Effects of recombination on densovirus phylogeny

详细信息    查看全文

• 作者：Elena U. Martynova ; Coby Schal ; Dmitry V. Mukha
• 刊名：Archives of Virology
• 出版年：2016
• 出版时间：January 2016
• 年：2016
• 卷：161
• 期：1
• 页码：63-75
• 全文大小：569 KB
• 参考文献：1.Baquerizo-Audiot E, Abd-Alla A, Jousset FX, Cousserans F, Tijssen P, Bergoin M (2009) Structure and expression strategy of the genome of Culex pipiens densovirus, a mosquito densovirus with an ambisense organization. J Virol 83:6863–6873PubMed PubMedCentral CrossRef
  2.Barreau C, Jousset FX, Bergoin M (1996) Pathogenicity of the Aedes albopictus parvovirus (AaPV), a Denso-like virus, for Aedes aegypti mosquitoes. J Invert Pathol 68:299–309CrossRef
  3.Beczkowski PM, Hughes J, Biek R, Litster A, Willett BJ, Hosie MJ (2014) Feline Immunodeficiency virus (FIV) env recombinants are common in natural infections. Retrovirology 11:80PubMed PubMedCentral CrossRef
  4.Bergoin M, Tijssen P (2000) Molecular biology of Densovirinae. In: Faisst S, Rommelaere J (eds) Parvoviruses: From molecular biology to pathology and therapeutic uses. Contributions to Microbiology 4:12–32
  5.Bonami J-R, Mari J, Poulos BT, Lightner DV (1995) Characterization of hepatopancreatic parvo-like virus, a second unusual parvovirus pathogenic for penaeid shrimps. J Gen Virol 76:813–817PubMed CrossRef
  6.Boulila M (2011) Positive selection, molecular recombination structure and phylogenetic reconstruction of members of the family Tombusviridae: Implication in virus taxonomy. Genet Mol Biol 22:647–660CrossRef
  7.Bull JJ, Badgett MR, Wichman HA, Huelsenbeck JP, Hillis DM, Gulati A, Ho C, Molineux IJ (1997) Exceptional convergent evolution in a virus. Genetics 147:1497–1507PubMed PubMedCentral
  8.Carvajal-Rodrigues A (2008) Detecting recombination and diversifying selection in human alpha-papillomavirus. Infect Genet Evol 8:689–692CrossRef
  9.Castresana J (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17:540–552PubMed CrossRef
  10.Chenault KD, Melcher U (1994) Phylogenetic relationships reveal recombination among isolates of Cauliflower Mosaic Virus. J Mol Evol 39:496–505PubMed CrossRef
  11.Combelas N, Holmblat B, Joffret M-L, Colbere-Garapin F, Delpeyroux F (2011) Recombination between Poliovirus and Coxsackie A viruses of species C: a model of viral genetic plasticity and emergence. Viruses 3:1460–1484PubMed PubMedCentral CrossRef
  12.Cook S, Moureau G, Kitchen A, Gould EA, de Lamballerie X, Holmes EC, Harbach RE (2012) Molecular evolution of the insect-specific flaviviruses. J Gen Virol 93:223–234PubMed PubMedCentral CrossRef
  13.Cotmore SF, Agbandje-McKenna M, Chiorini JA, Mukha DV, Pintel DJ, Qiu J, Soderlund-Venermo M, Tattersall P, Tijssen P, Gatherer D, Davison AJ (2014) The family parvoviridae. Arch Virol 159:1239–1247PubMed PubMedCentral CrossRef
  14.Drummond AJ, Rambaut A (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7:214PubMed PubMedCentral CrossRef
  15.Fediere G (2000) Epidemiology and pathology of Densovirinae. Molecular biology of Densovirinae. In: Faisst S, Rommelaere J (eds) Parvoviruses: From molecular biology to pathology and therapeutic uses. Contributions to Microbiology 4:1–11
  16.Fediere G, Li Y, Zadori Z, Szelei J, Tijssen (2002) Genome organization of Casphalia extranes Densovirus, a new Iteravirus. Virology 292:299–308PubMed CrossRef
  17.Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376PubMed CrossRef
  18.Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791CrossRef
