An evolutionary analysis of the Secoviridae family of viruses

PLoS ONE

Volumn 9, Issue 9, 2014, Pages

  Thompson, Jeremy R ^a   Kamath, Nitin ^a,b   Perry, Keith L ^a  

^a Department of Plant Pathology and Plant Microbe Biology Cornell University ^*  (United States)

^b NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COAT PROTEIN; CAPSID PROTEIN; NUCLEOTIDE;

ARTICLE; CODON; COMOVIRINAE; EVOLUTION; GENE SEQUENCE; MONOPHYLY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLANT VIRUS; PROTEIN DOMAIN; SECOVIRIDAE; SEQUENCE ALIGNMENT; SPECIES DISTRIBUTION; SPECIES DIVERSITY; TAXONOMY; UNINDEXED SEQUENCE; VIRUS IDENTIFICATION; VIRUS ISOLATION; VIRUS MUTATION; ANIMAL; BIOLOGICAL MODEL; CHEMISTRY; GENETIC SELECTION; GENETIC VARIABILITY; GENETICS; HOST PATHOGEN INTERACTION; ISOLATION AND PURIFICATION; METABOLISM; PICORNAVIRIDAE; PLANT; PROTEIN TERTIARY STRUCTURE; SEQUENCE HOMOLOGY; SPECIES DIFFERENCE; STATISTICAL MODEL; VIROLOGY; VIRUS GENOME;

ANIMALS; BIOLOGICAL EVOLUTION; CAPSID PROTEINS; GENETIC VARIATION; GENOME, VIRAL; HOST-PATHOGEN INTERACTIONS; LIKELIHOOD FUNCTIONS; MODELS, BIOLOGICAL; NUCLEOTIDES; PHYLOGENY; PICORNAVIRIDAE; PLANT VIRUSES; PLANTS; PROTEIN STRUCTURE, TERTIARY; SELECTION, GENETIC; SEQUENCE HOMOLOGY, AMINO ACID; SPECIES SPECIFICITY;

EID: 84907459087     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0106305     Document Type: Article

References (77)

