A genome-wide pairwise-identity-based proposal for the classification of viruses in the genus Mastrevirus (family Geminiviridae)

Archives of Virology

Volumn 158, Issue 6, 2013, Pages 1411-1424

  Muhire, Brejnev ^a   Martin, Darren P ^a   Brown, Judith K ^b   Navas Castillo, Jesús ^c   Moriones, Enrique ^c   Zerbini, F Murilo ^d   Rivera Bustamante, Rafael ^e   Malathi, V G ^f   Briddon, Rob W ^g   Varsani, Arvind ^a,h  

^a UNIVERSITY OF CAPE TOWN   (South Africa)

^b UNIVERSITY OF ARIZONA   (United States)

^c INSTITUTO DE HORTOFRUTICULTURA SUBTROPICAL Y MEDITERRÁNEA LA MAYORA   (Spain)

^d FEDERAL UNIVERSITY OF VIÇOSA   (Brazil)

^e DEPARTAMENTO DE INGENIERÍA GENÉTICA   (Mexico)

^f INDIAN AGRICULTURAL RESEARCH INSTITUTE   (India)

^g NATIONAL INSTITUTE FOR BIOTECHNOLOGY AND GENETIC ENGINEERING NIBGE   (Pakistan)

^h UNIVERSITY OF CANTERBURY   (New Zealand)

Author keywords

[No Author keywords available]

Indexed keywords

VIRUS DNA;

ARTICLE; CLASSIFICATION; GEMINIVIRUS; GENETICS; NOMENCLATURE; NUCLEOTIDE SEQUENCE; PHYLOGENY; SEQUENCE ALIGNMENT; VIRUS GENOME;

BASE SEQUENCE; DNA, VIRAL; GEMINIVIRIDAE; GENOME, VIRAL; PHYLOGENY; SEQUENCE ALIGNMENT; TERMINOLOGY AS TOPIC;

DNA VIRUSES; GEMINIVIRIDAE; MASTREVIRUS;

EID: 84878598727     PISSN: 03048608     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00705-012-1601-7     Document Type: Article

References (60)

