Species diversity, phylogeny and genetic variability of begomovirus populations infecting leguminous weeds in northeastern Brazil

Plant Pathology

Volumn 61, Issue 3, 2012, Pages 457-467

  Silva, S J C ^a,c   Castillo Urquiza, G P ^a   Hora Junior B T ^a   Assuncao I P ^b   Lima, G S A ^b,c   Pio Ribeiro, G ^c   Mizubuti, E S G ^a   Zerbini, F M ^a  

^a FEDERAL UNIVERSITY OF VIÇOSA   (Brazil)

^b FEDERAL UNIVERSITY OF ALAGOAS   (Brazil)

^c UNIVERSIDADE FEDERAL RURAL DE PERNAMBUCO   (Brazil)

Author keywords

Fabaceae; Geminivirus; Macroptilium; MaYSV; Recombination

Indexed keywords

CLONE; EPIDEMIC; GENETIC VARIATION; INFECTIOUS DISEASE; LEGUME; PHYLOGENETICS; PHYLOGENY; RECOMBINATION; SPECIES DIVERSITY; VIRAL DISEASE;

BRAZIL; CENTRAL AMERICA;

BEGOMOVIRUS; EUPHORBIA; FABACEAE; GEMINIVIRIDAE; MACROPTILIUM; MACROPTILIUM LATHYROIDES;

EID: 84860765229     PISSN: 00320862     EISSN: 13653059     Source Type: Journal    
DOI: 10.1111/j.1365-3059.2011.02543.x     Document Type: Article

References (55)

