Sequence variability within the 3′-proximal part of the Sweet potato mild mottle virus genome

Archives of Virology

Volumn 148, Issue 3, 2003, Pages 487-496

  Mukasa, S B ^a,b   Rubaihayo, P R ^b   Valkonen, Jari P T ^a,c  

^a SWEDISH UNIVERSITY OF AGRICULTURAL SCIENCES   (Sweden)

^b MAKERERE UNIVERSITY   (Uganda)

^c UNIVERSITY OF HELSINKI   (Finland)

Author keywords

[No Author keywords available]

Indexed keywords

3' UNTRANSLATED REGIONS; AMINO ACID SEQUENCE; CAPSID PROTEINS; IPOMOEA BATATAS; MOLECULAR SEQUENCE DATA; PLANT DISEASES; POTYVIRIDAE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; UGANDA; VARIATION (GENETICS);

IPOMOEA BATATAS; IPOMOVIRUS; POTYVIRIDAE; SOLANUM TUBEROSUM; SWEET POTATO MILD MOTTLE VIRUS;

EID: 0344838340     PISSN: 03048608     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00705-002-0930-3     Document Type: Article

References (37)

1. Alicai T, Fenby NS, Gibson RW, Adipala E, Vetten HJ, Foster GD, Seal SE (1999) Occurrence of two serotypes of sweet potato chlorotic stunt virus in East Africa and their associated differences in coat protein and HSP70 homologue gene sequences. Plant Pathol 48: 718-726
2. Badge JL, Robinson DJ, Brunt AA, Foster GD (1997) 3′ end terminal sequences of the RNA genomes of Narcissus latent and Maclura mosaic viruses suggest that they represent a new genus of the Potyviridae. J Gen Virol 78: 253-257
3. Bos L (1999) Plant viruses, unique and intriguing pathogens. A textbook of plant virology. Backhuys Publishers, Leiden
4. Clark CA, Moyer JW (1988) Compendium of sweet potato diseases. American Phytopathological Society, St Paul, MN
5. Colinet D, Kummert J, Lepoivre P (1996) Molecular evidence that the whitefly-transmitted sweet potato mild mottle virus belongs to distinct genus of the Potyviridae. Arch Virol 141: 125-135
6. Colinet D, Kummert P, Lepoivre P (1998) The nucleotide sequence and genome organisation of the whitefly transmitted sweet potato mild mottle virus: a close relationship with members of the family Potyviridae. Virus Res 53: 187-196
7. Felsenstein J (1993) PHYLIP (Phylogeny Inference Package) version 3.57c. Department of Genetics, University of Washington, Seattle, WA
8. Foulds IJ, Lea VJ, Sidebottom C, James CM, Boulton RE, Brears T, Slabas AR, Jack PL, Stratford R (1993) Cloning and sequence-analysis of the coat protein gene of barley mild mottle mosaic virus. Virus Res 27: 79-89
9. García-Arenal F, Fraile A, Malpica JM (2001) Variability and genetic structure of plant virus populations. Annu Rev Phytopathol 39: 157-186
10. Gibbs A, Mackenzie A (1997) A primer pair for amplifying part of the genome of all potyvirids by RT-PCR. J Virol Methods 63: 9-16
11. Gibbs KS, Padovan AC (1993) Detection of sweet potato feathery mottle in sweet potato grown in Northern Australia using an efficient and simple assay. Int J Pest Management 39: 223-228
12. Gibson RW, Mpembe I, Alicai T, Carey EE, Mwanga ROM, Seal SE, Vetten HJ (1998) Symptoms, etiology and serological analysis of sweet potato virus disease in Uganda. Plant Pathol 47: 95-102
13. Haldeman-Cahill R, Daros J-A, Carrington JC (1998) Secondary structures in the coding sequences and 3′ non-translated region involved in amplification of the tobacco etch virus genome. J Virol 72: 4072-4079
14. Hollings M, Stone OM, Bock KR (1976) Purification and properties of sweet potato mild mottle, a whitefly borne virus from sweet potato (Ipomoea batatas) in East Africa. Ann Appl Biol 82: 511-528
15. Jacquet C, Delecolle B, Raccah B, Lecoq H, Dunez J, Ravelonandro M (1998) Use of modified plum pox virus coat protein genes developed to limit heteroencapsidation-associated risks in transgenic plants. J Gen Virol 79: 1509-1517
16. Karyeija RF, Gibson RW, Valkonen JPT (1998) The significance of sweet potato feathery mottle virus in subsistence sweet potato production in Africa. Plant Dis 82: 4-15
