Identification and phylogenetic analysis of sequences of Bean pod mottle virus, Soybean mosaic virus, and Cowpea chlorotic mottle virus in expressed sequence tag data from soybean

Canadian Journal of Plant Pathology

Volumn 28, Issue 2, 2006, Pages 289-301

  Stromvik M V ^a   Latour, F ^a   Archambault, A ^a   Vodkin, L O ^b  

^a MCGILL UNIVERSITY   (Canada)

^b UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

Bean pod mottle virus; Bioinformatics; Expressed sequence tags; Genomics; Glycine max; Soybean mosaic virus

Indexed keywords

ALFALFA MOSAIC VIRUS; ARACHIS HYPOGAEA; BEAN POD MOTTLE VIRUS; BEAN YELLOW MOSAIC VIRUS; COWPEA CHLOROTIC MOTTLE VIRUS; COWPEA MOSAIC VIRUS; COWPEA SEVERE MOSAIC VIRUS; CUCUMBER MOSAIC VIRUS; GLYCINE MAX; GLYCINE SOJA; NICOTIANA TABACUM; PEANUT MOTTLE VIRUS; PEANUT STUNT VIRUS; SOYBEAN MOSAIC VIRUS; TOBACCO MOSAIC VIRUS; TOBACCO RINGSPOT VIRUS; TOBACCO STREAK VIRUS;

EID: 33846473744     PISSN: 07060661     EISSN: 17152992     Source Type: Journal    
DOI: 10.1080/07060660609507298     Document Type: Article

References (49)

