Australian monocot-infecting mastrevirus diversity rivals that in Africa

Virus Research

Volumn 169, Issue 1, 2012, Pages 127-136

  Kraberger, Simona ^a   Thomas, John E ^b   Geering, Andrew D W ^b   Dayaram, Anisha ^a   Stainton, Daisy ^a   Hadfield, James ^a   Walters, Matthew ^a   Parmenter, Kathleen S ^c   van Brunschot, Sharon ^b   Collings, David A ^a   Martin, Darren P ^d   Varsani, Arvind ^a,d  

^a UNIVERSITY OF CANTERBURY   (New Zealand)

^b UNIVERSITY OF QUEENSLAND   (Australia)

^c DEPARTMENT OF AGRICULTURE AND FISHERIES   (Australia)

^d UNIVERSITY OF CAPE TOWN   (South Africa)

Author keywords

Australia; Geminivirus; Grass; Mastrevirus; Recombination

Indexed keywords

AFRICA; ARTICLE; AUSTRALIA; EUDICOT; GEMINIVIRUS; MONOCOT; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; SPECIES COMPARISON; SPECIES DIVERSITY; SPECIES IDENTIFICATION; VIRUS GENOME; VIRUS ISOLATION;

AUSTRALIA; CLUSTER ANALYSIS; DNA, VIRAL; GEMINIVIRIDAE; GENETIC VARIATION; MOLECULAR SEQUENCE DATA; PHYLOGENY; POACEAE; SEQUENCE ANALYSIS, DNA;

DICOTYLEDONEAE; GEMINIVIRIDAE; MASTREVIRUS; POACEAE; SPOROBOLUS;

EID: 84867194652     PISSN: 01681702     EISSN: 18727492     Source Type: Journal    
DOI: 10.1016/j.virusres.2012.07.018     Document Type: Article

References (57)

