Detection of members of the Tombusviridae in the Tallgrass Prairie Preserve, Osage County, Oklahoma, USA

Virus Research

Volumn 160, Issue 1-2, 2011, Pages 256-263

  Scheets, Kay ^a   Blinkova, Olga ^a   Melcher, Ulrich ^a   Palmer, Michael W ^a   Wiley, Graham B ^b   Ding, Tao ^a   Roe, Bruce A ^b  

^a OKLAHOMA STATE UNIVERSITY   (United States)

^b UNIVERSITY OF OKLAHOMA   (United States)

Author keywords

Carmovirus; Ecogenomics; Fern host; Genomic sequence; Tombusviridae; Tombusvirus

Indexed keywords

COAT PROTEIN; COMPLEMENTARY DNA; VIRUS DNA; VIRUS RNA;

ARTICLE; CARMOVIRUS; DNA POLYMORPHISM; LESPEDEZA; LESPEDEZA PROCUMBENS; MOLECULAR PHYLOGENY; NONHUMAN; NUCLEOTIDE SEQUENCE; PANICOVIRUS; PELLAEA ATROPURPUREA; PRAIRIE; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; PTERIDACEAE; RNA STRUCTURE; SEQUENCE ANALYSIS; TOMBUSVIRUS; UNITED STATES; VIRUS DETECTION; VIRUS GENOME; VIRUS IDENTIFICATION;

CLUSTER ANALYSIS; LESPEDEZA; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; OKLAHOMA; PHYLOGENY; PLANT DISEASES; PTERIDACEAE; RNA, VIRAL; SEQUENCE ANALYSIS, DNA; TOMBUSVIRIDAE;

CARMOVIRUS; FILICOPHYTA; LESPEDEZA PROCUMBENS; PANICOVIRUS; PELLAEA ATROPURPUREA; TOMBUSVIRIDAE; TOMBUSVIRUS;

EID: 80052161956     PISSN: 01681702     EISSN: 18727492     Source Type: Journal    
DOI: 10.1016/j.virusres.2011.06.023     Document Type: Article

References (44)