1. Le Gall O, Christian P, Fauquet CM, King AM, Knowles NJ, et al. (2008) Picornavirales, a proposed order of positive-sense single-stranded RNA viruses with a pseudo-T = 3 virion architecture. Arch Virol 153: 715-727.
2. Sanfacon H, Wellink J, Le Gall O, Karasev A, van der Vlugt R, et al. (2009) Secoviridae: a proposed family of plant viruses within the order Picornavirales that combines the families Sequiviridae and Comoviridae, the unassigned genera Cheravirus and Sadwavirus, and the proposed genus Torradovirus. Arch Virol 154: 899-907.
3. Li CJ, Yoshikawa N, Takahashi T, Ito T, Yoshida K, et al. (2000) Nucleotide sequence and genome organization of Apple latent spherical virus: a new virus classified into the family Comoviridae. JGen Virol 81: 541-547. (Pubitemid 30077299)
4. Thompson JR, Perry KL, De Jong W (2004) A new potato virus in a new lineage of picorna-like viruses. Arch Virol 149: 2141-2154. (Pubitemid 39508956)
5. Iwanami T, Kondo Y, Karasev AV (1999) Nucleotide sequences and taxonomy of satsuma dwarf virus. J Gen Virol 80: 793-797. (Pubitemid 29101236)
6. Thompson JR, Leone G, Lindner JL, Jelkmann W, Schoen CD (2002) Characterization and complete nucleotide sequence of Strawberry mottle virus: a tentative member of a new family of bipartite plant picorna-like viruses. J Gen Virol 83: 229-239. (Pubitemid 34030827)
7. Tzanetakis IE, Postman JD, Gergerich RC, Martin RR (2006) A virus between families: nucleotide sequence and evolution of Strawberry latent ringspot virus. Virus Res 121: 199-204. (Pubitemid 44436624)
8. Verbeek M, Dullemans AM, van den Heuvel JFJM, Maris PC, van der Vlugt RAA (2007) Identification and characterisation of tomato torrado virus, a new plant picorna-like virus from tomato. Arch Virol 152: 881-890. (Pubitemid 46664064)
9. Martelli GP, Boudon-Padieu E (2006) Directory of Infectious Diseases of Grapevines. In: Martelli GP, Boudon-Padieu E, editors. Options mediterraneennes. Bari: CIHEAM.
10. Chancellor TCB, Holt J, Villareal S, Tiongco ER, Venn J (2006) Spread of plant virus disease to new plantings: A case study of rice tungro disease. Adv Virus Res 66: 1-29. (Pubitemid 44107831)
11. Alfaro-Fernandez A, Cordoba-Selles MD, Juarez M, Herrera-Vasquez JA, Sanchez-Navarro JA, et al. (2010) Occurrence and Geographical Distribution of the 'Torrado' Disease in Spain. J Phytopathol 158: 457-469.
12. Verbeek M, Dullemans AM, van den Heuvel J, Maris PC, van der Vlugt RAA (2007) Identification and characterisation of tomato torrado virus, a new plant picorna-like virus from tomato. Arch Virol 152: 881-890. (Pubitemid 46664064)
13. Sanfaçon H, Iwanami T, Karasev AV, van der Vlugt R, Wellink J, et al. (2012) Secoviridae. In: King AMQ, Adams MJ, Carstens EB, Lefkowitz EJ, editors. Virus Taxonomy - Ninth report of the International Committee on Taxonomy of Viruses. London, U.K.: Academic Press. pp. 881-899.
14. Oliver JE, Vigne E, Fuchs M (2010) Genetic structure and molecular variability of Grapevine fanleaf virus populations. Virus Res 152: 30-40.
15. Azzam O, Yambao MLM, Muhsin M, McNally KL, Umadhay KML (2000) Genetic diversity of rice tungro spherical virus in tungro-endemic provinces of the Philippines and Indonesia. Arch Virol 145: 1183-1197. (Pubitemid 30446107)
16. 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: 1445-1450.
17. Lamprecht RL, Maree HJ, Stephan D, Burger JT (2012) Complete nucleotide sequence of a South African isolate of Grapevine fanleaf virus. Virus Genes 45: 406-410.
18. Vigne E, Marmonier A, Fuchs M (2008) Multiple interspecies recombination events within RNA2 of Grapevine fanleaf virus and Arabis mosaic virus. Arch Virol 153: 1771-1776.
19. Mekuria TA, Gutha LR, Martin RR, Naidu RA (2009) Genome Diversity and Intra- and Interspecies Recombination Events in Grapevine fanleaf virus. Phytopathology 99: 1394-1402.
20. Vigne E, Marmonier A, Komar V, Lemaire O, Fuchs M (2009) Genetic structure and variability of virus populations in cross-protected grapevines superinfected by Grapevine fanleaf virus. Virus Res 144: 154-162.
21. 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: 2435-2445. (Pubitemid 39162617)
22. Elbeaino T, Digiaro M, Ghebremeskel S, Martelli GP (2012) Grapevine deformation virus: Completion of the sequence and evidence on its origin from recombination events between Grapevine fanleaf virus and Arabis mosaic virus. Virus Res 166: 136-140.
