Identification and in silico characterisation of defective molecules associated with isolates of banana bunchy top virus

详细信息    查看全文

• 作者：Daisy Stainton ; Darren P. Martin ; David A. Collings ; John E. Thomas…
• 关键词：Banana bunchy top virus ; Nanovirus ; Defective molecules
• 刊名：Archives of Virology
• 出版年：2016
• 出版时间：April 2016
• 年：2016
• 卷：161
• 期：4
• 页码：1019-1026
• 全文大小：584 KB
• 参考文献：1.Aronson MN, Meyer AD, Györgyey J, Katul L, Vetten HJ, Gronenborn B, Timchenko T (2000) Clink, a nanovirus-encoded protein, binds both pRB and SKP1. J Virol 74:2967–2972CrossRef PubMed PubMedCentral
  2.Bach J, Jeske H (2014) Defective DNAs of beet curly top virus from long-term survivor sugar beet plants. Virus Res 183:89–94CrossRef PubMed
  3.Bell KE, Dale JL, Ha CV, Vu MT, Revill PA (2002) Characterisation of Rep-encoding components associated with banana bunchy top nanovirus in Vietnam. Arch Virol 147:695–707CrossRef PubMed
  4.Burns TM, Harding RM, Dale JL (1995) The genome organisation of banana bunchy top virus: analysis of six ssDNA components. J Gen Virol 76:1471–1482CrossRef PubMed
  5.Casado CG, Javier Ortiz G, Padron E, Bean SJ, McKenna R, Agbandje-McKenna M, Boulton MI (2004) Isolation and characterization of subgenomic DNAs encapsidated in “single” T = 1 isometric particles of Maize streak virus. Virology 323:164–171CrossRef PubMed
  6.Dale JL (1987) Banana bunchy top—an economically important tropical plant-virus disease. Adv Virus Res 33:301–325CrossRef PubMed
  7.Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797CrossRef PubMed PubMedCentral
  8.Frischmuth T, Stanley J (1992) Characterization of beet curly top virus subgenomic DNA localizes sequences required for replication. Virology 189:808–811CrossRef PubMed
  9.Fu HC, Hu JM, Hung TH, Su HJ, Yeh HH (2009) Unusual events involved in banana bunchy top virus strain evolution. Phytopathology 99:812–822CrossRef PubMed
  10.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 166:13–22CrossRef PubMed
  11.Hafner GJ, Harding RM, Dale JL (1995) Movement and transmission of banana bunchy top virus DNA component one in bananas. J Gen Virol 76:2279–2285CrossRef PubMed
  12.Hafner GJ, Harding RM, Dale JL (1997) A DNA primer associated with banana bunchy top virus. J Gen Virol 78:479–486CrossRef PubMed
  13.Hafner GJ, Stafford MR, Wolter LC, Harding RM, Dale JL (1997) Nicking and joining activity of banana bunchy top virus replication protein in vitro. J Gen Virol 78:1795–1799CrossRef PubMed
  14.Harding RM, Burns TM, Dale JL (1991) Virus-like particles associated with banana bunchy top disease contain small single-stranded DNA. J Gen Virol 72:225–230CrossRef PubMed
  15.Herrera-Valencia VA, Dugdale B, Harding RM, Dale JL (2006) An iterated sequence in the genome of banana bunchy top virus is essential for efficient replication. J Gen Virol 87:3409–3412CrossRef PubMed
  16.Horn J, Lauster S, Krenz B, Kraus J, Frischmuth T, Jeske H (2011) Ambivalent effects of defective DNA in beet curly top virus-infected transgenic sugarbeet plants. Virus Res 158:169–178CrossRef PubMed
  17.Horser CL, Karan M, Harding RM, Dale JL (2001) Additional Rep-encoding DNAs associated with banana bunchy top virus. Arch Virol 146:71–86CrossRef PubMed
  18.Idris AM, Shahid MS, Briddon RW, Khan AJ, Zhu JK, Brown JK (2011) An unusual alphasatellite associated with monopartite begomoviruses attenuates symptoms and reduces betasatellite accumulation. J Gen Virol 92:706–717CrossRef PubMed
  19.Liu Y, Robinson DJ, Harrison BD (1998) Defective forms of cotton leaf curl virus DNA-A that have different combinations of sequence deletion, duplication, inversion and rearrangement. J Gen Virol 79:1501–1508CrossRef PubMed
  20.Martin DP, Lemey P, Lott M, Moulton V, Posada D, Lefeuvre P (2010) RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics 26:2462–2463CrossRef PubMed PubMedCentral
  21.Martin DP, Murrell B, Golden M, Khoosal A, Muhire B (2015) RDP4: Detection and analysis of recombination patterns in virus genomes. Virus Evol. doi:10.​1093/​ve/​vev003
  22.Ndunguru J, Legg JP, Fofana IBF, Aveling TAS, Thompson G, Fauquet CM (2006) Identification of a defective molecule derived from DNA-A of the bipartite begomovirus of East African cassava mosaic virus. Plant Pathol 55:2–10CrossRef
  23.Paprotka T, Boiteux LS, Fonseca MEN, Resende RO, Jeske H, Faria JC, Ribeiro SG (2010) Genomic diversity of sweet potato geminiviruses in a Brazilian germplasm bank. Virus Res 149:224–233CrossRef PubMed
  24.Patil BL, Dasgupta I (2006) Defective interfering DNAs of plant viruses. Crit Rev Plant Sci 25:47–64CrossRef