1. Accotto G.P., Donson J., Mullineaux P.M. Mapping of Digitaria streak virus transcripts reveals different RNA species from the same transcription unit. EMBO Journal 1989, 8:1033-1039.
2. Andersen M.T., Richardson K.A., Harbison S.-A., Morris B.A.M. Nucleotide sequence of the geminivirus chloris striate mosaic virus. Virology 1988, 164:443-449.
3. Boni M.F., Posada D., Feldman M.W. An exact nonparametric method for inferring mosaic structure in sequence triplets. Genetics 2007, 176:1035-1047.
4. Briddon R.W., Heydarnejad J., Khosrowfar F., Massumi H., Martin D.P., Varsani A. Turnip curly top virus, a highly divergent geminivirus infecting turnip in Iran. Virus Research 2010, 152:169-175.
5. Briddon R.W., Martin D.P., Owor B.E., Donaldson L., Markham P.G., Greber R.S., Varsani A. A novel species of mastrevirus (family Geminiviridae) isolated from Digitaria didactyla grass from Australia. Archives of Virology 2010, 155:1529-1534.
6. Brown J.K., Fauquet C.M., Briddon R.W., Zerbini M., Moriones E., Navas-Castillo J. Geminivirdae. Virus Taxonomy: Classification and Nomenclature of Viruses: Ninth Report of the International Committee on Taxonomy of Viruses 2011, 251-374. Elsevier Academic Press, San Diego. A.M.Q. King, M.J. Adamas, E.B. Carstens, E.J. Lefkowitz (Eds.).
7. Dekker E.L., Woolston C.J., Xue Y., Cox B., Mullineaux P.M. Transcript mapping reveals different expression strategies for the bicistronic RNAs of the geminivirus wheat dwarf virus. Nucleic Acids Research 1991, 19:4075-4081.
8. Delport W., Poon A.F.Y., Frost S.D.W., Kosakovsky Pond S.L. Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology. Bioinformatics 2010, 26:2455-2457.
9. Edgar R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 2004, 32:1792-1797.
10. Geering A.D.W., Thomas J.E., Holton T., Hadfield J., Varsani A. Paspalum striate mosaic virus: an Australian mastrevirus from Paspalum dilatatum. Archives of Virology 2011, 157:193-197.
11. Gibbs M.J., Armstrong J.S., Gibbs A.J. Sister-scanning: a Monte Carlo procedure for assessing signals in recombinant sequences. Bioinformatics 2000, 16:573-582.
12. Giussani L.M., Cota-Sánchez J.H., Zuloaga F.O., Kellogg E.A. A molecular phylogeny of the grass subfamily Panicoideae (Poaceae) shows multiple origins of C4 photosynthesis. American Journal of Botany 2001, 88(11):1993-2012.
13. Greber R. Biological characteristics of grass geminiviruses from eastern Australia. Annals of Applied Biology 1989, 114:471-480.
14. Guindon S., Dufayard J.-F., Lefort V., Anisimova M., Hordijk W., Gascuel O. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Systematic Biology 2010, 59:307-321.
15. Hadfield J., Martin D., Stainton D., Kraberger S., Owor B., Shepherd D., Lakay F., Markham P., Greber R., Briddon R., Varsani A. Bromus catharticus striate mosaic virus: a new mastrevirus infecting Bromus catharticus from Australia. Archives of Virology 2011, 156:335-341.
16. Hadfield J., Thomas J.E., Schwinghamer M.W., Kraberger S., Stainton D., Dayaram A., Parry J.N., Pande D., Martin D.P., Varsani A. Molecular characterisation of dicot-infecting mastreviruses from Australia. Virus Research 2012, 166:13-22.
17. Harkins G.W., Martin D.P., Duffy S., Monjane A.L., Shepherd D.N., Windram O.P., Owor B.E., Donaldson L., van Antwerpen T., Sayed R.A., Flett B., Ramusi M., Rybicki E.P., Peterschmitt M., Varsani A. Dating the origins of the maize-adapted strain of maize streak virus, MSV-A. Journal of General Virology 2009, 90:3066-3074.
18. Harrison B.D. Advances in Geminivirus research. Annual Review of Phytopathology 1985, 23:55-82.
19. Heyraud F., Matzeit V., Schaefer S., Schell J., Gronenborn B. The conserved nonanucleotide motif of the geminivirus stem-loop sequence promotes replicational release of virus molecules from redundant copies. Biochimie 1993, 75:605-615.
20. Jeske H., Lutgemeier M., Preisz W. DNA forms indicate rolling circle and recombination-dependent replication of Abutilon mosaic virus. EMBO Journal 2001, 20:6158-6167.