1. Andersen MT, Richardson KA, Harbison SA, Morris BA (1988) Nucleotide sequence of the geminivirus chloris striate mosaic virus. Virology 164: 443-449.
2. Bao Y, Chetvernin V, Tatusova T (2012) PAirwise sequence comparison (PASC) and its application in the classification of Filoviruses. Viruses 4: 1318-1327.
3. Behjatnia A, Afsharifar A, Tahan V, Motlagh VA, Gandomani OE, Niazi A, Izadpanah K (2008) Widespread occurrence and molecular characterization of barley dwarf geminivirus in Iran. Phytopathology 98: S20-S20.
4. Bendahmane M, Schalk HJ, Gronenborn B (1995) Identification and characterization of wheat dwarf virus from France using a rapid method for geminivirus DNA preparation. Phytopathology 85: 1449-1455.
5. Bigarre L, Salah M, Granier M, Frutos R, Thouvenel J, Peterschmitt M (1999) Nucleotide sequence evidence for three distinct sugarcane streak mastreviruses. Arch Virol 144: 2331-2344.
6. Briddon RW, Martin DP, Owor BE, Donaldson L, Markham PG, Greber RS, Varsani A (2010) A novel species of mastrevirus (family Geminiviridae) isolated from Digitaria didactyla grass from Australia. Arch Virol 155: 1529-1534.
7. Brown JK, Fauquet CM, Briddon RW, Zerbini M, Moriones E, Navas-Castillo J (2012) Virus taxonomy: ninth report of the international committee on taxonomy of viruses. Academic Press, Waltham.
8. Chatani M, Matsumoto Y, Mizuta H, Ikegami M, Boulton MI, Davies JW (1991) The nucleotide sequence and genome structure of the geminivirus miscanthus streak virus. J Gen Virol 72: 2325-2331.
9. Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD (2003) Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res 31: 3497-3500.
10. Donson J, Accotto GP, Boulton MI, Mullineaux PM, Davies JW (1987) The nucleotide sequence of a geminivirus from Digitaria sanguinalis. Virology 161: 160-169.
11. Edgar RC (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5: 1-19.
12. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797.
13. Fauquet CM, Maxwell DP, Gronenborn B, Stanley J (2000) Revised proposal for naming geminiviruses. Arch Virol 145: 1743-1761.
14. Fauquet CM, Stanley J (2003) Geminivirus classification and nomenclature: progress and problems. Ann Appl Biol 142: 165-189.
15. Fauquet CM, Briddon RW, Brown JK, Moriones E, Stanley J, Zerbini M, Zhou X (2008) Geminivirus strain demarcation and nomenclature. Arch Virol 153: 783-821.
16. Felsenstein J (2004) Inferring phylogenies. Sinauer Associates, Sunderland.
17. Geering AD, Thomas JE, Holton T, Hadfield J, Varsani A (2012) Paspalum striate mosaic virus: an Australian mastrevirus from Paspalum dilatatum. Arch Virol 157: 193-197.
18. Greber R (1989) Biological characteristics of grass geminiviruses from eastern Australia. Ann App Biol 114: 471-480.
19. Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3. 0. Syst Biol 59: 307-321.
20. Hadfield J, Martin DP, Stainton D, Kraberger S, Owor BE, Shepherd DN, Lakay F, Markham PG, Greber RS, Briddon RW, Varsani A (2011) Bromus catharticus striate mosaic virus: a new mastrevirus infecting Bromus catharticus from Australia. Arch Virol 156: 335-341.
21. Hadfield J, Thomas JE, Schwinghamer MW, Kraberger S, Stainton D, Dayaram A, Parry JN, Pande D, Martin DP, Varsani A (2012) Molecular characterisation of dicot-infecting mastreviruses from Australia. Virus Res 166: 13-22.
22. Halley-Stott RP, Tanzer F, Martin DP, Rybicki EP (2007) The complete nucleotide sequence of a mild strain of Bean yellow dwarf virus. Arch Virol 152: 1237-1240.
23. Harkins GW, Martin DP, Duffy S, Monjane AL, Shepherd DN, Windram OP, Owor BE, Donaldson L, van Antwerpen T, Sayed RA, Flett B, Ramusi M, Rybicki EP, Peterschmitt M, Varsani A (2009) Dating the origins of the maize-adapted strain of maize streak virus, MSV-A. J Gen Virol 90: 3066-3074.
24. Hughes FL, Rybicki EP, Kirby R (1993) Complete nucleotide sequence of sugarcane streak monogeminivirus. Arch Virol 132: 171-182.
25. Katoh K, Kuma K, Toh H, Miyata T (2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res 33: 511-518.
26. Koklu G, Ramsell JN, Kvarnheden A (2007) The complete genome sequence for a Turkish isolate of Wheat dwarf virus (WDV) from barley confirms the presence of two distinct WDV strains. Virus Genes 34: 359-366.
27. Kraberger S, Thomas JE, Geering AD, Dayaram A, Stainton D, Hadfield J, Walters M, Parmenter KS, van Brunschot S, Collings DA, Martin DP, Varsani A (2012) Australian monocot-infecting mastrevirus diversity rivals that in Africa. Virus Res 169: 127-136.
28. Kumar J, Singh SP, Tuli R (2012) A novel mastrevirus infecting wheat in India. Archi Virol 257: 2031-2034.
29. Kundu JK, Gadiou S, Cervena G (2009) Discrimination and genetic diversity of wheat dwarf virus in the Czech Republic. Virus genes 38: 468-474.
30. Kvarnheden A, Lindblad M, Lindsten K, Valkonen JP (2002) Genetic diversity of wheat dwarf virus. Arch Virol 147: 205-216.
31. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007) Clustal W and Clustal X version 2. 0. Bioinformatics 23: 2947-2948.
32. Lauber C, Gorbalenya AE (2012) Partitioning the genetic diversity of a virus family: approach and evaluation through a case study of picornaviruses. J Virol 86: 3890-3904.
33. Lauber C, Gorbalenya AE (2012) Toward genetics-based virus taxonomy: comparative analysis of a genetics-based classification and the taxonomy of picornaviruses. J Virol 86: 3905-3915.
34. Lawry R, Martin DP, Shepherd DN, van Antwerpen T, Varsani A (2009) A novel sugarcane-infecting mastrevirus from South Africa. Arch Virol 154: 1699-1703.