  25.Patil BL, Dutt N, Briddon RW, Bull SE, Rothenstein D, Borah BK, Dasgupta I, Stanley J, Jeske H (2007) Deletion and recombination events between the DNA-A and DNA-B components of Indian cassava-infecting geminiviruses generate defective molecules in Nicotiana benthamiana. Virus Res 124:59–67CrossRef PubMed
  26.Rey MEC, Ndunguru J, Berrie LC, Paximadis M, Berry S, Cossa N, Nuaila VN, Mabasa KG, Abraham N, Rybicki EP, Martin D, Pietersen G, Esterhuizen LL (2012) Diversity of dicotyledenous-infecting geminiviruses and their associated DNA molecules in Southern Africa, including the South-west Indian Ocean Islands. Viruses 4:1753–1791CrossRef PubMed PubMedCentral
  27.Rybicki EP, Pietersen G (1999) Plant virus disease problems in the developing world. Adv Virus Res 53:127–175CrossRef PubMed
  28.Rybicki EP (2015) A Top Ten list for economically important plant viruses. Arch Virol 160:17–20CrossRef PubMed
  29.Schubert J, Habekuß A, Wu B, Thieme T, Wang X (2014) Analysis of complete genomes of isolates of the Wheat dwarf virus from new geographical locations and descriptions of their defective forms. Virus Genes 48:133–139CrossRef PubMed
  30.Stainton D, Kraberger S, Walters M, Wiltshire EJ, Rosario K, Halafihi M, Lolohea S, Katoa I, Faitua TH, Aholelei W, Taufa L, Thomas JE, Collings DA, Martin DP, Varsani A (2012) Evidence of inter-component recombination, intra-component recombination and reassortment in banana bunchy top virus. J Gen Virol 93:1103–1119CrossRef PubMed
  31.Stainton D, Martin D, Muhire B, Lolohea S, Halafihi M, Lepoint P, Blomme G, Crew KS, Sharman M, Kraberger S, Dayaram A, Walters M, Collings DA, Mabvakure B, Lemey P, Harkins G, Thomas JE, Varsani A (2015) The global distribution of Banana bunchy top virus reveals little evidence for frequent recent, human-mediated long distance dispersal events. Virus Evol. doi:10.​1093/​ve/​vev009
  32.Stamatakis A (2014) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312–1313CrossRef PubMed PubMedCentral
  33.Stanley J, Townsend R (1985) Characterisation of DNA forms associated with cassava latent virus infection. Nucleic Acids Res 13:2189–2206CrossRef PubMed PubMedCentral
  34.Stanley J, Frischmuth T, Ellwood S (1990) Defective viral DNA ameliorates symptoms of geminivirus infection in transgenic plants. Proc Natl Acad Sci USA 87:6291–6295CrossRef PubMed PubMedCentral
  35.Stanley J, Saunders K, Pinner MS, Wong SM (1997) Novel defective interfering DNAs associated with ageratum yellow vein geminivirus infection of Ageratum conyzoides. Virology 239:87–96CrossRef PubMed
  36.Stenger DC, Stevenson MC, Hormuzdi SG, Bisaro DM (1992) A number of subgenomic DNAs are produced following agroinoculation of plants with beet curly top virus. J Gen Virol 73:237–242CrossRef PubMed
  37.Su HJ, Tsao LY, Wu ML, Hung TH (2003) Biological and molecular categorization of strains of Banana bunchy top virus. J Phytopathol 151:290–296CrossRef
  38.Thomas JE, Dietzgen RG (1991) Purification, characterization and serological detection of virus-like particles associated with banana bunchy top disease in Australia. J Gen Virol 72:217–224CrossRef PubMed
  39.van der Walt E, Rybicki EP, Varsani A, Polston JE, Billharz R, Donaldson L, Monjane AL, Martin DP (2009) Rapid host adaptation by extensive recombination. J Gen Virol 90:734–746CrossRef PubMed PubMedCentral
  40.Wanitchakorn R, Hafner GJ, Harding RM, Dale JL (2000) Functional analysis of proteins encoded by banana bunchy top virus DNA-4 to -6. J Gen Virol 81:299–306CrossRef PubMed
  41.Wanitchakorn R, Harding RM, Dale JL (2000) Sequence variability in the coat protein gene of two groups of banana bunchy top isolates. Arch Virol 145:593–602CrossRef PubMed
  42.Wu R-Y, You L-R, Soong T-S (1994) Nucleotide sequences of two circular single-stranded DNAs associated with banana bunchy top virus. Phytopathology 84:952–957CrossRef
  43.Yu NT, Zhang YL, Feng TC, Wang JH, Kulye M, Yang WJ, Lin ZS, Xiong Z, Liu ZX (2012) Cloning and sequence analysis of two banana bunchy top virus genomes in Hainan. Virus Genes 44:488–494CrossRef PubMed
  44.Zaffalon V, Mukherjee SK, Reddy VS, Thompson JR, Tepfer M (2012) A survey of geminiviruses and associated satellite DNAs in the cotton-growing areas of northwestern India. Arch Virol 157:483–495CrossRef PubMed
  45.Zhou XP, Xie Y, Zhang ZK, Qi YJ, Wu JJ (2001) Molecular characterization of a novel defective DNA isolated from tobacco tissues infected with tobacco leaf curl virus. Acta Virol 45:45–50PubMed
  
