Evolution of cassava brown streak disease-associated viruses

Journal of General Virology

Volumn 92, Issue 4, 2011, Pages 974-987

  Mbanzibwa, D R ^a,b,c   Tian, Y P ^b   Tugume, A K ^b,c   Patil, B L ^d   Yadav, J S ^d   Bagewadi, B ^d   Abarshi, M M ^e   Alicai, T ^f   Changadeya, W ^g   Mkumbira, J ^g   Muli, M B ^h   Mukasa, S B ^c   Tairo, F ^a   Baguma, Y ^f   Kyamanywa, S ^c   Kullaya, A ^a   Maruthi, M N ^e   Fauquet, C M ^d   Valkonen, J P T ^b  

^a Mikocheni Agricultural Research Institute   (Tanzania)

^b UNIVERSITY OF HELSINKI   (Finland)

^c MAKERERE UNIVERSITY   (Uganda)

^d Danforth Plant Science Center   (United States)

^e UNIVERSITY OF GREENWICH   (United Kingdom)

^f National Crops Resources Research Institute   (Uganda)

^g UNIVERSITY OF MALAWI   (Malawi)

^h KENYA AGRICULTURAL RESEARCH INSTITUTE   (Kenya)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEOTIDE; POLYPROTEIN;

AMINO ACID SEQUENCE; ARTICLE; CASSAVA BROWN STREAK DISEASE; CASSAVA BROWN STREAK VIRUS; DNA VIRUS; EVOLUTION; HOMOLOGOUS RECOMBINATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; VIRUS GENOME; VIRUS INFECTION; VIRUS ISOLATION;

AFRICA; CLUSTER ANALYSIS; EVOLUTION, MOLECULAR; GENOME, VIRAL; INDIA; MANIHOT; MOLECULAR SEQUENCE DATA; PHYLOGENY; PLANT DISEASES; POTYVIRIDAE; RECOMBINATION, GENETIC; RNA, VIRAL; SELECTION, GENETIC; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY;

CASSAVA BROWN STREAK VIRUS; IPOMOVIRUS; MANIHOT ESCULENTA; PICORNA; POTYVIRIDAE;

EID: 79955750036     PISSN: 00221317     EISSN: 14652099     Source Type: Journal    
DOI: 10.1099/vir.0.026922-0     Document Type: Article

References (56)