35. Lemey P, Salemi M, Vandamme A-M (2009) The phylogenetic handbook: a practical approach to phylogenetic analysis and hypothesis testing, 2nd edn. Cambridge University Press, New York.
36. MacDowell SW, Macdonald H, Hamilton WD, Coutts RH, Buck KW (1985) The nucleotide sequence of cloned wheat dwarf virus DNA. EMBO journal 4: 2173-2180.
37. Martin DP, Willment JA, Billharz R, Velders R, Odhiambo B, Njuguna J, James D, Rybicki EP (2001) Sequence diversity and virulence in Zea mays of maize streak virus isolates. Virology 288: 247-255.
38. Martin DP, Linderme D, Lefeuvre P, Shepherd DN, Varsani A (2011) Eragrostis minor streak virus: an Asian streak virus in Africa. Arch Virol 156: 1299-1303.
39. Monjane AL, Harkins GW, Martin DP, Lemey P, Lefeuvre P, Shepherd DN, Oluwafemi S, Simuyandi M, Zinga I, Komba EK, Lakoutene DP, Mandakombo N, Mboukoulida J, Semballa S, Tagne A, Tiendrebeogo F, Erdmann JB, van Antwerpen T, Owor BE, Flett B, Ramusi M, Windram OP, Syed R, Lett JM, Briddon RW, Markham PG, Rybicki EP, Varsani A (2011) Reconstructing the history of maize streak virus strain a dispersal to reveal diversification hot spots and its origin in southern Africa. J Virol 85: 9623-9636.
40. Morris BA, Richardson KA, Haley A, Zhan X, Thomas JE (1992) The nucleotide sequence of the infectious cloned DNA component of tobacco yellow dwarf virus reveals features of geminiviruses infecting monocotyledonous plants. Virology 187: 633-642.
41. Mumtaz H, Kumari SG, Mansoor S, Martin DP, Briddon RW (2011) Analysis of the sequence of a dicot-infecting mastrevirus (family Geminiviridae) originating from Syria. Virus genes 42: 422-428.
42. Nahid N, Amin I, Mansoor S, Rybicki EP, van der Walt E, Briddon RW (2008) Two dicot-infecting mastreviruses (family Geminiviridae) occur in Pakistan. Arch Virol 153: 1441-1451.
43. Needleman SB, Wunsch CD (1970) A general method applicable to search for similarities in amino acid sequence of 2 proteins. J Mol Biol 48: 443.
44. Ogdenw TH, Rosenberg MS (2006) Multiple sequence alignment accuracy and phylogenetic inference. Syst Biol 55: 314-328.
45. Oluwafemi S, Varsani A, Monjane AL, Shepherd DN, Owor BE, Rybicki EP, Martin DP (2008) A new African streak virus species from Nigeria. ArchVirol 153: 1407-1410.
46. Owor BE, Martin DP, Shepherd DN, Edema R, Monjane AL, Rybicki EP, Thomson JA, Varsani A (2007) Genetic analysis of maize streak virus isolates from Uganda reveals widespread distribution of a recombinant variant. J Gen Virol 88: 3154-3165.
47. Pande D, Kraberger S, Lefeuvre P, Lett JM, Shepherd DN, Varsani A, Martin DP (2012) A novel maize-infecting mastrevirus from La Reunion Island. Arch Virol 157: 1617-1621.
48. Posada D (2008) jModelTest: phylogenetic model averaging. Mol Biol Evol 25: 1253-1256.
49. Ramsell JNE, Lemmetty A, Jonasson J, Andersson A, Sigvald R, Kvarnheden A (2008) Sequence analyses of wheat dwarf virus isolates from different hosts reveal low genetic diversity within the wheat strain. Plant Pathol 57: 834-841.
50. Ramsell JNE, Boulton MI, Martin DP, Valkonen JPT, Kvarnheden A (2009) Studies on the host range of the barley strain of Wheat dwarf virus using an agroinfectious viral clone. Plant Pathol 58: 1161-1169.
51. Rybicki EP (1994) A phylogenetic and evolutionary justification for three genera of Geminiviridae. Arch Virol 139: 49-77.
52. Schubert J, Habekuss A, Kazmaier K, Jeske H (2007) Surveying cereal-infecting geminiviruses in Germany-diagnostics and direct sequencing using rolling circle amplification. Virus Res 127: 61-70.
53. Shepherd DN, Varsani A, Windram OP, Lefeuvre P, Monjane AL, Owor BE, Martin DP (2008) Novel sugarcane streak and sugarcane streak reunion mastreviruses from southern Africa and La Reunion. Arch Virol 153: 605-609.
54. Thomas JE, Parry JN, Schwinghamer MW, Dann EK (2010) Two novel mastreviruses from chickpea (Cicer arietinum) in Australia. Arch Virol 155: 1777-1788.
55. Thompson JD, Plewniak F, Poch O (1999) A comprehensive comparison of multiple sequence alignment programs. Nucleic Acids Res 27: 2682-2690.
56. Tobias I, Shevchenko O, Kiss B, Bysov A, Snihur H, Polischuk V, Salanki K, Palkovics L (2011) Comparison of the nucleotide sequences of wheat dwarf virus (WDV) isolates from Hungary and Ukraine. Polish J Microbiol/Polskie Towarzystwo Mikrobiologow = Polish Soc Microbiologists 60: 125-131.
57. Varsani A, Oluwafemi S, Windram OP, Shepherd DN, Monjane AL, Owor BE, Rybicki EP, Lefeuvre P, Martin DP (2008) Panicum streak virus diversity is similar to that observed for maize streak virus. Arch Virol 153: 601-604.
58. Varsani A, Shepherd DN, Monjane AL, Owor BE, Erdmann JB, Rybicki EP, Peterschmitt M, Briddon RW, Markham PG, Oluwafemi S, Windram OP, Lefeuvre P, Lett JM, Martin DP (2008) Recombination, decreased host specificity and increased mobility may have driven the emergence of maize streak virus as an agricultural pathogen. J Gen Virol 89: 2063-2074.
59. Varsani A, Monjane AL, Donaldson L, Oluwafemi S, Zinga I, Komba EK, Plakoutene D, Mandakombo N, Mboukoulida J, Semballa S, Briddon RW, Markham PG, Lett JM, Lefeuvre P, Rybicki EP, Martin DP (2009) Comparative analysis of Panicum streak virus and maize streak virus diversity, recombination patterns and phylogeography. Virol J 6: 194.
60. Wu BL, Melcher U, Guo XY, Wang XF, Fan LJ, Zhou GH (2008) Assessment of codivergence of Mastreviruses with their plant hosts. BMC Evol Biol 8: 335.