1. Ambrozevicius LP, Calegario RF, Fontes EPB, Carvalho MG, Zerbini FM, 2002. Genetic diversity of begomoviruses infecting tomato and associated weeds in Southeastern Brazil. Fitopatologia Brasileira 27, 372-7.
2. Andrade EC, Manhani GG, Alfenas PF, Calegario RF, Fontes EPB, Zerbini FM, 2006. Tomato yellow spot virus, a tomato-infecting begomovirus from Brazil with a closer relationship to viruses from Sida sp., forms pseudorecombinants with begomoviruses from tomato but not from Sida. Journal of General Virology 87, 3687-96.
3. Bull SE, Briddon RW, Sserubombwe WS, Ngugi K, Markham PG, Stanley J, 2006. Genetic diversity and phylogeography of cassava mosaic viruses in Kenya. Journal of General Virology 87, 3053-65.
4. Calegario RF, Ferreira SS, Andrade EC, Zerbini FM, 2007. Characterization of Tomato yellow spot virus, (ToYSV), a novel tomato-infecting begomovirus from Brazil. Brazilian Journal of Agricultural Research 42, 1335-43.
5. Castillo-Urquiza GP, Beserra Júnior JEA, Alfenas-Zerbini P et al., 2007. Genetic diversity of begomoviruses infecting tomato in Paty do Alferes, Rio de Janeiro state, Brazil. Virus Reviews and Research 12, 233.
6. Castillo-Urquiza GP, Beserra JEA, Bruckner FP et al., 2008. Six novel begomoviruses infecting tomato and associated weeds in Southeastern Brazil. Archives of Virology 153, 1985-9.
7. Castillo-Urquiza GP, Alfenas-Zerbini P, Beserra-Junior JEA et al., 2010. Genetic structure of tomato-infecting begomovirus populations in two tomato-growing regions of Southeastern Brazil. In: Program and Abstracts, 6th International Geminivirus Symposium and 4th International ssDNA Comparative Virology Workshop, 2010, Guanajuato, Mexico.
8. Chagas CM, Barradas MM, Vicente M, 1981. Espécies hospedeiras do vírus do mosaico dourado do feijoeiro. Arquivos do Instituto Biologico de São Paulo 48, 123-7.
9. Costa AS, 1976. Whitefly-transmitted plant diseases. Annual Review of Phytopathology 14, 429-40.
10. Doyle JJ, Doyle JL, 1987. A rapid DNA isolation procedure for small amounts of fresh leaf tissue. Phytochemical Bulletin 19, 11-15.
11. Duffy S, Holmes EC, 2008. Phylogenetic evidence for rapid rates of molecular evolution in the single-stranded DNA begomovirus Tomato yellow leaf curl virus. Journal of Virology 82, 957-65.
12. Duffy S, Holmes EC, 2009. Validation of high rates of nucleotide substitution in geminiviruses: phylogenetic evidence from East African cassava mosaic viruses. Journal of General Virology 90, 1539-47.
13. Excoffier L, Laval G, Schneider S, 2005. Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online 1, 47-50.
14. Faria JC, Maxwell DP, 1999. Variability in geminivirus isolates associated with Phaseolus spp. in Brazil. Phytopathology 89, 262-8.
15. Faria JC, Bezerra IC, Zerbini FM, Ribeiro SG, Lima MF, 2000. Current status of geminivirus diseases in Brazil. Fitopatologia Brasileira 25, 125-37.
16. Fauquet CM, Briddon RW, Brown JK et al., 2008. Geminivirus strain demarcation and nomenclature. Archives of Virology 153, 783-821.
17. Fernandes JJ, Carvalho MG, Andrade EC, Brommonschenkel SH, Fontes EPB, Zerbini FM, 2006. Biological and molecular properties of Tomato rugose mosaic virus (ToRMV), a new tomato-infecting begomovirus from Brazil. Plant Pathology 55, 513-22.
18. Fernandes FR, Cruz ARR, Faria JC, Zerbini FM, Aragão FJL, 2009. Three distinct begomoviruses associated with soybean in central Brazil. Archives of Virology 154, 1567-70.
19. Frischmuth T, Engel M, Lauster S, Jeske H, 1997. Nucleotide sequence evidence for the occurrence of three distinct whitefly-transmitted, Sida-infecting bipartite geminiviruses in Central America. Journal of General Virology 78, 2675-82.
20. Galvão RM, Mariano AC, Luz DF et al., 2003. A naturally occurring recombinant DNA-A of a typical bipartite begomovirus does not require the cognate DNA-B to infect Nicotiana benthamiana systemically. Journal of General Virology 84, 715-26.
21. García-Andrés S, Monci F, Navas-Castillo J, Moriones E, 2006. Begomovirus genetic diversity in the native plant reservoir Solanum nigrum: evidence for the presence of a new virus species of recombinant nature. Virology 350, 433-42.
22. García-Andrés S, Accotto GP, Navas-Castillo J, Moriones E, 2007a. Founder effect, plant host, and recombination shape the emergent population of begomoviruses that cause the tomato yellow leaf curl disease in the Mediterranean basin. Virology 359, 302-12.
23. García-Andrés S, Tomas DM, Sanchez-Campos S, Navas-Castillo J, Moriones E, 2007b. Frequent occurrence of recombinants in mixed infections of tomato yellow leaf curl disease-associated begomoviruses. Virology 365, 210-19.
24. Ge LM, Zhang JT, Zhou XP, Li HY, 2007. Genetic structure and population variability of tomato yellow leaf curl China virus. Journal of Virology 81, 5902-7.
25. Harkins GW, Delport W, Duffy S et al., 2009. Experimental evidence indicating that mastreviruses probably did not co-diverge with their hosts. Virology Journal 6, 104.
26. Huson DH, Bryant D, 2006. Application of phylogenetic networks in evolutionary studies. Molecular Biology and Evolution 23, 254-67.
27. Idris AM, Hiebert E, Bird J, Brown JK, 2003. Two newly described begomoviruses of Macroptilium lathyroides and common bean. Phytopathology 93, 774-83.