1. Alicai, T., Omongo, C. A., Maruthi, M. N., Hillocks, R. J., Baguma, Y., Kawuki, R., Bua, A., Otim-Nape, G. W. & Colvin, J. (2007). Reemergence of cassava brown streak disease in Uganda. Plant Dis 91, 24-29.
2. Anisimova, M., Nielsen, R. & Yang, Z. (2003). Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites. Genetics 164, 1229-1236.
3. Chare, E. R. & Holmes, E. C. (2004). Selection pressures in the capsid genes of plant RNA viruses reflect mode of transmission. J Gen Virol 85, 3149-3157.
4. Chare, E. R. & Holmes, E. C. (2006). A phylogenetic survey of recombination frequency in plant RNA viruses. Arch Virol 151, 933-946.
5. Chung, B.-N., Canto, T. & Palukaitis, P. (2007). Stability of recombinant plant viruses containing genes of unrelated plant viruses. J Gen Virol 88, 1347-1355.
6. Chung, B. Y. W., Miller, W. A., Atkins, J. F. & Firth, A. E. (2008). An overlapping essential gene in the Potyviridae. Proc Natl Acad Sci U S A 105, 5897-5902.
7. Deng, D., Otim-Nape, W. G., Sangare, A., Ogwal, S., Beachy, R. N. & Fauquet, C. M. (1997). Presence of a new virus closely related to East African cassava mosaic geminivirus, associated with cassava mosaic outbreak in Uganda. Afr J Root Tuber Crops 2, 23-28.
8. Dolja, V. V., Haldeman, R., Robertson, N. L., Dougherty, W. G. & Carrington, J. C. (1994). Distinct functions of capsid protein in assembly and movement of tobacco etch potyvirus in plants. EMBO J 13, 1482-1491.
9. Dolja, V. V., Haldeman-Cahill, R., Montgomery, A. E., Vandenbosch, K. A. & Carrington, J. C. (1995). Capsid protein determinants involved in cell-to-cell and long distance movement of tobacco etch potyvirus. Virology 206, 1007-1016.
10. Dolja, V. V., Kreuze, J. F. & Valkonen, J. P. T. (2006). Comparative and functional genomics of closteroviruses. Virus Res 117, 38-51.
11. Escriu, F., Fraile, A. & García-Arenal, F. (2007). Constraints to genetic exchange support gene coadaptation in a tripartite RNA virus. PLoS Pathog 3, e8.
12. Fauquet, C. M., Mayo, M. A., Maniloff, J., Desselberger, U. & Ball, L. A. (2005). Virus taxonomy: The Eighth Report of the International Committee on Taxonomy of Viruses. San Diego, CA: Elsevier Academic Press.
13. Galperin, M. Y., Moroz, O. V., Wilson, K. S. & Murzin, A. G. (2006). House cleaning, a part of good housekeeping. Mol Microbiol 59, 5-19.
14. García-Arenal, F., Fraile, A. & Malpica, J. M. (2001). Variability and genetic structure of plant virus populations. Annu Rev Phytopathol 39, 157-186.
15. Hall, T. A. (1999). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41, 95-98.
16. Hillocks, R. J. & Jennings, D. K. (2003). Cassava brown streak disease: a review of present knowledge and research needs. Int J Pest Manage 49, 225-234.
17. Janssen, D., Velasco, L., Martín, G., Segundo, E. & Cuadrado, I. M. (2007). Low genetic diversity among Cucumber vein yellowing virus isolates from Spain. Virus Genes 34, 367-371.
18. Kimura, M. (1980). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16, 111-120.
19. Kimura, M. & Takahata, N. (1983). Selective constraint in protein polymorphism: study of the effectively neutral mutation model by using an improved pseudosampling method. Proc Natl Acad Sci U S A 80, 1048-1052.
20. Lalić, J., Agudelo-Romero, P., Carrasco, P. & Elena, S. F. (2010). Adaptation of tobacco etch potyvirus to a susceptible ecotype of Arabidopsis thaliana capacitates it for systemic infection of resistant ecotypes. Philos Trans R Soc Lond B Biol Sci 365, 1997-2007.
21. Librado, P. & Rozas, J. (2009). DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25, 1451-1452.
22. Lodhi, M. A., Ye, G.-N., Weedon, N. F. & Reisch, B. L. (1994). A simple and efficient method for DNA extraction from grapevine cultivars and Vitis species. Plant Mol Biol Rep 12, 6-13.
23. Lole, K. S., Bollinger, R. C., Paranjape, R. S., Gadkari, D., Kulkarni, S. S., Novak, N. G., Ingersoll, R., Sheppard, H. W. & Ray, S. C. (1999). Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination. J Virol 73, 152-160.
24. Mangrauthia, S. K., Parameswari, B., Jain, R. K. & Praveen, S. (2008). Role of genetic recombination in the molecular architecture of Papaya ringspot virus. Biochem Genet 46, 835-846.
25. Martin, D. P., van der Walt, E., Posada, D. & Rybicki, E. P. (2005a). The evolutionary value of recombination is constrained by genome modularity. PLoS Genet 1, e51. doi:10.1371/journal.pgen.0010051.
26. Martin, D. P., Williamson, C. & Posada, D. (2005b). RDP2: recombination detection and analysis from sequence alignments. Bioinformatics 21, 260-262.
27. Maruthi, M. N., Hillocks, R. J., Mtunda, K., Raya, M. D., Muhanna, M., Kiozia, H., Rekha, A. R., Colvin, J. & Thresh, J. M. (2005). Transmission of Cassava brown streak virus by Bemisia tabaci (Gennadius). J Phytopathol 153, 307-312.
28. Mbanzibwa, D. R., Tian, Y., Mukasa, S. B. & Valkonen, J. P. T. (2009a). Cassava brown streak virus (Potyviridae) encodes a putative Maf/HAM1 pyrophosphatase implicated in reduction of mutations and a P1 proteinase that suppresses RNA silencing but contains no HC-Pro. J Virol 83, 6934-6940.