1. Abascal F., Zardoya R., Posada D. ProtTest: selection of best-fit models of protein evolution. Bioinformatics 2005, 21:2104-2105.
2. Allen M.S., Hamilton R.G., Melcher U., Palmer M.W. Lessons from the Prairie: Research at The Nature Conservancy's Tallgrass Prairie Preserve 2009, Oklahoma Academy of Sciences, Stillwater, OK.
3. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25:3389-3402.
4. Castaño A., Hernández C. Complete nucleotide sequence and genome organization of Pelargonium line pattern virus and its relationship with the family Tombusviridae. Arch. Virol. 2005, 150:949-965.
5. Castaño A., Ruiz L., Hernández C. Insights into the translational regulation of biologically active open reading frames of Pelargonium line pattern virus. Virology 2009, 386:417-426.
6. Ciuffreda P., Rubino L., Russo M. Molecular cloning and complete nucleotide sequence of Galinsoga mosaic virus genomic RNA. Arch. Virol. 1998, 143:173-180.
7. Cooper I., Jones R.A.C. Wild plants and viruses: under-investigated ecosystems. Adv. Virus Res. 2006, vol. 67. Academic Press, pp. 1-47.
8. Culley A.I., Lang A.S., Suttle C.A. Metagenomic analysis of coastal RNA virus communities. Science 2006, 312:1795-1798.
9. Culley A.I., Lang A.S., Suttle C.A. The complete genomes of three viruses assembled from shotgun libraries of marine RNA virus communities. Virol. J. 2007, 4:69.
10. Djikeng A., Kuzmickas R., Anderson N.G., Spiro D.J. Metagenomic analysis of RNA viruses in a fresh water lake. PLoS One 2009, 4:e7264.
11. Virus Taxonomy 2005, Elsevier, London. C.M. Fauquet, M.A. Mayo, J. Maniloff, U. Desselberger, L.A. Ball (Eds.).
12. Felsenstein J. PHYLIP - Phylogeny Inference Package. Cladistics 1989, 5:164-166.
13. Hamilton R.G. Restoring heterogeneity on the Tallgrass Prairie Preserve: applying the fire-grazing interaction model. Proceedings of the 23rd Tall Timbers Fire Ecology Conference: Fire in Grassland and Shrubland Ecosystems 2007, Tall Timbers Research Station, Tallahassee, FL. R.E. Masters, K.E.M. Galley (Eds.).
14. Harkins G.W., Delport W., Duffy S., Wood N., Monjane A.L., Owor B.E., Donaldson L., Saumtally S., Triton G., Briddon R.W., Shepherd D.N., Rybicki E.P., Martin D.P., Varsani A. Experimental evidence indicating that mastreviruses probably did not co-diverge with their hosts. Virol. J. 2009, 6:104.
15. Harrell L., Melcher U., Atkins J.F. Predominance of six different hexanucleotide recoding signals 3' of read-through stop codons. Nucleic Acids Res. 2002, 30:2011-2017.
16. Hull R. A virus disease of harts-tongue fern. Virology 1968, 35(2):333-335.
17. Kinard G.R., Jordan R. Genome organization of Pelargonium chlorotic ring pattern virus: further implications for Tombusviridae taxonomy. Acta Hortic. 2002, 568:17-27.
18. Kneller E.L.P., Rakotondrafara A.M., Miller W.A. Cap-independent translation of plant viral RNAs. Virus Res. 2006, 119:63-75.
19. Le S.Q., Gascuel O. An improved general amino acid replacement matrix. Mol. Biol. Evol. 2008, 25:1307-1320.
20. Li L., Victoria J.G., Wang C., Jones M., Fellers G.M., Kunz T.H., Delwart E. Bat guano virome: predominance of dietary viruses from insects and plants plus novel mammalian viruses. J. Virol. 2010, 84:6955-6965.
21. Liang X.-Z., Lucy A.P., Ding S.-W., Wong S.-M. The p23 protein of Hibiscus chlorotic ringspot virus is indispensable for host-specific replication. J. Virol. 2002, 76:12312-12319.
22. López-Bueno A., Tamames J., Velázquez D., Moya A., Quesada A., Alcamí A. High diversity of the viral community from an Antarctic lake. Science 2009, 326:858-861.
23. Melcher U. Similarities between putative transport proteins of plant viruses. J. Gen. Virol. 1990, 71:1009-1018.
24. Melcher U., Muthukumar V., Wiley G.B., Min B.E., Palmer M.W., Verchot-Lubicz J., Nelson R.S., Roe B.A., Ali A., Thapa V., Pierce M.L. Evidence for novel viruses by analysis of nucleic acids in virus-like particle fractions from Ambrosia psilostachya. J. Virol. Methods 2008, 152:49-55.
25. Meyer F., Paarmann D., D'Souza M., Olson R., Glass E.M., Kubal M., Paczian T., Rodriguez A., Stevens R., Wilke A., Wilkening J., Edwards R.A. The Metagenomics RAST server-a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 2008, 9:386.
26. Miller W.A., White K.A. Long-distance RNA-RNA interactions in plant virus gene expression and replication. Annu. Rev. Phytopathol. 2006, 44:447-467.
27. Min, B-E, Feldman, T., Ali, A.,Wiley, G., Muthukumar, V., Roe, B., Roossinck, M., Melcher, U., Palmer, M.W., Nelson, R.S. Physiological and ecological analysis of a novel tymovirus in Asclepias viridis (milkweed) from the Tallgrass Prairie Preserve of Oklahoma. Phytopathology, submitted for publication.
28. Muthukumar V., Melcher U., Pierce M., Wiley G.B., Roe B.A., Palmer M.W., Thapa V., Ali A., Ding T. Non-cultivated plants of the Tallgrass Prairie Preserve of northeastern Oklahoma frequently contain virus-like sequences in particulate fractions. Virus Res. 2009, 141:169-173.
29. Na H., White K.A. Structure and prevalence of replication silencer-3' terminus RNA interactions in Tombusviridae. Virology 2006, 345:305-316.
30. Nameth S.T., Steininger J. Cucumber mosaic virus associated with leaf malformation and stunting in Adiantum pedatum. Plant Dis. 1997, 81:1333.
31. Nicholson B.L., Wu B., Chevtchenko I., White K.A. Tombusvirus recruitment of host translational machinery via the 3' UTR. RNA 2010, 16:1402-1419.
32. Nienhaus F., Mack C., Schinzer U. The isolation of viruses from fern plants. Z. Pflkrankh. Pflsch. 1974, 81:533-537.
33. O'Reilly E.K., Kao C.C. Analysis of RNA-dependent RNA polymerase structure and function as guided by known polymerase structures and computer predictions of secondary structure. Virology 1998, 252:287-303.
34. Rancurel C., Khosravi M., Dunker A.K., Romero P.R., Karlin D. Overlapping genes produce proteins with unusual sequence properties and offer insight into de novo protein creation. J. Virol. 2009, 83:10719-10736.
35. Roossinck M.J., Saha P., Wiley G.B., Quan J., White J.D., Lai H., Chavarría F., Shen G., Roe B.A. Ecogenomics: using massively parallel pyrosequencing to understand virus ecology. Mol. Ecol. 2010, 19:81-88.
36. Scheets K. Maize chlorotic mottle machlomovirus expresses its coat protein from a 1.47-kb subgenomic RNA and makes a 0.34-kb subgenomic RNA. Virology 2000, 267:90-101.
37. Turina M., Desvoyes B., Scholthof K.-B.G. A gene cluster encoded by Panicum mosaic virus is associated with virus movement. Virology 2000, 266:120-128.
38. Valverde R.A., Sabanadzovic S. A novel plant virus with unique properties infecting Japanese holly fern. J. Gen. Virol. 2009, 90:2542-2549.
39. Wang Z., Parisien M., Scheets K., Miller W.A. The cap-binding translation initiation factor, eIF4E, binds a pseudoknot in a viral cap-independent translation element. Structure 2011, 19:868-880.
40. Wren J.D., Roossinck M.J., Nelson R.S., Scheets K., Palmer M.W., Melcher U. Plant virus biodiversity and ecology. PLoS Biol. 2006, 4:e80.
41. Yuan X., Shi K., Young M.Y., Simon A.E. The terminal loop of a 3' proximal hairpin plays a critical role in replication and the structure of the 3' region of Turnip crinkle virus. Virology 2010, 402:271-280.
42. Zhang T., Breitbart M., Lee W.H., Run J.Q., Wei C.L., Soh S.W., Hibberd M.L., Liu E.T., Rohwer F., Ruan Y. RNA viral community in human feces: prevalence of plant pathogenic viruses. PLoS Biol. 2006, 4:e3.
43. Ziegler A., Cowan G., Torrance L. Comparative sequence analysis and serological and infectivity studies indicate that Cocksfoot mild mosaic virus is a member of the genus Panicovirus. Arch. Virol. 2009, 154:1545-1549.
44. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003, 31:3406-3415.