1. Allison, R. F., Janda, M., and Ahlquist, P., 1989. Sequence of Cowpea chlorotic mottle virus RNAs 2 and 3 and evidence of a recombination event during Bromovirus evolution. Virology, 172:321–330.
2. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D. J., 1997. Gapped BLAST and PSI-BLAST:a new generation of protein database search programs. Nucleic Acids Res., 25:3389–3402.
3. Anandalakshmi, R., Pruss, G. J., Ge, X., Marathe, R., Mallory, A. C., Smith, T. H., and Vance, V. B., 1998. A viral suppressor of gene silencing in plants. Proc. Natl. Acad. Sci. USA, 95:13 079–13 084.
4. Anjos, J. R., Jarlfors, U., and Ghabrial, S. A., 1992. Soybean mosaic potyvirus enhances the titer of two Comoviruses in dually infected soybean plants. Phytopathology, 82:1022–1027.
5. Barker, R. F., Jarvis, N. P., Thompson, D. V., Loesch-Fries, L. S., and Hall, T. C., 1983. Complete nucleotide sequence of Alfalfa mosaic virus RNA3. Nucleic Acids Res., 11:2881–2891.
6. Calvert, L. A., and Ghabrial, S. A., 1983. Enhancement by Soybean mosaic virus of Bean pod mottle virus titer in doubly infected soybean. Phytopathology, 73:992–997.
7. Chen, J., Zheng, H.-Y., Lin, L., Adams, M. J., Antoniw, J. F., Zhao, M.-F., Shang, Y.-F., and Chen, J.-P., 2004. A virus related to Soybean mosaic virus from Pinellia ternata in China and its comparison with local soybean SMV isolates. Arch. Virol., 149:349–363.
8. Chen, X., and Bruening, G., 1992a. Cloned DNA copies of Cowpea severe mosaic virus genomic RNAs:infectious transcripts and complete nucleotide sequence of RNA 1. Virology, 191:607–618.
9. Chen, X., and Bruening, G., 1992b. Nucleotide sequence and genetic map of Cowpea severe mosaic virus RNA 2 and comparisons with RNA 2 of other Comoviruses. Virology, 187:682–692.
10. Chisholm, S. T., Parra, M. A., Anderberg, R. J., and Carrington, J. C., 2001. Arabidopsis RTM1 and RTM2 genes function in phloem to restrict long-distance movement of Tobacco etch virus. Plant Physiol., 127:1667–1675.
11. Cornelissen, B. J., Brederode, F. T., Veeneman, G. H., van Boom, J. H., and Bol, J. F., 1983. Complete nucleotide sequence of Alfalfa mosaic virus RNA 2. Nucleic Acids Res., 11:3019–3025.
12. Cornelissen, B. J., Janssen, H., Zuidema, D., and Bol, J. F., 1984. Complete nucleotide sequence of Tobacco streak virus RNA 3. Nucleic Acids Res., 12:2427–2437.
13. Di, R., Hu, C.-C., and Ghabrial, S. A., 1999. Complete nucleotide sequence of Bean pod mottle virus RNA1:sequence comparisons and evolutionary relationships to other Comoviruses. Virus Genes, 18:129–137.
14. Dzianott, A. M., and Bujarski, J. J., 1991. The nucleotide sequence and genome organization of the RNA-1 segment in two bromo viruses:Broad bean mottle virus and Cowpea chlorotic mottle virus. Virology, 185:553–562.
15. Eggenberger, A. L., Stark, D. M., and Beachy, R. N., 1989. The nucleotide sequence of a Soybean mosaic virus coat protein-coding region and its expression in Escherichia coli, Agrobacterium tumefaciens and Tobacco callus. J. Gen. Virol., 70:1853–1860.
16. Felsenstein, J., 1985. Confidence limits on phylogenies:an approach using bootstrap. Evolution, 39:783–791.
17. Giesler, L. J., Ghabrial, S. A., Hunt, T. E., and Hill, J. H., 2002. Bean pod mottle virus:a threat to U.S. soybean production. Plant Dis., 86:1280–1289.
18. Graham, M. A., Silverstein, K. A., Cannon, S. B., and VandenBosch, K. A., 2004. Computational identification and characterization of novel genes from legumes. Plant Physiol., 135:1179–1197.
19. Gu, H., and Ghabrial, S. A., 2005. The Bean pod mottle virus proteinase cofactor and putative helicase are symptom severity determinants. Virology, 333:271–283.
20. Gu, H., Clark, A. J., de Sá, P. B., Pfeiffer, T. W., Tolin, S., and Ghabrial, S. A., 2002. Diversity among isolates of Bean pod mottle virus. Phytopathology, 92:446–452.
21. Hajimorad, M. R., Eggenberger, A. L., and Hill, J. H., 2003. 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. Virology, 314:497–509.
22. Hall, T., 1997. BioEdit tool, version 7.05, Carlsbad, Calif.:Ibis Therapeutics.
23. Hobbs, H. A., Hartman, G. L., Wang, Y., Hill, C. B., Bernard, R. L., Pedersen, W. L., and Domier, L. L., 2003. Occurrence of seed coat mottling in soybean plants inoculated with Bean pod mottle virus and Soybean mosaic virus. Plant Dis., 87:1333–1336.
24. Jayaram, C., Hill, J. H., and Miller, W. A., 1992. Complete nucleotide sequences of two Soybean mosaic virus strains differentiated by response of soybean containing the Rsv resistance gene. J. Gen. Virol., 73:2067–2077.
25. Koper-Zwarthoff, E. C., Brederode, F. T., Veeneman, G., van Boom, J. H., and Bol, J. F., 1980. Nucleotide sequences at the 5'-termini of the Alfalfa mosaic virus RNAs and the intercistronic junction in RNA 3. Nucleic Acids Res., 8:5635–5647.
26. Krell, R. K., Pedigo, L. P., Hill, J. H., and Rice, M. E., 2003. Potential primary inoculum sources of Bean pod mottle virus in Iowa. Plant Dis., 87:1416–1422.