• 作者单位：Daisy Stainton (1)
  Darren P. Martin (2)
  David A. Collings (1)
  John E. Thomas (3)
  Arvind Varsani (1) (2) (4)
  
  1. School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
  2. Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town, South Africa
  3. Ecosciences Precinct, Queensland Alliance for Agriculture and Food Innovation, Centre for Plant Science, The University of Queensland, PO Box 46, Brisbane, QLD, 4001, Australia
  4. Department of Plant Pathology, Emerging Pathogens Institute, University of Florida, Gainesville, FL, 32611, USA
  
• 刊物类别：Biomedical and Life Sciences
• 刊物主题：Biomedicine
  Virology
  Medical Microbiology
  Infectious Diseases
  
• 出版者：Springer Wien
• ISSN：1432-8798

文摘

Banana bunchy top virus (BBTV) is a multi-component single-stranded DNA virus. From 267 potentially infected Musa plants, 24 apparently ‘defective’ BBTV components have been identified. Interestingly, 23/24 of these defective molecules were apparently derived from DNA-R. All of the identified defective molecules had retained at least part of the CR-SL and CR-M but had insertions and/or deletions that in most cases resulted in open reading frame disruptions. Our detection of three monophyletic but diverse (and therefore likely circulating) defective DNA-R lineages suggests that, in many cases, defective DNA-R molecules might remain associated with BBTV genomes for prolonged periods.