Genetic diversity and molecular evolution of arabis mosaic virus based on the CP gene sequence

详细信息    查看全文

• 作者：Fangluan Gao ; Wuzhen Lin ; Jianguo Shen ; Furong Liao
• 刊名：Archives of Virology
• 出版年：2016
• 出版时间：April 2016
• 年：2016
• 卷：161
• 期：4
• 页码：1047-1051
• 全文大小：739 KB
• 参考文献：1.King AM, Lefkowitz E, Adams MJ, Carstens EB (2011) Virus taxonomy, Ninth Report of the International Committee on Taxonomy of Viruses. Elsevier Academic Press, Amsterdam
  2.Wetzel T, Chisholm J, Bassler A, Sanfacon H (2008) Characterization of proteinase cleavage sites in the N-terminal region of the RNA1-encoded polyprotein from Arabis mosaic virus (subgroup A nepovirus). Virology 375(1):159–169CrossRef PubMed
  3.Vigne E, Marmonier A, Fuchs M (2008) Multiple interspecies recombination events within RNA2 of Grapevine fanleaf virus and Arabis mosaic virus. Arch Virol 153(9):1771–1776CrossRef PubMed
  4.Nourinejhad Zarghani S, Dupuis-Maguiraga L, Bassler A, Wetzel T (2014) Mapping of the exchangeable and dispensable domains of the RNA 2-encoded 2AHP protein of arabis mosaic nepovirus. Virology 458–459:106–113CrossRef PubMed
  5.Vigne E, Bergdoll M, Guyader S, Fuchs M (2004) Population structure and genetic variability within isolates of Grapevine fanleaf virus from a naturally infected vineyard in France: evidence for mixed infection and recombination. J Gen Virol 85(Pt 8):2435–2445CrossRef PubMed
  6.Moury B, Simon V (2011) dN/dS-based methods detect positive selection linked to trade-offs between different fitness traits in the coat protein of potato virus Y. Mol Biol Evol 28(9):2707–2717CrossRef PubMed
  7.Thompson JR, Kamath N, Perry KL (2014) An evolutionary analysis of the Secoviridae family of viruses. PLoS One 9(9):e106305CrossRef PubMed PubMedCentral
  8.Cuevas J, Delaunay A, Rupar M, Jacquot E, Elena SF (2012) Molecular evolution and phylogeography of Potato virus Y based on the CP gene. J Gen Virol 93(Pt 11):2496–2501CrossRef PubMed
  9.Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32(5):1792–1797CrossRef PubMed PubMedCentral
  10.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. Mol Biol Evol 28(10):2731–2739CrossRef PubMed PubMedCentral
  11.Muhire BM, Varsani A, Martin DP (2014) SDT: A virus classification tool based on pairwise sequence alignment and identity calculation. PLoS One 9(9):e108277CrossRef PubMed PubMedCentral
  12.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(19):2462–2463CrossRef PubMed PubMedCentral
  13.Talavera G, Castresana J (2007) Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol 56(4):564–577CrossRef PubMed
  14.Parker J, Rambaut A, Pybus OG (2008) Correlating viral phenotypes with phylogeny: accounting for phylogenetic uncertainty. Infect Genet Evol 8(3):239–246CrossRef PubMed
  15.Librado P, Rozas J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25(11):1451–1452CrossRef PubMed
  16.Hudson RR, Boos DD, Kaplan NL (1992) A statistical test for detecting geographic subdivision. Mol Biol Evol 9(1):138–151PubMed
  17.Hudson RR (2000) A new statistic for detecting genetic differentiation. Genetics 155(4):2011–2014PubMed PubMedCentral
  18.Excoffier L, Lischer HE (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 10(3):564–567CrossRef PubMed
  19.Balloux F, Lugon-Moulin N (2002) The estimation of population differentiation with microsatellite markers. Mol Ecol 11(2):155–165CrossRef PubMed
  20.Yang Z (2007) PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol 24(8):1586–1591CrossRef PubMed
  21.Yang Z, Nielsen R (2000) Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol Biol Evol 17(1):32–43CrossRef PubMed
  22.Pond SLK, Frost SDW, Muse SV (2005) HyPhy: hypothesis testing using phylogenies. Bioinformatics 21(5):676–679CrossRef PubMed
  23.Gibbs A, Ohshima K (2010) Potyviruses and the digital revolution. Annu Rev Phytopathol 48:205–223CrossRef PubMed
  24.Tugume AK, Mukasa SB, Kalkkinen N, Valkonen JPT (2010) Recombination and selection pressure in the ipomovirus sweet potato mild mottle virus(Potyviridae) in wild species and cultivated sweetpotato in the centre of evolution in East Africa. J Gen Virol 91:1092–1108CrossRef PubMed
  25.Stracke S, Presterl T, Stein N, Perovic D, Ordon F, Graner A (2007) Effects of introgression and recombination on haplotype structure and linkage disequilibrium surrounding a locus encoding Bymovirus resistance in Barley. Genetics 175(2):805–817CrossRef PubMed PubMedCentral
  26.Mekuria TA, Gutha LR, Martin RR, Naidu RA (2009) Genome diversity and intra- and interspecies recombination events in Grapevine fanleaf virus. Phytopathology 99(12):1394–1402CrossRef PubMed
  27.Azzam O, Yambao ML, Muhsin M, McNally KL, Umadhay KM (2000) Genetic diversity of rice tungro spherical virus in tungro-endemic provinces of the Philippines and Indonesia. Arch Virol 145(6):1183–1197CrossRef PubMed
  28.Oliver JE, Vigne E, Fuchs M (2010) Genetic structure and molecular variability of Grapevine fanleaf virus populations. Virus Res 152(1–2):30–40CrossRef PubMed
  29.Ferrer RM, Ferriol I, Moreno P, Guerri J, Rubio L (2011) Genetic variation and evolutionary analysis of broad bean wilt virus 2. Arch Virol 156(8):1445–1450CrossRef PubMed
  30.Moury B, Morel C, Johansen E, Jacquemond M (2002) Evidence for diversifying selection in Potato virus Y and in the coat protein of other potyviruses. J Gen Virol 83(Pt 10):2563–2573CrossRef PubMed
  
• 作者单位：Fangluan Gao (1)
  Wuzhen Lin (1)
  Jianguo Shen (2)
  Furong Liao (3)
  
  1. Key Lab for Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, 350002, People’s Republic of China
  2. Inspection and Quarantine Technology Center, Fujian Exit-Entry, Inspection and Quarantine Bureau, Fuzhou, 350001, People’s Republic of China
  3. Inspection and Quarantine Technology Center, Xiamen Exit-Entry Inspection and Quarantine Bureau, Xiamen, 361012, People’s Republic of China
  
• 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

Arabis mosaic virus (ArMV) is a virus with a wide host range. In this study, the genetic diversity of ArMV and the molecular mechanisms underlying its evolution were investigated using the coat protein (CP) sequence. Of the 33 ArMV isolates studied, three were found to be recombinants. The other 30 recombination-free ArMV isolates could be separated into two major lineages with a significant F _ST value (0.384) and tended to cluster according to their geographical origin. Different evolutionary constraints were detected for the two linages, pointing to a role of natural selection in the differentiation of ArMV.