27. Lim, W. S., Kim, Y. H., and Kim, K. H., 2003. Complete genome sequences of the genomic RNA of Soybean mosaic virus strains G7H and G5. Plant Pathol. J., 19:171–176.
28. Lomonossoff, G. P., and Shanks, M., 1983. The nucleotide sequence of Cowpea mosaic virus B RNA. EMBO (Eur. Mol. Biol. Organ.) J., 2:2253–2258.
29. Macfarlane, S. A., Shanks, M., Davies, J. M., Zlotnick, A., and Lomonossoff, G. P., 1991. Analysis of the nucleotide sequence of Bean pod mottle virus middle component RNA. Virology, 183:405–409.
30. Naidu, R. A., Hu, C.-C., Pennington, C.-C., and Ghabrial, S. A., 1995. Differentiation of eastern and western strains of Peanut stunt cucumovirus based on satellite RNA support and nucleotide sequence homology. Phytopathology, 85:502–507.
31. Nakamura, S., Honkura, R., Ugaki, M., Ohshima, M., and Ohashi, Y., 1994. Nucleotide sequence of the 3'-terminal region of Bean yellow mosaic virus RNA and resistance to viral infection in transgenic Nicotiana benthamiana expressing its coat protein gene. Ann. Phytopathol. Soc. Jpn., 60:295–304.
32. Owen, J., Shintaku, M., Aeschleman, P., Ben Tahar, S., and Palukaitis, P., 1990. Nucleotide sequence and evolutionary relationships of Cucumber mosaic virus (CMV) strains:CMV RNA 3. J. Gen. Virol., 71:2243–2249.
33. Owens, R. A., Blackburn, M., and Ding, B., 2001. Possible involvement of the phloem lectin in long-distance viroid movement. Mol. Plant-Microbe Interact., 14:905–909.
34. Reddy, S. M. S., Ghabrial, S. A., Redmond, C. T., Dinkins, R. D., and Collins, G. B., 2001. Resistance to Bean pod mottle virus in transgenic soybean lines expressing the capsid polyprotein. Phytopathology, 91:831–838.
35. Rizzo, T. M., and Palukaitis, P., 1988. Nucleotide sequence and evolutionary relationships of Cucumber mosaic virus (CMV) strains:CMV RNA 2. J. Gen. Virol., 69:1777–1787.
36. Rizzo, T. M., and Palukaitis, P., 1989. Nucleotide sequence and evolutionary relationships of Cucumber mosaic virus (CMV) strains:CMV RNA 1. J. Gen. Virol., 70:1–11.
37. Ross, J. P., 1987. “ Viral and bacterial diseases ”. In Soybeans:improvement, production and uses, Edited by:Wilcox, J. R., 729–755. Madison, Wisc.:American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America.
38. Scott, S. W., Zimmerman, M. T., and Ge, X., 1998. The sequence of RNA 1 and RNA 2 of Tobacco streak virus:additional evidence for the inclusion of Alfalfa mosaic virus in the genus Ilarvirus. Arch. Virol., 143:1187–1198.
39. Shoemaker, R., Keim, P., Vodkin, L. O., Retzel, E., Clifton, S. W., Waterston, R., Smoller, D., Coryell, V., Khanna, A., Erpelding, J., Gai, X., Brendel, V., Raph-Schmidt, C., Shoop, E. G., Vielweber, C. J., Schmatz, M., Pape, D., Bowers, Y., Theising, B., Martin, J., Dante, M., Wylie, T., and Granger, C., 2002. A compilation of soybean ESTs:generation and analysis. Genome, 45:329–338.
40. Strömvik, M. V., Thibaud-Nissen, F., and Vodkin, L. O., 2004. Mining soybean expressed sequence tag and microarray data. Recent Adv. Phytochem., 38:177–195.
41. Sundararaman, V. P., Strömvik, M. V., and Vodkin, L. O., 2000. A putative defective interfering RNA from Bean pod mottle virus. Plant Dis., 84:1309–1313.
42. Swofford, D. L., 2002. PAUP*:phylogenetic analysis using parsimony (and other methods), Sunderland, Mass.:Sinauer Associates. Version 4.0 Beta test 10
43. Theuri, J. M., and Sehgal, O. P., 1996. In planta behavior of Bean pod mottle and Cowpea mosaicComoviruses:infectivity and structural alterations. Physiol. Mol. Plant Pathol., 48:193–207.
44. Thompson, J. D., Higgins, D. G., and Gibson, T. J., 1994. CLUSTAL W:improving the sensitivity of progressive multiple sequence alignment through sequence weighing, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22:4673–4680.
45. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F., and Higgins, D. G., 1997. The ClustalX windows interface:flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res., 24:4876–4882.
46. Thompson, J. R., Perry, K. L., and De Jong, W., 2004. A new potato virus in a new lineage of picorna-like viruses. Arch. Virol., 149:2141–2154.
47. van Wezenbeek, P., Verver, J., Harmsen, J., Vos, P., and van Kammen, A., 1983. Primary structure and gene organization of the middle-component RNA of Cowpea mosaic virus. EMBO (Eur. Mol. Biol. Organ.) J., 2:941–946.
48. Vodkin, L. O., Khanna, A., Shealy, R., Clough, S., Gonzalez, O., Philip, R., Zabala, G., Thibaud-Nissen, F., Sidarous, M., Strömvik, M. V., Shoop, E., Schmidt, C., Retzel, E., Erpelding, J., Shoemaker, R., Rodriguez-Huete, A., Polocco, J., Coryell, V., Keim, P., Gong, G., Liu, L., Pardinas, J., and Schweitzer, P., 2004. Microarrays for global expression constructed with a low redundancy set of 27,500 sequenced cDNAs representing an array of developmental stages and physiological conditions of the soybean plant. BMC (Biomed. Chromatogr.) Genomics, 5:73
49. Zalloua, P. A., Buzayan, J. M., and Bruening, G., 1996. Chemical cleavage of 5'-linked protein from Tobacco ringspot virus genomic RNAs and characterization of the protein-RNA linkage. Virology, 219:1–8.