23. Zhang CQ, Gu HC, Ghabrial SA (2007) Molecular characterization of naturally occurring RNA1 recombinants of the Comovirus Bean pod mottle virus. Phytopathology 97: 1255-1262.
24. Le Gall O, Candresse T, Dunez J (1995) Transfer of the 3′ Non-Translated Region of Grapevine Chrome Mosaic-Virus Rna-1 by Recombination to Tomato Black Ring Virus Rna-2 in Pseudorecombinant Isolates. J Gen Virol 76: 1285-1289.
25. Verbeek M, Dullemans AM, van den Heuvel JFJM, Maris PC, van der Vlugt RAA (2008) Tomato marchitez virus, a new plant picorna-like virus from tomato related to tomato torrado virus. Arch Virol 153: 127-134.
26. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797.
27. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biology Evol 28: 2731-2739.
28. Pond SLK, Frost SDW (2005) Datamonkey: rapid detection of selective pressure on individual sites of codon alignments. Bioinformatics 21: 2531-2533.
29. Xia X, Xie Z (2001) DAMBE: software package for data analysis in molecular biology and evolution. The J Hered 92: 371-373. (Pubitemid 32848767)
30. Pond SLK, Frost SDW, Muse SV (2005) HyPhy: hypothesis testing using phylogenies. Bioinformatics 21: 676-679. (Pubitemid 40424796)
31. Pond SLK, Murrell B, Fourment M, Frost SDW, Delport W, et al. (2011) A Random Effects Branch-Site Model for Detecting Episodic Diversifying Selection. Mol Biol Evol 28: 3033-3043.
32. Murrell B, Moola S, Mabona A, Weighill T, Sheward D, et al. (2013) FUBAR: a fast, unconstrained bayesian approximation for inferring selection. Mol Biol Evol 30: 1196-1205.
33. Posada D (2008) jModelTest: phylogenetic model averaging. Mol Biol Evol 25: 1253-1256.
34. Drummond AJ, Rambaut A (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7.
35. Drummond AJ, Suchard MA, Xie D, Rambaut A (2012) Bayesian Phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol 29: 1969-1973.
36. Swofford DL (1993) Paup - a Computer-Program for Phylogenetic Inference Using Maximum Parsimony. JGen Physiol 102: A9-A9.
37. Kishino H, Hasegawa M (1989) Evaluation of the Maximum-Likelihood Estimate of the Evolutionary Tree Topologies from DNA-Sequence Data, and the Branching Order in Hominoidea. J Mol Evol 29: 170-179. (Pubitemid 19206089)
38. Martin DP, Lemey P, Lott M, Moulton V, Posada D, et al. (2010) RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics 26: 2462-2463.
39. Thompson JR, Fuchs M, Perry KL (2012) Genomic analysis of grapevine leafroll associated virus-5 and related viruses. Virus Res 163: 19-27.
40. Altschul SF, Madden TL, Schaffer AA, Zhang JH, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402. (Pubitemid 27359211)
41. Pond SLK, Posada D, Gravenor MB, Woelk CH, Frost SDW (2006) GARD: a genetic algorithm for recombination detection. Bioinformatics 22: 3096-3098. (Pubitemid 44884087)
42. Drummond AJ, Rambaut A (2009) Bayesian evolutionary analysis by sampling trees. In: Lemey P, Salemi M, Vandamme A-M, editors. The Phylogenetic Handbook: Cambridge University Press. pp. 564-591.
43. Pagan I, Holmes EC (2010) Long-Term Evolution of the Luteoviridae: Time Scale and Mode of Virus Speciation. J Virol 84: 6177-6187.
44. Sun BJ, Sun LY, Tugume AK, Adams MJ, Yang J, et al. (2013) Selection Pressure and Founder Effects Constrain Genetic Variation in Differentiated Populations of Soilborne Bymovirus Wheat yellow mosaic virus (Potyviridae) in China. Phytopathology 103: 949-959.
45. 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: 1092-1108.
46. Nolasco G, Santos C, Santos MT, Cortez I, Fonseca F, et al. (2006) Rupestris stem pitting associated virus isolates are composed by mixtures of genomic variants which share a highly conserved coat protein. Arch Virol 151: 83-96. (Pubitemid 41813771)
47. Chare ER, Holmes EC (2004) Selection pressures in the capsid genes of plant RNA viruses reflect mode of transmission. J Gen Virol 85: 3149-3157. (Pubitemid 39360059)
48. Woelk CH, Holmes EC (2002) Reduced positive selection in vector-borne RNA viruses. Mol Biol Evol 19: 2333-2336. (Pubitemid 35440469)
49. Holmes EC (2009) The Evolutionary Genetics of Emerging Viruses. Annu Rev Ecol Evol S 40: 353-372.
50. Murray GG, Kosakovsky Pond SL, Obbard DJ (2013) Suppressors of RNAi from plant viruses are subject to episodic positive selection. Proc Biol Sci 280: 20130965.
51. Harper SJ (2013) Citrus tristeza virus: Evolution of Complex and Varied Genotypic Groups. Front Microbiol 4: 93.
