Asymmetric patterns of reassortment and concerted evolution in Cardamom bushy dwarf virus

Infection, Genetics and Evolution

Volumn 24, Issue , 2014, Pages 15-24

  Savory, F R ^a   Ramakrishnan, U ^a  

^a TATA INSTITUTE OF FUNDAMENTAL RESEARCH   (India)

Author keywords

Concerted evolution; Nanovirus; Reassortment; Recombination

Indexed keywords

NUCLEOTIDE; VIRUS DNA;

ARTICLE; CARDAMOM BUSHY DWARF VIRUS; CONTROLLED STUDY; GENE FREQUENCY; GENE SEQUENCE; GENETIC REASSORTMENT; GENETIC VARIABILITY; HOMOLOGOUS RECOMBINATION; MOLECULAR EVOLUTION; NANOVIRIDAE; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; VIRUS GENOME; VIRUS ISOLATION; VIRUS RECOMBINATION; BABUVIRUS; DNA SEQUENCE; ELETTARIA; GENETICS; HAPLOTYPE; ISOLATION AND PURIFICATION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PLANT DISEASE; SEQUENCE ALIGNMENT; VIROLOGY;

BABUVIRUS; BASE SEQUENCE; DNA, VIRAL; ELETTARIA; EVOLUTION, MOLECULAR; GENETIC VARIATION; GENOME, VIRAL; HAPLOTYPES; HOMOLOGOUS RECOMBINATION; MOLECULAR SEQUENCE DATA; PHYLOGENY; PLANT DISEASES; REASSORTANT VIRUSES; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

EID: 84897875550     PISSN: 15671348     EISSN: 15677257     Source Type: Journal    
DOI: 10.1016/j.meegid.2014.02.012     Document Type: Article

References (52)

