Genome sequences of Agropyron mosaic virus and Hordeum mosaic virus support reciprocal monophyly of the genera Potyvirus and Rymovirus in the family Potyviridae

Archives of Virology

Volumn 150, Issue 2, 2005, Pages 299-312

  French, R ^a   Stenger, D C ^b  

^a UNIVERSITY OF NEBRASKA LINCOLN   (United States)

^b NONE

Author keywords

[No Author keywords available]

Indexed keywords

POLYPROTEIN;

AGROPYRON; ARTICLE; BARLEY; CLASSIFICATION; COMPARATIVE STUDY; GENETICS; PHYLOGENY; POTYVIRUS; SEQUENCE HOMOLOGY; SPECIES DIFFERENCE; VIROLOGY; VIRUS GENOME;

AGROPYRON; GENOME, VIRAL; HORDEUM; PHYLOGENY; POLYPROTEINS; POTYVIRIDAE; SEQUENCE HOMOLOGY, AMINO ACID; SEQUENCE HOMOLOGY, NUCLEIC ACID; SPECIES SPECIFICITY;

ACARI; AGROPYRON; AGROPYRON MOSAIC VIRUS; HORDEUM; HORDEUM MOSAIC VIRUS; HORDEUM VULGARE SUBSP. VULGARE; LOLIUM; POTYVIRIDAE; POTYVIRUS; RYEGRASS MOSAIC VIRUS; RYMOVIRUS;

EID: 12944271899     PISSN: 03048608     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00705-004-0396-6     Document Type: Article

References (41)