52. Hicks AL, Duffy S (2011) Genus-Specific Substitution Rate Variability among Picornaviruses. J Virol 85: 7942-7947.
53. Fargette D, Pinel-Galzi A, Sereme D, Lacombe S, Hebrard E, et al. (2008) Diversification of Rice yellow mottle virus and related viruses spans the history of agriculture from the Neolithic to the present. Plos Pathog 4.
54. Duffy S, Shackelton LA, Holmes EC (2008) Rates of evolutionary change in viruses: patterns and determinants. Nat Rev Genet 9: 267-276. (Pubitemid 351399833)
55. Wertheim JO, Fourment M, Kosakovsky Pond SL (2012) Inconsistencies in estimating the age of HIV-1 subtypes due to heterotachy. Mol Biol Evol29: 451-456.
56. Gibbs AJ, Fargette D, Garcia-Arenal F, Gibbs MJ (2010) Time-the emerging dimension of plant virus studies. J Gen Virol 91: 13-22.
57. Wertheim JO, Worobey M (2009) Dating the age of the SIV lineages that gave rise to HIV-1 and HIV-2. PLoS Comput Biol 5: e1000377.
58. Gibbs AJ, Ohshima K, Phillips MJ, Gibbs MJ (2008) The prehistory of potyviruses: their initial radiation was during the dawn of agriculture. PLoS One 3: e2523.
59. Aravind L, Koonin EV (1999) Gleaning non-trivial structural, functional and evolutionary information about proteins by iterative database searches. J Mol Biol 287: 1023-1040. (Pubitemid 29188885)
60. Koonin EV, Dolja VV (1993) Evolution and Taxonomy of Positive-Strand Rna Viruses - Implications of Comparative-Analysis of Amino-Acid-Sequences. Crit Rev Biochem Mol 28: 375-430. (Pubitemid 23294324)
61. Melcher U (2000) The '30K' superfamily of viral movement proteins. J Gen Virol 81: 257-266.
62. Chen YP, Becnel JJ, Valles SM (2012) RNA viruses infecting pest insects. In: Vega FE, Kaya HK, editors. Insect Pathology: Elsevier. pp.133-169.
63. Ahlquist P, Noueiry AO, Lee WM, Kushner DB, Dye BT (2003) Host factors in positive-strand RNA virus genome replication. J Virol 77: 8181-8186. (Pubitemid 36871445)
64. Roossinck MJ, Sabanadzovic S, Okada R, Valverde RA (2011) The remarkable evolutionary history of endornaviruses. J Gen Virol 92: 2674-2678.
65. Leconte AM, Dickinson BC, Yang DD, Chen IA, Allen B, et al. (2013) A Population-Based Experimental Model for Protein Evolution: Effects of Mutation Rate and Selection Stringency on Evolutionary Outcomes. Biochemistry-US 52: 1490-1499.
66. Kuzmin IV, Shi M, Orciari LA, Yager PA, Velasco-Villa A, et al. (2012) Molecular Inferences Suggest Multiple Host Shifts of Rabies Viruses from Bats to Mesocarnivores in Arizona during 2001-2009. Plos Pathog 8.
67. Ivanov KI, Makinen K (2012) Coat proteins, host factors and plant viral replication. Curr Opin Virol 2: 712-718.
68. Campbell BC, Steffen-Campbell JD, Gill RJ (1994) Evolutionary origin of whiteflies (Hemiptera: Sterorrhyncha: Aleyrodidae) inferred from 18S rDNA sequences. Insect Mol Biol 3: 73-88. (Pubitemid 2110848)
69. Rehm P, Borner J, Meusemann K, von Reumont BM, Simon S, et al. (2011) Dating the arthropod tree based on large-scale transcriptome data. Mol Phylogenet Evol 61: 880-887.
70. Anon (2011) Virus Taxonomy: Ninth Report of the International Committee on Taxonomy of Viruses: Elsevier.
71. Li JL, Cornman RS, Evans JD, Pettis JS, Zhao Y, et al. (2014) Systemic Spread and Propagation of a Plant-Pathogenic Virus in European Honeybees, Apis mellifera. mBio 5.
72. Gildow FE, Darcy CJ (1988) Barley and Oats as Reservoirs for an Aphid Virus and the Influence on Barley Yellow Dwarf Virus Transmission. Phytopathology 78: 811-816.
73. Ban L, Didon A, Jonsson LMV, Glinwood R, Delp G (2007) An improved detection method for the Rhopalosiphum padi virus (RhPV) allows monitoring of its presence in aphids and movement within plants. J Virol Methods 142: 136-142. (Pubitemid 46590412)
74. Koonin EV, Wolf YI, Nagasaki K, Dolja VV (2008) The Big Bang of picorna-like virus evolution antedates the radiation of eukaryotic supergroups. Nat Rev Microbiol 6: 925-939.
75. Dasgupta R, Garcia BH, Goodman RM (2001) Systemic spread of an RNA insect virus in plants expressing plant viral movement protein genes. P Natl Acad Sci USA 98: 4910-4915. (Pubitemid 32397056)
76. Gibbs MJ, Weiller GF (1999) Evidence that a plant virus switched hosts to infect a vertebrate and then recombined with a vertebrate-infecting virus. P Natl Acad Sci USA 96: 8022-8027. (Pubitemid 29328401)
77. Tuthill TJ, Groppelli E, Hogle JM, Rowlands DJ (2010) Picornaviruses. Curr Top Microbiol 343: 43-89.