1. Almeida R.P.P., Bennett G.M., Anhalt M.D., Tsai C.W., O'Grady P. Spread of an introduced vector-borne banana virus in Hawaii. Mol. Ecol. 2009, 18:136-146.
2. Beaty B.J., Holterman M., Tabachnick W., Shope R.E., Rozhon E.J., Bishop D.H. Molecular basis of bunyavirus transmission by mosquitoes: role of the middle-sized RNA segment. Science 1981, 211:1433-1435.
3. Bell K.E., Dale J.L., Ha C.V., Vu M.T., Revill P.A. Characterisation of rep-encoding components associated with banana bunchy top nanovirus in Vietnam. Arch. Virol. 2002, 147:695-707.
4. Boni M.F., Posada D., Feldman M.W. An exact nonparametric method for inferring mosaic structure in sequence triplets. Genetics 2007, 176:1035-1047.
5. Croll D., Sanders I.R. Recombination in Glomus intraradices, a supposed ancient asexual arbuscular mycorrhizal fungas. BMC Evol. Biol. 2009, 9:13.
6. Darriba D., Taboada G.L., Doallo R., Posada D. JModelTest 2: more models, new heuristics and parallel computing. Nat. Meth. 2012, 9:772.
7. Drummond A.J., Suchard M.A., Xie D., Rambaut A. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol. Biol. Evol. 2012, 29:1969-1973.
8. Drummond A.J., Ho S.Y.W., Phillips M.J., Rambaut A. Relaxed phylogenetics and dating with confidence. PLoS Biol. 2006, 4(5):e88.
9. Escriu F., Fraile A., Garcia-Arenal F. Constraints to genetic exchange support gene coadaptation in a tripartite RNA virus. PLoS Pathog. 2007, 3. e8.
10. Fraile A., Alonso-Prados J.L., Aranda M.A., Bernal J.J., Malpica J.M., García-Arenal F. Genetic exchange by recombination or reassortment is infrequent in natural populations of a tripartite RNA plant virus. J. Virol. 1997, 71(2):934-940.
11. Fu H.C., Hu J.M., Hung T.H., Su H.J., Yeh H.H. Unusual events in Banana bunchy top virus strain evolution. Phytopathology 2009, 99(7):812-822.
12. Gibbs M.J., Weiller G.F. Evidence that a plant virus switched hosts to infect a vertebrate and then recombined with a vertebrate-infecting virus. Proc. Natl. Acad. Sci. USA 1999, 96:8022-8027.
13. 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.
14. Grigoras I., Timchenko T., Grande-Perez A., Katul L., Vetten H.J., Gronenborn B. High variability and rapid evolution of a nanovirus. J. Virol. 2010, 84:9105-9117.
15. Grigoras I., Del Cueto Ginzo A.I., Martin D.P., Varsani A., Romero J., Mammadov A.C., Huseynova I.M., Aliyev J.A., Kheyr-Pour A., Huss H., Ziebell H., Timchenko T., Vetten H.-J., Gronenborn B. Genome diversity and evidence of recombination and reassortment in Nanoviruses from Europe. J. Gen. Virol. 2014, 10.1099/vir.0.063115-0.
16. Heath L., van der Walt E., Varsani A., Martin D.P. Recombination patterns in aphthoviruses mirror those found in other picornaviruses. J. Virol. 2006, 80:11827-11832.
17. Herrera-Valencia V.A., Dugdale B., Harding R.M., Dale J.L. An iterated sequence in the genome of Banana bunchy top virus is essential for efficient replication. J. Gen. Virol. 2006, 87(11):3409-3412.
18. Horser C.L., Karan M., Harding R.M., Dale J.L. Additional rep-encoding DNAs associated with Banana bunchy top virus. Arch. Virol. 2001, 146(1):71-86.
19. Hou Y.M., Gilbertson R.L. Increased pathogenicity in a pseudorecombinant bipartite geminivirus correlates with intermolecular recombination. J. Virol. 1996, 70(8):5430-5436.
20. Hu J.M., Fu H.C., Lin C.H., Su H.J., Yeh H.H. Reassortment and concerted evolution in Banana bunchy top virus genomes. J. Virol. 2007, 81:1746-1761.
21. Hughes A.L. Birth-and-death evolution of protein-coding regions and concerted evolution of non-coding regions in the multi-component genomes of nanoviruses. Mol. Phylogenet. Evol. 2004, 30:287-294.
22. Hyder M.Z., Shah S.H., Hameed S., Naqvi S.M. Evidence of recombination in the Banana bunchy top virus genome. Infect. Genet. Evol. 2011, 11:1293-1300.
23. Idris A.M., Mills-Lujan K., Martin K., Brown J.K. Melon chlorotic leaf curl virus: characterisation and differential reassortment with closest relatives reveal adaptive virulence in the squash leaf curl virus clade and host shifting by the host-restricted bean calico mosaic virus. J. Virol. 2008, 82(4):1959-1967.
24. Islam M.N., Naqvi A.V., Jan A.T., Rizwanul Haq Q.M. Genetic diversity and possible evidence of recombination among Banana Bunch Top Virus (BBTV) isolates. Int. Res. J. Microbiol. 2010, 1(1):1-12.
25. Lefeuvre P., Lett J.M., Varsani A., Martin D.P. Widely conserved recombination patterns among single-stranded DNA viruses. J. Virol. 2009, 83:2697-2707.
26. Li C., Hatta M., Nidom C.A., Muramoto Y., Watanabe S., Neumann G. Reassortment between avian H5N1 and human H3N2 influenza viruses creates hybrid viruses with substantial virulence. Proc. Natl. Acad. Sci. USA 2010, 107:4687-4692.
