Revisiting the classification of curtoviruses based on genome-wide pairwise identity

Archives of Virology

Volumn 159, Issue 7, 2014, Pages 1873-1882

  Varsani, Arvind ^a,b   Martin, Darren P ^b   Navas Castillo, Jesús ^c   Moriones, Enrique ^c   Hernández Zepeda, Cecilia ^d   Idris, Ali ^e   Murilo Zerbini, F ^f   Brown, Judith K ^g  

^a UNIVERSITY OF CANTERBURY   (New Zealand)

^b UNIVERSITY OF CAPE TOWN   (South Africa)

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

^d CENTRO DE INVESTIGACIÓN CIENTÍFICA DE YUCATÁN   (Mexico)

^e KING ABDULLAH UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Saudi Arabia)

^f FEDERAL UNIVERSITY OF VIÇOSA   (Brazil)

^g UNIVERSITY OF ARIZONA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARMORACIA RUSTICANA; BEET CURLY TOP VIRUS; BETA VULGARIS SUBSP. VULGARIS; CURTOVIRUS; GEMINIVIRIDAE; HORSERADISH CURLY TOP VIRUS; SPINACIA OLERACEA;

ARTICLE; CLASSIFICATION; GEMINIVIRUS; GENETICS; NOMENCLATURE; VIRUS GENOME;

GEMINIVIRIDAE; GENOME, VIRAL; TERMINOLOGY AS TOPIC;

EID: 84903595327     PISSN: 03048608     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00705-014-1982-x     Document Type: Article

References (40)

