A Wang, J Gen Virol 2008 89 1069 1080 10.1099/vir.0.83531-0 18343851
5. Potyvirus proteins: a wealth of functions. S Urcuqui-Inchima AL Haenni F Bernardi, Virus Res 2001 74 157 175 10.1016/S0168-1702(01)00220-9 11226583
6. An overlapping essential gene in the Potyviridae. BY-W Chung WA Miller JF Atkins AE Firth, Proc Natl Acad Sci USA 2008 105 5897 5902 18408156 10.1073/pnas.0800468105
7. Strains of soybean mosaic virus classification based on virulence in resistanct soybean cultivars. EK Cho RM Goodman, Phytopathology 1979 69 467 470 10.1094/Phyto-69-467
8. Evaluation of resistance in soybeans to soybean mosaic virus strains. EK Cho RM Goodman, Crop Sci 1982 22 1133 1136
9. Studies on virus diseases and causal viruses of soybean in Japan. K Takahashi T Tanaka W Iida Y Tsuda, Tohoku Natl Agric Exp Stn Bull 1980 62 1 130
10. Identification of two new starins of soybean mosaic virus. YX Chen BD Xue YZ Hu ZD Fang, Acta Phytophyl Sin 1986 13 221 226
11. Identification of strains of soybean mosaic virus. ZQ Pu Q Cao DC Fang BD Xi CT Fang, Acta Phytophyl Sin 1982 9 15 20
12. Variation and evolution of plant virus populations. F García-Arenal A Fraile JM Malpica, Int Microbiol 2003 6 225 232 10.1007/s10123-003-0142-z 13680390
13. RNA recombination in animal and plant viruses. MM Lai, Microbiol Rev 1992 56 61 79 1579113
14. RNA recombination in vivo in the absence of viral replication. A Gallei A Pankraz HJ Thiel P Becher, J Virol 2004 78 6271 6281 15163720 10.1128/JVI.78.12.6271-6281.2004
15. Emergence of Rsv-resistance breaking Soybean mosaic virus isolates from Korean soybean cultivars. BK Choi JM Koo HJ Ahn HJ Yum CW Choi KH Ryu P Chen SA Tolin, Virus Res 2005 112 42 51 10.1016/j.virusres.2005.03.020 15869819
16. Identification and molecular characterization of two naturally occurring Soybean mosaic virus isolates that are closely related but differ in their ability to overcome Rsv4 resistance. AG Gagarinova M Babu V Poysa JH Hill A Wang, Virus Res 2008 18793685
17. Evolution of Soybean mosaic virus-G7 molecularly cloned genome in Rsv1-genotype soybean results in emergence of a mutant capable of evading Rsv1-mediated recognition. MR Hajimorad AL Eggenberger JH Hill, Virology 2003 314 497 509 10.1016/S0042-6822(03)00456-2 14554079
18. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. JD Thompson DG Higgins TJ Gibson, Nucleic Acids Res 1994 22 4673 4680 7984417 10.1093/nar/22.22.4673
19. RDP2: recombination detection and analysis from sequence alignments. DP Martin C Williamson D Posada, Bioinformatics 2005 21 260 262 10.1093/bioinformatics/bth490 15377507
20. Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of inter subtype recombination. KS Lole RC Bollinger RS Paranjape D Gadkari SS Kulkarni NG Novak R Ingersoll HW Sheppard SC Ray, J Virol 1999 73 152 160 9847317
21. Recombination in AIDS viruses. DL Robertson BH Hahn PM Sharp, J Mol Evol 1995 40 249 259 10.1007/BF00163230 7723052
22. Recombination in HIV-1. DL Robertson PM Sharp FE McCutchan BH Hahn, Nature 1995 374 124 126 10.1038/374124b0 7877682
23. Analyzing the mosaic structure of genes. JM Smith, J Mol Evol 1992 34 126 129 1556748
24. Complete genome sequences of the genomic RNA of Soybean mosaic virus strains G7H and G5. WS Lim YH Kim KH Kim, Plant Pathol 2003 19 171 176
25. RNAvirus mutations and fitness for survival. E Domingo JJ Holland, Annu Rev Microbiol 1997 51 151 78 10.1146/annurev.micro.51.1.151 9343347
26. Loss and gain of elicitor function of Soybean mosaic virus G7 provoking Rsv1-mediated lethal systemic hypersensitive response maps to P3. MR Hajimorad AL Eggenberger JH Hill, J Virol 2005 79 1215 1222 15613348 10.1128/JVI.79.2. 1215-1222.2005
27. The 6K2 protein and the VPg of potato virus A are determinants of systemic infection in Nicandra physaloides. ML Rajamaki JPT Valkonen, Mol Plant-Microbe Interact 1999 12 1074 1081 10.1094/MPMI.1999.12.12.1074 10624016
28. The cylindrical inclusion gene of Turnip mosaic virus encodes a pathogenic determinant to the Brassicaresistance gene TuRB01. CE Jenner F Sanchez SB Nettleship GD Foster F Ponz JA Walsh, Mol Plant-Microbe Interact 2000 13 1102 1108 10.1094/MPMI.2000.13.10.1102 11043471
29. The ability of a bymovirus to overcome the rym4-mediated resistance in barley correlates with a codon change in the VPg coding region on RNA1. T Kühne N Shi G Proeseler MJ Adams K Kanyuka, J General Virol 2003 84 2853 2859 10.1099/vir.0.19347-0
30. The recessive potyvirus resistance gene pot-1 is the tomato orthologue of the pepper pvr2-eIF4E gene. S Ruffel JL Gallois ML Lesage C Caranta, Mol Gen Genomics 2005 274 346 353 10.1007/s00438-005-0003-x
31. Multiple determinants in the coding region of Pea seed-borne mosaic virus P3 are involved in virulence against sbm-2 resistance. CK Hjulsager BS Olsen DM Kjaer Jensen MI Cordea BN Krath IE Johansen OS Lund, Virology 2006 355 52 61 10.1016/j.virol.2006.07.016 16908044
32. Increase in Zucchini yellow mosaic virus symptom severity in tolerant zucchini cultivars is related to a point mutation in P3 protein and is associated with a loss of relative fitness on susceptible plants. C Desbiez A Gal-On M Girard C Wipf-Scheibel H Lecoq, Phytopathology 2003 93 1478 1484 10.1094/PHYTO.2003.93.12.1478 18943611
33. A phylogenetic survey of recombination frequency in plant RNA viruses. ER Chare EC Holmes, Arch Virol 2006 151 933 946 10.1007/s00705-005-0675-x 16292597
34. The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. JD Thompson TJ Gibson F Plewniak F Jeanmougin DG Higgins, Nucleic Acids Res 1997 24 4876 4882 10.1093/nar/25.24. 4876
35. MRBAYES 3:Bayesian phylogenetic inference under mixed models. F Ronquist JP Huelsenbeck, Bioinformatics 2003 19 1572 1574 10.1093/bioinformatics/btg180 12912839
36. PHYLIP - Phylogeny Inference Package (Version 3.2). J Felsenstein, Cladistics 1989 5 164 166
37. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. S Guindon O Gascuel, Syst Biol 2003 52 696 704 10.1080/10635150390235520 14530136
38. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. H Shimodaira M Hasegawa, Mol Biol Evol 1999 16 1114 1116