29. Mbanzibwa, D. R., Tian, Y. P., Tugume, A. K., Mukasa, S. B., Tairo, F., Kyamanywa, S., Kullaya, A. & Valkonen, J. P. T. (2009b). Genetically distinct strains of Cassava brown streak virus in the Lake Victoria basin and the Indian Ocean coastal area of East Africa. Arch Virol 154, 353-359.
30. Miyata, T., Miyazawa, S. & Yasunaga, T. (1979). Two types of amino acid substitutions in protein evolution. J Mol Evol 12, 219-236.
31. Monger, W. A., Seal, S., Cotton, S. & Foster, G. D. (2001a). Identification of different isolates of Cassava brown streak virus and development of a diagnostic test. Plant Pathol 50, 768-775.
32. Monger, W. A., Seal, S., Isaac, A. M. & Foster, G. D. (2001b). Molecular characterization of the Cassava brown streak virus coat protein. Plant Pathol 50, 527-534.
33. Monger, W. A., Alicai, T., Ndunguru, J., Kinyua, Z. M., Potts, M., Reeder, R. H., Miano, D. W., Adams, I. P., Boonham, N. & other authors (2010). The complete genome sequence of the Tanzanian strain of Cassava brown streak virus and comparison with the Ugandan strain sequence. Arch Virol 155, 429-433.
34. Moury, B., Morel, C., Johansen, E. & Jacquemond, M. (2002). Evidence for diversifying selection in Potato virus Y and in the coat protein of other potyviruses. J Gen Virol 83, 2563-2573.
35. Muse, S. V. & Gaut, B. S. (1994). A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. Mol Biol Evol 11, 715-724.
36. Mware, B., Narla, R., Amata, R., Olubayo, F., Songa, J., Kyamanywa, S. & Ateka, E. M. (2009). Efficiency of Cassava brown streak virus transmission by two whitefly species in coastal Kenya. J Gen Mol Virol 1, 40-45.
37. Pagán, I. & Holmes, E. C. (2010). Long-term evolution of the Luteoviridae: time scale and mode of virus speciation. J Virol 84, 6177-6187.
38. Patil, B. L. & Fauquet, C. M. (2009). Cassava mosaic geminiviruses: actual knowledge and perspectives. Mol Plant Pathol 10, 685-701.
39. Patil, B. L., Ogwok, E., Wagaba, H., Mohammed, I. U., Yadav, J. S., Bagewadi, B., Taylor, N. J., Kreuze, J. F., Maruthi, M. N. & other authors (2011). RNAi-mediated resistance to diverse isolates belonging to two virus species involved in Cassava brown streak disease. Mol Plant Pathol 12, 31-41.
40. Posada, D. (2002). Evaluation of methods for detecting recombination from DNA sequences: empirical data. Mol Biol Evol 19, 708-717.
41. Posada, D. & Crandall, K. A. (2002). The effect of recombination on the accuracy of phylogeny estimation. J Mol Evol 54, 396-402.
42. Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406-425.
43. Scotto-Lavino, E., Du, G. & Frohman, M. A. (2007). 59 end cDNA amplification using classic RACE. Nat Protoc 1, 2555-2562.
44. Storey, H.H. (1936). Virus diseases of East African plants. VI. A progress report on studies of the disease of cassava. East Afr Agric J 2, 34-39.
45. Tajima, F. & Nei, M. (1984). Estimation of evolutionary distance between nucleotide sequences. Mol Biol Evol 1, 269-285.
46. Tamura, K., Dudley, J., Nei, M. & Kumar, S. (2007). MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24, 1596-1599.
47. Tugume, A. K., Cuéllar, W. J., Mukasa, S. B. & Valkonen, J. P. T. (2010a). Molecular genetic analysis of virus isolates from wild and cultivated plants demonstrates that East Africa is a hotspot for the evolution and diversification of Sweet potato feathery mottle virus. Mol Ecol 19, 3139-3156.
48. Tugume, A. K., Mukasa, S. B., Kalkkinen, N. & Valkonen, J. P. T. (2010b). Recombination and selection pressure in the ipomovirus Sweet potato mild mottle virus (Potyviridae) in wild species and cultivated sweetpotato in the centre of evolution in East Africa. J Gen Virol 91, 1092-1108.
49. Valli, A., López-Moya, J. J. & García, J. A. (2007). Recombination and gene duplication in the evolutionary diversification of P1 proteins in the family Potyviridae. J Gen Virol 88, 1016-1028.
50. Varrelmann, M. & Maiss, E. (2000). Mutations in the coat protein gene of Plum pox virus suppress particle assembly, heterologous encapsidation and complementation in transgenic plants of Nicotiana benthamiana. J Gen Virol 81, 567-576.
51. Winter, S., Koerbler, M., Stein, B., Pietruszka, A., Paape, M. & Butgereitt, A. (2010). Analysis of cassava brown streak viruses reveals the presence of distinct virus species causing cassava brown streak disease in East Africa. J Gen Virol 91, 1365-1372.
52. Wong, W. S. W., Yang, Z., Goldman, N. & Nielsen, R. (2004). Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites. Genetics 168, 1041-1051.
53. Yang, Z. (2007). PAML4: phylogenetic analysis by maximum likelihood. Mol Biol Evol 24, 1586-1591.
54. Yang, Z., Nielsen, R., Goldman, N. & Pedersen, A. M. (2000). Codonsubstitution models for heterogeneous selection pressure at amino acid sites. Genetics 155, 431-449.
55. Yang, Z., Wong, W. S. W. & Nielsen, R. (2005). Bayes Empirical Bayes inference of amino acid sites under positive selection. Mol Biol Evol 22, 1107-1118.
56. Zhou, X., Liu, Y., Calvert, L., Munoz, C., Otim-Nape, G. W., Robinson, D. J. & Harrison, B. D. (1997). Evidence that DNA-A of a geminivirus associated with severe cassava mosaic disease in Uganda has arisen by interspecific recombination. J Gen Virol 78, 2101-2111.