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

References

• 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 .
   Google Scholar
• 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 .
   PubMed Web of Science ®Google Scholar
• 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 .
   Web of Science ®Google Scholar
• 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 .
   Google Scholar
• 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 .
   PubMed Web of Science ®Google Scholar
• 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 .
   Google Scholar
• 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 .
   PubMed Web of Science ®Google Scholar
• 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 .
   Google Scholar
• 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 .
   Google Scholar
• 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 .
   PubMed Web of Science ®Google Scholar
• 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 .
   PubMed Web of Science ®Google Scholar
• 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 .
   PubMed Web of Science ®Google Scholar
• 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 .
   Google Scholar
• 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 .
   Google Scholar
• 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 .
   PubMed Web of Science ®Google Scholar
• Felsenstein , J. 1985 . Confidence limits on phylogenies: an approach using bootstrap . Evolution , 39 : 783 – 791 .
   PubMed Web of Science ®Google Scholar
• 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 .
   Google Scholar
• 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 .
   PubMedGoogle Scholar
• 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 .
   Google Scholar
• 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 .
   Google Scholar
• 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 .
   PubMed Web of Science ®Google Scholar
• Hall , T. 1997 . BioEdit tool, version 7.05 , Carlsbad, Calif. : Ibis Therapeutics .
   Google Scholar
• 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 .
   Google Scholar
• 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 .
   PubMed Web of Science ®Google Scholar
• 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 .
   Google Scholar
• 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 .
   Google Scholar
• 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 .
   Google Scholar
• 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 .
   Google Scholar
• 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 .
   Google Scholar
• 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 .
   Web of Science ®Google Scholar
• 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 .
   Google Scholar
• 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 .
   PubMed Web of Science ®Google Scholar
• 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 .
   Google Scholar
• 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 .
   PubMed Web of Science ®Google Scholar
• 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 .
   Google Scholar
• 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 .
   Google Scholar
• 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 .
   Google Scholar
• 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 .
   Google Scholar
• 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 .
   PubMedGoogle Scholar
• 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 .
   Google Scholar
• 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 .
   Google Scholar
• Swofford , D. L. 2002 . PAUP*: phylogenetic analysis using parsimony (and other methods) , Sunderland, Mass. : Sinauer Associates . Version 4.0 Beta test 10
   Google Scholar
• Theuri , J. M. and Sehgal , O. P. 1996 . In planta behavior of Bean pod mottle and Cowpea mosaic Comoviruses : infectivity and structural alterations . Physiol. Mol. Plant Pathol. , 48 : 193 – 207 .
   Google Scholar
• 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 .
   PubMed Web of Science ®Google Scholar
• 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 .
   Web of Science ®Google Scholar
• 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 .
   Google Scholar
• 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 .
   Google Scholar
• 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
   Google Scholar
• 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 .
   Google Scholar