  19.Francois S, Bernardo P, Filloux D, Roumagnac P, Yaverkovski N, Froissart R, Ogliastro M (2014) A novel Itera-like densovirus isolatedby viral metagenomics from the sea barley Hordeum marinum. Genome Announcements 2:e01196–e01214PubMed PubMedCentral CrossRef
  20.Fu X, Wang X, Ni B, Shen H, Wang H, Zhang X, Chen S, Shao S, Zhang W (2011) Virol J 8:182PubMed PubMedCentral CrossRef
  21.Huelsenbeck JP, Ronquist R, Nielsen R, Bollback JP (2001) Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294:2310–2314PubMed CrossRef
  22.Jackwood MW, Boynton TO, Hilt DA, McKinley ET, McKinley ET, Kissinger JC, Paterson AH, Robertson J, Lemke C, McCall AW, Williams SM, Jackwood JW, Byrd LA (2010) Emergence of a group 3 coronavirus through recombination. Virology 398:98–108PubMed CrossRef
  23.Jackwood MW, Hall D, Handel A (2012) Molecular evolution and emergence of avian gammacoronavirus. Infect Genet Evol 12:1305–1311PubMed CrossRef
  24.Jetzt AE, Yu H, Klarmann GJ, Ron Y, Preston BD, Dougherty JP (2000) High rate of recombination throughout the human immunodeficiency virus type 1 genome. J Virol 74:1234–1240PubMed PubMedCentral CrossRef
  25.Jousset FX, Baquerizo E, Bergoin M (2000) A new densovirus isolated from the mosquito Culex pipiens (Diptera: Culicidae). Virus Res 67:11–16PubMed CrossRef
  26.Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30:772–780PubMed PubMedCentral CrossRef
  27.Kawase S, Kurstak E (1991) Parvoviridae of invertebrates: Densonucleosis viruses. In: Kurstak E (ed) Viruses of Invertebrates. Dekker, New York, pp 315–343
  28.Koonin EV, Dolja VV, Krupovic M (2015) Origins and evolution of viruses of eukaryotes: The ultimate modularity. Virology 479–480:2–25PubMed CrossRef
  29.Kosakovsky Pond SL, Frost SDW (2005) Not so different after all: a comparison of methods for detecting amino acid sites under selection. Mol Biol Evol 22:1208–1222PubMed CrossRef
  30.Lai MMC (1992) RNA recombination in animal and plant viruses. Microbiol Rev 56:61–79PubMed PubMedCentral
  31.Le SQ, Lartillot N, Gascuel O (2008) Phylogenetic mixture models for proteins. Philos Trans R Soc Lond B Biol Sci 363:3965–3976PubMed PubMedCentral CrossRef
  32.Leal E, Villanova FE, Lin W, Hu F, Liu Q, Liu Y, Cui S (2012) Interclade recombination in porcine parvovirus strains. J Gen Virol 93:2692–2704PubMed CrossRef
  33.Lefebvre DJ, Van Doorsselaere J, Delputte PI, Nauwynck HJ (2009) Recombination of two porcine circovirus type 2 strains. Arch Virol 154:875–879PubMed CrossRef
  34.Liu W, Zhai J, Liu J, Xie Y (2010) Identification of recombination between subgenotypes IA and IB of hepatitis A virus. Virus Genes 40:222–224PubMed CrossRef
  35.Martin DP, Lemey P, Lott M, Moulton V, Posada D, Lefeuvre P (2010) Rdp3: a flexible and fast computer program for analyzing recombination. Bioinformatics 26:2462–2463PubMed PubMedCentral CrossRef
  36.Martin DP, Biagini P, Lefeuvre P, Golden M, Roumagnac P, Varsani A (2011) Recombination in eukaryotic single stranded DNA viruses. Viruses 3:1699–1738PubMed PubMedCentral CrossRef
  37.Mochizuki M, Ohshima T, Une Y, Yachi A (2008) Recombination between vaccine and field strains of Canine Parvovirus is revealed by isolation of virus in canine and feline cell cultures. J Vet Med Sci 70:1305–1314PubMed CrossRef
  38.Mukha DV, Chumachenko AG, Dykstra MJ, Kurtti TJ, Schal C (2006) Characterization of a new densovirus infecting the German cockroach, Blattella germanica. J Gen Virol 87:1567–1575PubMed CrossRef