28. Inoue-Nagata AK, Albuquerque LC, Rocha WB, Nagata T, 2004. A simple method for cloning the complete begomovirus genome using the bacteriophage phi 29 DNA polymerase. Journal of Virological Methods 116, 209-11.
29. Inoue-Nagata AK, Martin DP, Boiteux LS, Giordano LD, Bezerra IC, De Avila AC, 2006. New species emergence via recombination among isolates of the Brazilian tomato infecting Begomovirus complex. Brazilian Journal of Agricultural Research 41, 1329-32.
30. Jovel J, Reski G, Rothenstein D, Ringel M, Frischmuth T, Jeske H, 2004. Sida micrantha mosaic is associated with a complex infection of begomoviruses different from Abutilon mosaic virus. Archives of Virology 149, 829-41.
31. Lefeuvre P, Lett JM, Reynaud B, Martin DP, 2007a. Avoidance of protein fold disruption in natural virus recombinants. PLoS Pathogens 3, e181.
32. Lefeuvre P, Martin DP, Hoareau M et al., 2007b. Begomovirus 'melting pot' in the south-west Indian Ocean islands: molecular diversity and evolution through recombination. Journal of General Virology 88, 3458-68.
33. Lefeuvre P, Martin DP, Harkins G et al., 2010. The spread of tomato yellow leaf curl virus from the Middle East to the world. PLoS Pathogens 6, e1001164.
34. 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, 2462-3.
35. Monci F, Sanchez-Campos S, Navas-Castillo J, Moriones E, 2002. A natural recombinant between the geminiviruses Tomato yellow leaf curl Sardinia virus and Tomato yellow leaf curl virus exhibits a novel pathogenic phenotype and is becoming prevalent in Spanish populations. Virology 303, 317-26.
36. Morales FJ, 2006. History and current distribution of begomoviruses in Latin America. Advances in Virus Research 67, 127-62.
37. Morales FJ, Anderson PK, 2001. The emergence and dissemination of whitefly-transmitted geminiviruses in Latin America. Archives of Virology 146, 415-41.
38. Nylander JAA, 2004. MrModeltest v2. Uppsala, Sweden: Evolutionary Biology Centre, Uppsala University.
39. Padidam M, Sawyer S, Fauquet CM, 1999. Possible emergence of new geminiviruses by frequent recombination. Virology 265, 218-24.
40. Paprotka T, Metzler V, Jeske H, 2010a. The complete nucleotide sequence of a new bipartite begomovirus from Brazil infecting Abutilon. Archives of Virology 155, 813-16.
41. Paprotka T, Metzler V, Jeske H, 2010b. The first DNA 1-like alpha satellites in association with New World begomoviruses in natural infections. Virology 404, 148-57.
42. Pita JS, Fondong VN, Sangare A, Otim-Nape GW, Ogwal S, Fauquet CM, 2001. Recombination, pseudorecombination and synergism of geminiviruses are determinant keys to the epidemic of severe cassava mosaic disease in Uganda. Journal of General Virology 82, 655-65.
43. Ramos-Sobrinho R, Silva SJC, Silva TAL et al., 2010. Genetic structure of a population of the begomovirus Bean golden mosaic virus (BGMV) that infects lima bean (Phaseolus lunatus L.) in the state of Alagoas, Brazil. In: Program and Abstracts, 6th International Geminivirus Symposium and 4th International ssDNA Comparative Virology Workshop, 2010, Guanajuato, Mexico.
44. Ribeiro SG, Ávila AC, Bezerra IC et al., 1998. Widespread occurrence of tomato geminiviruses in Brazil, associated with the new biotype of the whitefly vector. Plant Disease 82, 830.
45. Ribeiro SG, Martin DP, Lacorte C, Simões IC, Orlandini DRS, Inoue-Nagata AK, 2007. Molecular and biological characterization of Tomato chlorotic mottle virus suggests that recombination underlies the evolution and diversity of Brazilian tomato begomoviruses. Phytopathology 97, 702-11.
46. Rodríguez-Pardina PE, Hanada K, Laguna IG, Zerbini FM, Ducasse DA, 2010. Molecular characterisation and relative incidence of bean- and soybean-infecting begomoviruses in northwestern Argentina. Annals of Applied Biology 158, 69-78.
47. Rojas MR, Gilbertson RL, Russell DR, Maxwell DP, 1993. Use of degenerate primers in the polymerase chain reaction to detect whitefly-transmitted geminiviruses. Plant Disease 77, 340-7.
48. Rojas MR, Hagen C, Lucas WJ, Gilbertson RL, 2005. Exploiting chinks in the plant's armor: evolution and emergence of geminiviruses. Annual Review of Phytopathology 43, 361-94.
49. Ronquist F, Huelsenbeck JP, 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19, 1572-4.
50. Roye ME, Spence J, McLaughlin WA, Maxwell DP, 1999. The common weed Macroptilium lathyroides is not a source of crop-infecting geminiviruses from Jamaica. Tropical Agriculture 76, 256-62.
51. Rozas J, Sánchez-DelBarrio JC, Messeguer X, Rozas R, 2003. DnaSP: DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19, 2496-7.
52. Seal SE, Van den Bosch F, Jeger MJ, 2006. Factors influencing begomovirus evolution and their increasing global significance: implications for sustainable control. Critical Reviews in Plant Sciences 25, 23-46.
53. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S, 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution 28, 2731-9.
54. Webster CG, Coutts BA, Jones RAC, Jones MGK, Wylie SJ, 2007. Virus impact at the interface of an ancient ecosystem and a recent agroecosystem: studies on three legume-infecting potyviruses in the southwest Australian floristic region. Plant Pathology 56, 729-42.
55. Weir BS, 1996. Genetic Data Analysis II: Methods for Discrete Population Genetic Data. Sunderland, MA, USA: Sinauer Associated Inc.