27. Mandal B., Mandal S., Pun K.B., Varma A. First report of the association of a nanovirus with foorkey disease of large cardamom in India. Plant Dis. 2004, 88:428.
28. Mandal B. Advances in small isometric multicomponent ssDNA viruses infecting plants. Ind. J. Virol. 2010, 21(1):18-30.
29. Mandal B., Shilpi S., Barman A.R., Mandal S., Varma A. Nine novel DNA components associated with the foorkey disease of large cardamom: evidence of a distinct Babuvirus species in Nanoviridae. Virus Res. 2013, 178(2):297-305.
30. Martin D., Rybicki E. RDP: detection of recombination amongst aligned sequences. Bioinformatics 2000, 16:562-563.
31. Martin D.P., Posada D., Crandall K.A., Williamson C. A modified bootscan algorithm for automated identification of recombinant sequences and recombination breakpoints. AIDS Res. Hum. Retroviruses 2005, 21:98-102.
32. Martin D.P., van der Walt E., Posada D., Rybicki E.P. The evolutionary value of recombination is constrained by genome modularity. PLoS Genet. 2005, 1:e51.
33. 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.
34. Martin D.P., Biagini P., Lefeuvre P., Golden M., Roumagnac P., Varsani A. Recombination in eukaryotic single stranded DNA viruses. Viruses 2011, 3:1699-1738.
35. Martin D.P., Lefeuvre P., Varsani A., Hoareau M., Semegni J.-Y., Dijoux B., Vincent C., Reynaud B., Lett J.-M. Complex recombination patterns arising during geminivirus coinfections preserve and demarcate biologically important intra-genome interaction networks. PLoS Pathog. 2011, 7(9):e1002203.
36. Maynard Smith J. Analyzing the mosaic structure of genes. J. Mol. Evol. 1992, 34:126-129.
37. Nei M., Li W.H. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc. Natl. Acad. Sci. USA 1979, 76:5269-5273.
38. Padidam M., Sawyer S., Fauquet C. Possible emergence of new geminiviruses by frequent recombination. Virology 1999, 265:218-225.
39. Pamilo P., Nei M. Relationships between gene trees and species trees. Mol. Biol. Evol. 1988, 5(5):568-583.
40. Posada D., Crandall K.A. Evaluation of methods for detecting recombination from DNA sequences: computer simulations. Proc. Natl. Acad. Sci. USA 2001, 98:13757-13762.
41. Preiss W., Jeske H. Multitasking in replication is common among geminiviruses. J. Virol. 2003, 77:2972-2980.
42. Rambaut, A., Drummond, A.J., 2007. Tracer v. 1.5. Computer program and documentation distributed by the authors at <>. http://beast.bio.ed.ac.uk/Tracer.
43. Rambaut, A., 2009. FigTree v. 1.3.1. Computer program and documentation distributed by the author at <>. http://tree.bio.ed.ac.uk/software/.
44. Roberts S., Stanley J. Lethal mutations within the conserved stem-loop of African cassava mosaic virus DNA are rapidly corrected by genomic recombination. J. Gen. Virol. 1994, 7:3203-3209.
45. Roossnick M.J. Symbiosis versus competition in plant virus evolution. Nat. Rev. Microbiol. 2005, 3(12):917-924.
46. Scholtissek C., Bürger H., Kistner O., Shortridge K.F. The nucleoprotein as a possible major factor in determining host specificity of influenza H3N2 virus. Virology 1985, 147(2):287-294.
47. Selvarajan R., Sheeba M.M., Balasubramanian V., Rajmohan R., Dhevi N.L., Sasireka T. Molecular characterisation of geographically different Banana bunchy top virus isolates in India. Ind. J. Virol. 2010, 21(2):110-116.
48. Sharman M., Thomas J.E., Skabo S., Holton T.A. Abaca bunchy top virus, a new member of the genus Babuvirus (family Nanoviridae). Arch. Virol. 2008, 153(1):135-147.
49. Stainton D., Kraberger S., Walters M., Wiltshire E.J., Rosario K., Halafihi M., Lolohea S., Katoa I., Faitua T.H., Aholelei W., Taufa L., Thomas J.E., Collings A., Martin D.P., Varsani A. Evidence of inter-component recombination, intra-component recombination and reassortment in Banana bunchy top virus. J. Gen. Virol. 2012, 93:1103-1119.
50. Timchenko T., Katul L., Sano Y., de Kouchkovsky F., Vetten H.J., Gronenborn B. The master rep concept in nanovirus replication: identification of missing genome components and potential for natural genetic reassortment. Virology 2000, 274:189-195.
51. Wang H.I., Chang C.H., Lin P.H., Fu H.C., Tang C., Yeh H.H. Application of motif-based tools on evolutionary analysis of multipartite single-stranded DNA viruses. PLoS ONE 2013, 8(8):e71565.
52. Zhou X., Liu Y., Calvert L., Munoz C., Otim-Nape G., Robinson D., Harrison B. Evidence that DNA-A of a geminivirus associated with severe cassava mosaic disease in Uganda has arisen by interspecific recombination. J. Gen. Virol. 1997, 78:2101-2111.