1. Berger PH, Wyatt SD, Shiel PJ, Silbernagel MJ, Druffel K, Mink GI (1997) Phylogenetic analysis of the Potyviridae with emphasis on legume-infecting potyviruses. Arch Virol 142: 1979-1999
2. Carrington JC, Cary SM, Parks TD, Dougherty WG (1989) A second proteinase encoded by a plant potyviral genome. EMBO J 8: 365-370
3. Choi I-R, Hall JS, Henry M, Zhang L, Hein GL, French R, Stenger DC (2001) Contributions of genetic drift and negative selection on the evolution of three strains of wheat streak mosaic tritimovirus. Arch Virol 146: 619-628
4. Dolphin K, Belshaw R, Orme CDL, Quicke DLJ (2000) Noise and incongruence: interpreting results of the incongruence length difference test. Mol Phylogenet Evol 17: 401-406
5. Dougherty WG, Cary SM, Parks TD (1989) Molecular genetic analysis of a plant virus polyprotein cleavage site: a model. Virology 171: 356-364
6. Farris JS, Källersjö M, Kluge AG, Bult C (1995) Constructing a significance test for incongruence. Syst Biol 44: 570-572
7. Felsenstein J (1978) Cases in which parsimony or compatibility methods will be positively misleading. Syst Zool 27: 401-410
8. Gascuel O (1997) BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. Mol Biol Evol 14: 685-695
9. Glasa M, Kudela O, Subr Z (2003) Molecular analysis of the 3′ terminal region of the genome of Beet mosaic virus and its relation with other potyviruses. Arch Virol 148: 1863-1871
10. Goldman N, Anderson JP, Rodrigo AG (2000) Likelihood-based tests of topologies in phylogenetics. Syst Biol 49: 652-670
11. Götz R, Huth W, Lesemann D-E, Maiss E (2002) Molecular and serological relationships of Spartina mottle virus (SpMV) strains from Spartina spec, and from Cynodon dactylon to other members of the Potyviridae. Arch Virol 147: 379-391
12. Götz R, Maiss E (1995) The complete nucleotide sequence and genome organization of the mite-transmitted brome streak mosaic rymovirus in comparison to those of potyviruses. J Gen Virol 76: 2035-2042
13. Hall BG (2001) Phylogenetic trees made easy. Sinauer, Sunderland, Mass
14. Hall JS, Adams B, Parsons TJ, French R, Lane LC, Jensen SG (1998) Molecular cloning, sequencing, and phylogenetic relationships of a new potyvirus: sugarcane streak mosaic virus, and a reevaluation of the classification of the Potyviridae. Mol Phylogenet Evol 10: 323-332
15. Hasegawa M, Kishino H, Yano T (1985) Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 22: 160-174
16. Henikoff S, Henikoff JG (1992) Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci USA 89: 10915-10919
17. Hillis DM, Bull JJ (1993) An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analyses. Syst Biol 42: 182-192
18. Huelsenbeck JP, Ronquist F (2001) MrBayes: Bayesian inference of phylogeny. Bioinformatics 17: 754-755
19. Kumar S, Tamura K, Jakobsen IB, Nei M (2001) MEGA2: molecular evolutionary genetics analysis software. Bioinformatics 17: 1244-1245
20. Loytynoja A, Milinkovitch MC (2003) A hidden Markov model for progressive multiple alignment. Bioinformatics 19: 1505-1513
21. Mackenzie AM, Webster DE, Gibbs MJ, Thomas BJ, Gibbs AJ (1999) Australian isolates of ryegrass mosaic rymovirus and their relationships. Arch Virol 144: 309-316
22. Niblett CL, Zagula KR, Calvert LA, Kendall TL, Stark DM, Smith CE, Beachy RN, Lommel SA (1991) cDNA cloning and nucleotide sequence of the wheat streak mosaic virus capsid protein gene. J Gen Virol 72: 499-504
23. Page, RDM (1996) TREEVIEW: an application to display phylogenetic trees on personal computers. Comput Appl Biosci 12: 357-358
24. Rabenstein F, Seifers DL, Schubert J, French R, Stenger DC (2002) Phylogenetic relationships, strain diversity and biogeography of tritimoviruses. J Gen Virol 83: 895-906
25. Rice P, Longden I, Bleasby A (2000) EMBOSS: the European molecular biology open software suite. Trends Genet 16: 276-277
26. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406-425
27. Salm SN, Rey MEC, Robertson NL, French R, Rabenstein F, Schubert J (1996) Molecular cloning and nucleotide sequencing of the partial genomes of Agropyron and Hordeum mosaic viruses, two members of the Rymovirus genus in the taxonomic family Potyviridae. Arch Virol 141: 2115-2127
28. Salm SN, Rey MEC, Rybicki EP (1996) Phylogenetic justification for splitting the Rymovirus genus of the taxonomic family Potyviridae. Arch Virol 141: 2237-2242
29. Sanderson MJ, Shaffer HB (2002) Troubleshooting molecular phylogenetic analyses. Annu Rev Ecol Syst 33: 49-72
30. Schmidt HA, Strimmer K, Vingron M, von Haeseler A (2002) TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18: 502-504
31. Schubert J, Fauquet C, Merits A, Rabenstein F (1999) The complete nucleotide sequence of Ryegrass mosaic potyvirus indicates that it is a recombinant between members of two different genera in the family Potyviridae. J Plant Dis Protect 106: 392-404
32. Shimodaira H, Hasegawa M (1999) Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol Biol Evol 16: 1114-1116
33. Shukla DD, Ward CW, Brunt AA, Berger PH (1998) Potyviridae family. AAB/CMI Descriptions of Plant Viruses, no 366
34. Slykhuis JT, Bell W (1966) Differentiation of Agropyron mosaic, wheat streak mosaic, and a hitherto unrecognized Hordeum mosaic virus in Canada. Can J Bot 44: 1191-1208
35. Stenger DC, French R (2004) Complete nucleotide sequence of Oat necrotic mottle virus: a distinct Tritimovirus species (family Potyviridae) most closely related to Wheat streak mosaic virus. Arch Virol 149: 633-640
36. Stenger DC, Hall JS, Choi I-R, French R (1998) Phylogenetic relationships within the family Potyviridae: wheat streak mosaic virus and brome streak mosaic vims are not members of the genus Rymovirus. Phytopathology 88: 782-787
37. Swofford DL (2003) PAUP*: phylogenetic analysis using parsimony (*and other methods). Version 4. Sinauer Associates, Sunderland, Mass
38. Van Regenmortel MHV, Fauquet CM, Bishop DHL, Carstens EB, Estes MK, Lemon SM, Maniloff J, Mayo MA, McGeoch DJ, Pringle CR, Wickner RB (2000) Virus taxonomy: the classification and nomenclature of viruses. The Seventh Report of the International Committee on Taxonomy of Viruses. Academic Press, San Diego
39. Verchot J, Koonin EV, Carrington JC (1991) The 35-kDa protein from the N-terminus of the potyviral polyprotein functions as a third virus-encoded proteinase. Virology 185: 527-535
40. Whelan S, Lio P, Goldman N (2001) Molecular phylogenetics: state-of-the-art methods for looking into the past. Trends Genet 17: 262-272
41. Zagula K, Niblett CL, Robertson NL, French R, Lommel SA (1992) Potyviridae: genus Rymovirus. Arch Virol Suppl 5: 269-276