1. Adams MJ, King AM, Carstens EB (2013) Ratification vote on taxonomic proposals to the International Committee on Taxonomy of Viruses (2013). Arch Virol 158: 2023-2030.
2. Baliji S, Black MC, French R, Stenger DC, Sunter G (2004) Spinach curly top virus: a newly described curtovirus species from Southwest Texas with incongruent gene phylogenies. Phytopathology 94: 772-779.
3. Baliji S, Sunter J, Sunter G (2007) Transcriptional analysis of complementary sense genes in Spinach curly top virus and functional role of C2 in pathogenesis. Mol Plant Microbe Interact 20: 194-206.
4. Bao Y, Chetvernin V, Tatusova T (2012) PAirwise Sequence Comparison (PASC) and its application in the classification of filoviruses. Viruses 4: 1318-1327.
5. Bennett CW, Tanrisever A (1957) Sugarbeet curly top disease in Turkey. Plant Dis Report 41: 721-725.
6. Bennett CW (1971) The curly top disease of sugarbeet and other plants Monograph 7. The American Phytopathological Society, St. Paul.
7. Boni MF, Posada D, Feldman MW (2007) An exact nonparametric method for inferring mosaic structure in sequence triplets. Genetics 176: 1035-1047.
8. Briddon RW, Stenger DC, Bedford ID, Stanley J, Izadpanah K, Markham PG (1998) Comparison of a beet curly top virus isolate originating from the old world with those from the new world. Europ J Plant Pathol 104: 77-84.
9. 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, London; Waltham.
10. Chen LF, Vivoda E, Gilbertson RL (2011) Genetic diversity in curtoviruses: a highly divergent strain of Beet mild curly top virus associated with an outbreak of curly top disease in pepper in Mexico. Arch Virol 156: 547-555.
11. Edgar RC (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinform 5: 113.
12. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acid 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, Briddon RW, Brown JK, Moriones E, Stanley J, Zerbini M, Zhou X (2008) Geminivirus strain demarcation and nomenclature. Arch Virol 153: 783-821.
15. Gibbs MJ, Armstrong JS, Gibbs AJ (2000) Sister-scanning: a Monte Carlo procedure for assessing signals in recombinant sequences. Bioinformatics 16: 573-582.
16. Guindon S, Delsuc F, Dufayard JF, Gascuel O (2009) Estimating maximum likelihood phylogenies with PhyML. Methods Mol Biol 537: 113-137.
17. Hernandez-Zepeda C, Varsani A, Brown JK (2013) Intergeneric recombination between a new, spinach-infecting curtovirus and a new geminivirus belonging to the genus Becurtovirus: first New World exemplar. Arch Virol 158: 2245-2254.
18. Hernandez C, Brown JK (2010) First report of a new Curtovirus species, Spinach severe curly top virus, in Commercial Spinach Plants (Spinacia oleracea) from South-Central Arizona. Plant Dis 94: 917.
19. Hormuzdi SG, Bisaro DM (1993) Genetic analysis of beet curly top virus: evidence for three virion sense genes involved in movement and regulation of single- and double-stranded DNA levels. Virology 193: 900-909.
20. 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.
21. Klute KA, Nadler SA, Stenger DC (1996) Horseradish curly top virus is a distinct subgroup II geminivirus species with rep and C4 genes derived from a subgroup III ancestor. J Gen Virol 77: 1369-1378.
22. Lam N, Creamer R, Rascon J, Belfon R (2009) Characterization of a new curtovirus, pepper yellow dwarf virus, from chile pepper and distribution in weed hosts in New Mexico. Arch Virol 154: 429-436.
23. Martin DP, Posada D, Crandall KA, Williamson C (2005) A modified bootscan algorithm for automated identification of recombinant sequences and recombination breakpoints. AIDS Res Hum Retroviruses 21: 98-102.
24. Martin DP, Lemey P, Lott M, Moulton V, Posada D, Lefeuvre P (2010) RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics 26: 2462-2463.
25. Muhire B, Martin DP, Brown JK, Navas-Castillo J, Moriones E, Zerbini FM, Rivera-Bustamante R, Malathi VG, Briddon RW, Varsani A (2013) A genome-wide pairwise-identity-based proposal for the classification of viruses in the genus Mastrevirus (family Geminiviridae). Arch Virol 158: 1411-1424.
26. Padidam M, Sawyer S, Fauquet CM (1999) Possible emergence of new geminiviruses by frequent recombination. Virology 265: 218-225.
27. Posada D, Crandall KA (2001) Evaluation of methods for detecting recombination from DNA sequences: Computer simulations. Proc Natl Acad Sci USA 98: 13757-13762.
28. Posada D (2008) jModelTest: phylogenetic model averaging. Mol Biol Evol 25: 1253-1256.
29. Severin HH (1927) Crops naturally infected with sugar beet curly-top. Science 66: 137-138.
30. Severin HHP (1929) Additional host-plants of curly top. Hilgardia 3: 595-636.
31. Smith JM (1992) Analyzing the mosaic structure of genes. J Mol Evol 34: 126-129.
32. Soto MJ, Gilbertson RL (2003) Distribution and rate of movement of the curtovirus Beet mild curly top virus (Family geminiviridae) in the beet leafhopper. Phytopathology 93: 478-484.
33. Stanley J, Markham PG, Callis RJ, Pinner MS (1986) The nucleotide sequence of an infectious clone of the geminivirus beet curly top virus. EMBO J 5: 1761-1767.
34. Stenger DC, Carbonaro D, Duffus JE (1990) Genomic characterization of phenotypic variants of beet curly top virus. J Gen Virol 71: 2211-2215.
35. Stenger DC (1994) Complete nucleotide sequence of the hypervirulent CFH strain of beet curly top virus. Mol Plant Microbe Interact 7: 154-157.
36. Sunter G, Sunter JL, Bisaro DM (2001) Plants expressing tomato golden mosaic virus AL2 or beet curly top virus L2 transgenes show enhanced susceptibility to infection by DNA and RNA viruses. Virology 285: 59-70.
37. Thompson JD, Plewniak F, Poch O (1999) A comprehensive comparison of multiple sequence alignment programs. Nucleic Acids Res 27: 2682-2690.
38. Thompson JD, Gibson TJ, Higgins DG (2002) Multiple sequence alignment using ClustalW and ClustalX. In: Andreas D Baxevanis et al., Current protocols in bioinformatics / editoral board, Chapter 2: Unit 2 3.
39. van Regenmortel MH, Ackermann HW, Calisher CH, Dietzgen RG, Horzinek MC, Keil GM, Mahy BW, Martelli GP, Murphy FA, Pringle C, Rima BK, Skern T, Vetten HJ, Weaver SC (2013) Virus species polemics: 14 senior virologists oppose a proposed change to the ICTV definition of virus species. Arch Virol 158: 1115-1119.
40. Velasquez-Valle R, Mena-Covarrubias J, Reveles-Torres LR, Arguello-Astorga GR, Salas-Luevano MA, Mauricio-Castillo JA (2012) First report of Beet mild curly top virus in Dry Bean in Zacatecas, Mexico. Plant Dis 96: 771-772.