21. Le S.Q., Gascuel O. An improved general amino acid replacement matrix. Molecular Biology and Evolution 2008, 25:1307-1320.
22. Martin D., Rybicki E. RDP: detection of recombination amongst aligned sequences. Bioinformatics 2000, 16:562-563.
23. Martin D.P., Briddon R.W., Varsani A. Recombination patterns in dicot-infecting mastreviruses mirror those found in monocot-infecting mastreviruses. Archives of Virology 2011, 156:1463-1469.
24. Martin D.P., Lemey P., Lott M., Moulton V., Posada D., Lefeuvre P. RDP3, a flexible and fast computer program for analyzing recombination. Bioinformatics 2010, 26:2462-2463.
25. Martin D.P., Linderme D., Lefeuvre P., Shepherd D.N., Varsani A. Eragrostis minor streak virus: an Asian streak virus in Africa. Archives of Virology 2011, 156:1299-1303.
26. Martin D.P., Posada D., Crandall K.A., Williamson C. A modified bootscan algorithm for automated identification of recombinant sequences and recombination breakpoints. AIDS Research and Human Retroviruses 2005, 21:98-102.
27. Martin D.P., Willment J.A., Billharz R., Velders R., Odhiambo B., Njuguna J., James D., Rybicki E.P. Sequence diversity and virulence in Zea mays of Maize streak virus isolates. Virology 2001, 288:247-255.
28. Monjane A.L., Harkins G.W., Martin D.P., Lemey P., Lefeuvre P., Shepherd D.N., Oluwafemi S., Simuyandi M., Zinga I., Komba E.K., Lakoutene D.P., Mandakombo N., Mboukoulida J., Semballa S., Tagne A., Tiendrebeogo F., Erdmann J.B., van Antwerpen T., Owor B.E., Flett B., Ramusi M., Windram O.P., Syed R., Lett J.M., Briddon R.W., Markham P.G., Rybicki E.P., Varsani A. Reconstructing the history of maize streak virus strain a dispersal to reveal diversification hot spots and its origin in southern Africa. Journal of Virology 2011, 85:9623-9636.
29. Monjane A.L., van der Walt E., Varsani A., Rybicki E.P., Martin D.P. Recombination hotspots and host susceptibility modulate the adaptive value of recombination during maize streak virus evolution. BMC Evolutionary Biology 2011, 11:1471-2148.
30. Mullineaux P.M., Guerineau F., Accotto G.-P. Processing of complementary sense RNAs of Digitaria streak virus in its host and in transgenic tobacco. Nucleic Acids Research 1990, 18:7259-7265.
31. Mumtaz H., Kumari S.G., Mansoor S., Martin D.P., Briddon R.W. Analysis of the sequence of a dicot-infecting mastrevirus (family Geminiviridae) originating from Syria. Virus Genes 2011, 42:422-428.
32. Nahid N., Amin I., Mansoor S., Rybicki E., van der Walt E., Briddon R. Two dicot-infecting mastreviruses (family Geminiviridae) occur in Pakistan. Archives of Virology 2008, 153:1441-1451.
33. Olmstead R.G., Reeves P.A. Evidence for the polyphyly of the Scrophulariaceae based on chloroplast rbcL and ndhF sequences. Annals of the Missouri Botanical Garden 1995, 82:176-193.
34. Owor B.E., Martin D.P., Shepherd D.N., Edema R., Monjane A.L., Rybicki E.P., Thomson J.A., Varsani A. Genetic analysis of maize streak virus isolates from Uganda reveals widespread distribution of a recombinant variant. Journal of General Virology 2007, 88:3154-3165.
35. ® Classic Card technology and use of bacteriophage phi 29 DNA polymerase for large-scale field sampling and cloning of complete maize streak virus genomes. Journal of Virological Methods 2007, 140:100-105.
36. Padidam M., Sawyer S., Fauquet C.M. Possible emergence of new geminiviruses by frequent recombination. Virology 1999, 265:218-225.
37. Pinner M., Markham P., Rybicki E., Greber R. Serological relationships of geminivirus isolates from Gramineae in Australia. Plant Pathology 1992, 41:618-625.
38. Pond S.L.K., Frost S.D.W. Not so different after all, a comparison of methods for detecting amino acid sites under selection. Molecular Biology and Evolution 2005, 22:1208-1222.
39. Pond S.L.K., Posada D., Gravenor M.B., Woelk C.H., Frost S.D.W. Automated phylogenetic detection of recombination using a genetic algorithm. Molecular Biology and Evolution 2006, 23:1891-1901.