17. Kimura M (1980) A simple method for estimating evolutionary rates on base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16: 111-120
18. Kreuze JF, Karyeija RF, Gibson RW, Valkonen JPT (2000) Comparisons of coat protein gene sequences show that East African isolates of sweet potato feathery mottle virus form a genetically distinct group. Arch Virol 145: 567-574
19. Lecoq H, Desbiez C, Delecolle B, Cohen S, Mansour A (2000) Cytological and molecular evidence that the whitefly-transmitted cucumber vein yellowing virus is a tentative member of the family Potyviridae. J Gen Virol 81: 2289-2293
20. Mathews DH, Sabina J, Zuker M, Tuner DH (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol 288: 911-940
21. Monger WA, Seal S, Isaac AM, Foster GD (2001) Molecular characterisation of the Cassava brown streak virus coat protein. Plant Pathol 50: 527-534
22. Monger WA, Spence NJ, Foster GD (2001) Molecular evidence that the aphid-transmitted tomato mild mottle virus belongs to the Potyviridae family but not the Potyvirus genus. Arch Virol 146: 2435-2441
23. Moyer JW, Salazar LF (1989) Virus and virus-like diseases of sweet potato. Plant Dis 73: 451-455
24. Nolasco G, de Blas C, Torres V, Ponz F (1993) A method combining immunocapture and PCR amplification in a microtiter plate for the detection of plant viruses and subviral pathogens. J Virol Methods 45: 201-218
25. Quemeda H, L'Hostis B, Gonsalves D, Reardon IM, Heinrikson R, Hiebert EL, Sieu LC, Slightom JL (1990) The nucleotide sequences of the 3′-terminal regions of papaya ringspot virus strains W and P. J Gen Virol 71: 203-210
26. Rajamäki M, Merits A, Rabenstein F, Andrejeva J, Paulin L, Kekarainen T, Kreuze JF, Forster RLS, Valkonen JPT (1998) Biological, serological and molecular differences among isolates of potato A potyvirus. Phytopathology 88: 311-321
27. Saitou N, Nei M (1987) The neighbour-joining method: A new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406-425
28. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual, 2nd edn. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
29. Schaeffers GA, Terry ER (1976) Insect transmission of sweet potato disease agents in Nigeria. Phytopathology 66:642-645
30. Schubert J, Fauquet C, Merits A, Rabenstein F (1999) The complete nucleotide sequence of the ryegrass mosaic potyvirus indicates that it is a recombinant between members of two different genera in the family Potyviridae. Z Pflanzenkr Plflanzenschutz 106: 392-404
31. Shukla DD, Ward CW, Brunt AA (1994) The Potyviridae. CAB International, Wallingford, UK
32. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673-4680
33. Van der Vlugt RA, Leunissen J, Goldbach R (1993) Taxonomic relationships between distinct potato virus Y isolates based on detailed comparisons of the viral coat proteins and 3′ non-translated regions. Arch Virol 131: 361-375
34. Van Regenmortel MHV, Fauquet CM, Bishop DHL, Carstens EB, Estes MK, Lemon SM, Maniloff J, Mayo MA, McGeoch DJ, Pringle CR, Wickner RB (2000) Virus Taxonomy. Classification and nomenclature of viruses. Seventh Report of the International Committee on Taxonomy of Viruses. Academic Press, San Diego, CA
35. Wu M, Yeong CY, Lee SC, Wong SM (1993) Nucleotide sequence of the 3′ half zucchini yellow mosaic virus (Singapore isolate) genome encoding the 4K protein, protease, polymerase and coat protein. Nucleic Acids Res 21: 1317
36. Wang CH, Bau HJ, Yeh SD (1994) Comparison of the nuclear inclusion b protein and coat protein genes of five papaya ringspot virus strains distinct in geographic origin and pathogenicity. Phytopathology 84: 1205-1210
37. Yeh S-D, Jan F-J, Chiang C-H, Doung T-J, Chen M-C, Chung P-H, Bau H-J (1992) Complete nucleotide sequence and genetic organisation of papaya ringspot virus RNA. J Gen Virol 73: 2531-2541