  39.Nei M, Gojobori T (1986) Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 3:418–426PubMed
  40.Nei M, Kumar S (2000) Molecular evolution and phylogenetics. Oxford University Press, New York
  41.Nylander JAA (2004) MrModeltest V2. Program Distributed by the Author, Evolutionary Biology Center, Uppsala University
  42.Ohshima T, Mochizuki M (2009) Evidence for recombination between Feline Panleukopenia Virus and Canine Parvovirus Type 2. J Vet Med Sci 71:403–408PubMed CrossRef
  43.O’Neill SL, Kittayapong P, Braig HR, Andreadis TG, Gonzalez JP (1995) 0 Insect densoviruses may be widespread in mosquito cell lines. J Gen Virol 76:2067–2074PubMed CrossRef
  44.Pei J, Kim BH, Grishin NV (2008) PROMALS3D: a tool for multiple sequence and structure alignment. Nucleic Acids Res 36:2295–2300PubMed PubMedCentral CrossRef
  45.Pham HT, Jousset FX, Perreault J, Shike H, Szelei J, Bergoin M, Tijssen P (2013) Expression strategy of Aedes albopictus densovirus. J Virol 87:9928–9932PubMed PubMedCentral CrossRef
  46.Robinson CM, Rajaiya J, Walsh MP, Seto D, Dyer DW, Jones MS, Chodosh J (2009) Computational analysis of human adenovirus type 22 provides evidence for recombination among species D human adenoviruses in the penton base gene. J Virol 83:8980–8985PubMed PubMedCentral CrossRef
  47.Ronquist F, Huelsenbeck JP (2003) Mrbayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572–1574PubMed CrossRef
  48.Shackelton LA, Hoelzer K, Parrish CR, Holmes EC (2007) Comparative analysis reveals frequent recombination in the parvoviruses. J Gen Virol 88:3294–3301PubMed PubMedCentral CrossRef
  49.Sharma S, Rabindran R, Robin S, Dasgupta I (2011) Analysis of the complete DNA sequence of rice tungro baciliformis virus from southern India indicates it to be a product of recombination. Arch Virol 156:2257–2262PubMed CrossRef
  50.Snoussi K, Kann M (2014) Interaction of parvoviruses with the nuclear envelope. Adv Biol Regul 54:39–49PubMed CrossRef
  51.Stern DL (2013) The genetic causes of convergent evolution. Nat Rev Gen 14:751–764CrossRef
  52.Sukhumsirichart W, Attasart P, Boonsaeng V, Panym S (2006) Complete nucleotide sequence and genomic organization of hepatopancreatic parvovirus (HPV) of Penaeus monodon. Virology 346:266–277PubMed CrossRef
  53.Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA 6: Molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729PubMed PubMedCentral CrossRef
  54.Tanada Y, Kaya HK (1993) Insect pathology. Academic Press, San Diego
  55.Theze J, Takatsuka J, Nakai M, Arif B, Herniou EA (2015) Gene Acquisition convergence between Entomopoxviruses and Baculoviruses. 7:1960–1974
  56.Thiry E, Meurens F, Muylkens B, McVoy M, Gogev S, Thiry J, Vanderplasschen A, Epstein A, Keil G, Schynts F (2005) Recombination in alphaherpesviruses. Rev Med Virol 15:89–103PubMed CrossRef
  57.Tiendrebeogo F, Lefeuvre P, Hoareau M, Harimala MA, De Bruyn A, Villemot J, Traore VSE, Konate G, Traore AS, Barro N, Reynaud B, Traore O, Lett J-M (2012) Evolution of African cassava mosaic virus by recombination between bipartite and monopartite begomoviruses. Virol J 9:67PubMed PubMedCentral CrossRef
  58.Tijssen P, Bergoin M (1995) Densonucleosis viruses constitute an increasingly diversified subfamily among the parvoviruses. Semin Virol 6:347–355CrossRef
  59.Tijssen P, Li Y, El-Far m, Szelei J, Letarte M, Zadori Z (2003) Organization and expression strategy of the ambisense genome of Densonucleosis Virus of Galleria mellonella. J Virol 77:10357–10365PubMed PubMedCentral CrossRef