40. Posada D., Crandall K.A. Evaluation of methods for detecting recombination from DNA sequences: computer simulations. Proceedings of the National Academy of Sciences of the United States of America 2001, 98(24):13757-13762.
41. Saunders K., Lucy A., Stanley J. DNA forms of the geminivirus African cassava mosaic virus consistent with a rolling circle mechanism of replication. Nucleic Acids Research 1991, 19:2325-2330.
42. Schalk H.J., Matzeit V., Schiller B., Schell J., Gronenborn B. Wheat dwarf virus, a geminivirus of graminaceous plants needs splicing for replication. EMBO Journal 1989, 8(2):359-364.
43. Schwinghamer M., Thomas J., Schilg M., Parry J., Dann E., Moore K., Kumari S. Mastreviruses in chickpea (Cicerarietinum) and other dicotyledonous crops and weeds in Queensland and northern New South Wales, Australia. Australasian Plant Pathology 2010, 39:551-561.
44. Shepherd D.N., Martin D.P., Lefeuvre P., Monjane A.L., Owor B.E., Rybicki E.P., Varsani A. A protocol for the rapid isolation of full geminivirus genomes from dried plant tissue. Journal of Virological Methods 2008, 149:97-102.
45. Shepherd D.N., Varsani A., Windram O.P., Lefeuvre P., Monjane A.L., Owor B.E., Martin D.P. Novel sugarcane streak and sugarcane streak Reunion mastreviruses from southern Africa and la Réunion. Archives of Virology 2008, 153(3):605-609.
46. Smith J.M. Analyzing the mosaic structure of genes. Journal of Molecular Evolution 1992, 34:126-129.
47. Stenger D.C., Revington G.N., Stevenson M.C., Bisaro D.M. Replicational release of geminivirus genomes from tandemly repeated copies: evidence for rolling-circle replication of a plant viral DNA. Proceedings of the National Academy of Sciences of the United States of America 1991, 88(18):8029-8033.
48. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. MEGA5, molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution 2011, 28:2713-2739.
49. Thomas J., Parry J., Schwinghamer M., Dann E. Two novel mastreviruses from chickpea (Cicer arietinum) in Australia. Archives of Virology 2010, 155:1777-1788.
50. Varsani A., Monjane A.L., Donaldson L., Oluwafemi S., Zinga I., Komba E.K., Plakoutene D., Mandakombo N., Mboukoulida J., Semballa S., Briddon R.W., Markham P.G., Lett J.M., Lefeuvre P., Rybicki E.P., Martin D.P. Comparative analysis of Panicum streak virus and Maize streak virus diversity, recombination patterns and phylogeography. Virology Journal 2009, 6:194.
51. Varsani A., Oluwafemi S., Windram O., Shepherd D., Monjane A., Owor B., Rybicki E., Lefeuvre P., Martin D. Panicum streak virus diversity is similar to that observed for maize streak virus. Archives of Virology 2008, 153:601-604.
52. Varsani A., Shepherd D.N., Dent K., Monjane A.L., Rybicki E.P., Martin D.P. A highly divergent South African geminivirus species illuminates the ancient evolutionary history of this family. Virology Journal 2009, 6:36.
53. Varsani A., Shepherd D.N., Monjane A.L., Owor B.E., Erdmann J.B., Rybicki E.P., Peterschmitt M., Briddon R.W., Markham P.G., Oluwafemi S., Windram O.P., Lefeuvre P., Lett J.M., Martin D.P. Recombination, decreased host specificity and increased mobility may have driven the emergence of maize streak virus as an agricultural pathogen. Journal of General Virology 2008, 89:2063-2074.
54. Willment J.A., Martin D.P., Rybicki E.P. Analysis of the diversity of African streak mastreviruses using PCR-generated RFLPs and partial sequence data. Journal of Virological Methods 2001, 93:75-87.
55. Wright E.A., Heckel T., Groenendijk J., Davies J.W., Boulton M.I. Splicing features in maize streak virus virion- and complementary-sense gene expression. Plant Journal 1997, 12:1285-1297.
56. Xie O., Suarez-Lopez P., Gutierrez C. Identification and analysis of a retinoblastoma binding motif in the replication protein of a plant DNA virus: requirement for efficient viral DNA replication. EMBO Journal 1995, 14:4073-4082.
57. Yazdi H., Heydarnejad J., Massumi H. Genome characterization and genetic diversity of beet curly top Iran virus: a geminivirus with a novel nonanucleotide. Virus Genes 2008, 36:539-545.