  60.Tijssen P, Agbandje-McKenna M, Almendral JM, Bergoin M, Flegel TW, Hedman K, Kleinschmidt J, Li Y, Pintel DJ, Tattersall P (2011) The family Parvoviridae. In: King AMQ, Adams MJ, Carstens EB, Lefkowitz EJ (eds) Virus taxonomy—ninth report of the international committee on taxonomy of viruses. Elsevier Academic Press, London, pp 405–425
  61.Wang Y, Abd-Alla AMM, Bossin H, Li Y, Bergoin M (2013) Analysis of the transcription strategy of the Juninia coenia (JcDNV) genome. Virus Res 174:101–107PubMed CrossRef
  62.Whelan S, Goldman N (2001) A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol Biol Evol 18:691–699PubMed CrossRef
  63.Worobey M (2000) Extensive homologous recombination among widely divergent TT viruses. J Virol 74:7666–7670PubMed PubMedCentral CrossRef
  64.van Munster M, Dulemans AM, Verbeek M, van den Heuvel JFJM, Reinbold C, Brault V, Clerivet A, van der Wilk F (2003) A new virus infecting Myzus persicae has a genome organization similar to the species of the genus Densovirus. J Gen Virol 84:165–172PubMed CrossRef
  65.Yu Q, Tijssen P (2014) Gene expression of five different iteradensoviruses: Bombyx mori densovirus, Casphalia extranea densovirus, Papilio polyxenes densovirus, Sibine fusca densovirus, and Danaus plexippus densovirus. J Virol 88:12152–12157PubMed PubMedCentral CrossRef
  66.Zhang J, Rosenberg HF, Nei M (1998) Positive Darwinian selection after gene duplication in primate ribonuclease genes. PNAS 95:3708–3713PubMed PubMedCentral CrossRef
  67.Zhou C, Tian H, Wang X, Liu W, Yang S, Shen Q, Wang Y, Ni B, Chen S, Fu X, Fei R, Zhang (2014) The genome sequence of a novel simian adenovirus in a chimpanzee reveals a close relationship to human adenoviruses. Arch Virol 159:1765–1770PubMed CrossRef
  
• 作者单位：Elena U. Martynova (1)
  Coby Schal (2)
  Dmitry V. Mukha (1)
  
  1. Vavilov Institute of General Genetics Russian Academy of Sciences, Moscow, 119991, Russia
  2. North Carolina State University, Raleigh, North Carolina, 27695-7613, 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

Densoviruses are a group of arthropod-infecting viruses with a small single-stranded linear DNA genome. These viruses constitute the subfamily Densovirinae of the family Parvoviridae. While recombination in between vertebrate-infecting parvoviruses has been investigated, to date, no systematic analysis of recombination has been carried out for densoviruses. The aim of the present work was to study possible recombination events in the evolutionary history of densoviruses and to assess possible effects of recombination on phylogenies inferred using amino acid sequences of nonstructural (NS) and capsid (viral protein, VP) proteins. For this purpose, the complete or nearly complete genome nucleotide sequences of 40 densoviruses from the GenBank database were used to construct a phylogenetic cladogram. The viruses under study clustered into five distinct groups corresponding to the five currently accepted genera. Recombination within each group was studied independently. The RDP4 software revealed three statistically highly credible recombination events, two of which involved viruses of the genus Ambidensovirus, and the other, viruses from the genus Iteradensovirus. These recombination events led to mismatches between phylogenetic trees constructed using comparison of amino acid sequences of proteins encoded by genome regions of recombinant and non-recombinant origin (regulatory NS1 and NS3 proteins and capsid VP protein).