Access the full text.
Sign up today, get DeepDyve free for 14 days.
J. Slykhuis, W. Bell (1966)
DIFFERENTIATION OF AGROPYRON MOSAIC, WHEAT STREAK MOSAIC, AND A HITHERTO UNRECOGNIZED HORDEUM MOSAIC VIRUS IN CANADABotany, 44
P. Rice, Ian Longden, A. Bleasby (2000)
EMBOSS: the European Molecular Biology Open Software Suite.Trends in genetics : TIG, 16 6
F. Rabenstein, D. Seifers, J. Schubert, R. French, D. Stenger (2002)
Phylogenetic relationships, strain diversity and biogeography of tritimoviruses.The Journal of general virology, 83 Pt 4
M. Sanderson, H. Shaffer (2002)
Troubleshooting Molecular Phylogenetic AnalysesAnnual Review of Ecology, Evolution, and Systematics, 33
K. Dolphin, R. Belshaw, C. Orme, D. Quicke (2000)
Noise and incongruence: interpreting results of the incongruence length difference test.Molecular phylogenetics and evolution, 17 3
Simon Whelan, Pietro Liò, Nick Goldman (2001)
Molecular phylogenetics: state-of-the-art methods for looking into the past.Trends in genetics : TIG, 17 5
R. Götz, W. Huth, D. Lesemann, E. Maiss (2002)
Molecular and serological relationships of Spartina mottle virus (SpMV) strains from Spartina spec. and from Cynodon dactylon to other members of the PotyviridaeArchives of Virology, 147
R. Page (1996)
TreeView: an application to display phylogenetic trees on personal computersComputer applications in the biosciences : CABIOS, 12 4
H. Schmidt, K. Strimmer, M. Vingron, A. Haeseler (2002)
TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computingBioinformatics, 18 3
D. Hillis, J. Bull (1993)
An Empirical Test of Bootstrapping as a Method for Assessing Confidence in Phylogenetic AnalysisSystematic Biology, 42
N. Saitou, M. Nei (1987)
The neighbor-joining method: a new method for reconstructing phylogenetic trees.Molecular biology and evolution, 4 4
M. Cummings (2004)
MEGA (Molecular Evolutionary Genetics Analysis)Dictionary of Bioinformatics and Computational Biology
M. Cummings (2004)
PAUP* [Phylogenetic Analysis Using Parsimony (and Other Methods)]Dictionary of Bioinformatics and Computational Biology
M. Glasa, O. Kúdela, Z. Šubr (2003)
Molecular analysis of the 3′ terminal region of the genome of Beet mosaic virus and its relation with other potyvirusesArchives of Virology, 148
D. Stenger, R. French (2004)
Complete nucleotide sequence of Oat necrotic mottle virus: A distinct Tritimovirus species (family Potyviridae) most closely related to Wheat streak mosaic virusArchives of Virology, 149
A. Löytynoja, M. Milinkovitch (2003)
A hidden Markov model for progressive multiple alignmentBioinformatics, 19 12
S. Henikoff, J. Henikoff (1992)
Amino acid substitution matrices from protein blocks.Proceedings of the National Academy of Sciences of the United States of America, 89 22
P. Berger, S. Wyatt, P. Shiel, M. Silbernagel, K. Druffel, G. Mink (1997)
Phylogenetic analysis of the Potyviridae with emphasis on legume-infecting potyvirusesArchives of Virology, 142
I. Choi, J. Hall, M. Henry, L. Zhang, G. Hein, R. French, D. Stenger (2001)
Contributions of genetic drift and negative selection on the evolution of three strains of wheat streak mosaic tritimovirusArchives of Virology, 146
J. Schubert, C. Fauquet, A. Merits, F. Rabenstein (1999)
The complete nucleotide sequence of the Ryegrass mosaic potyvirus* indicates that it is a recombinant between members of two different genera in the family Potyviridae, 106
R. Götz, E. Maiss (1995)
The complete nucleotide sequence and genome organization of the mite-transmitted brome streak mosaic rymovirus in comparison with those of potyviruses.The Journal of general virology, 76 ( Pt 8)
J. Carrington, S. Cary, T. Parks, W. Dougherty (1989)
A second proteinase encoded by a plant potyvirus genome.The EMBO Journal, 8
C. Niblett, K. Zagula, L. Calvert, T. Kendall, D. Stark, C. Smith, R. Beachy, S. Lommel (1991)
cDNA cloning and nucleotide sequence of the wheat streak mosaic virus capsid protein gene.The Journal of general virology, 72 ( Pt 3)
M. Hasegawa, H. Kishino, T. Yano (2005)
Dating of the human-ape splitting by a molecular clock of mitochondrial DNAJournal of Molecular Evolution, 22
N. Goldman, Jon Anderson, A. Rodrigo (2000)
Likelihood-based tests of topologies in phylogenetics.Systematic biology, 49 4
D. Stenger, J. Hall, I. Choi, R. French (1998)
Phylogenetic relationships within the family potyviridae: wheat streak mosaic virus and brome streak mosaic virus are not members of the genus rymovirus.Phytopathology, 88 8
S. Salm, M. Rey, Nancy Robertson, Roy French, F. Rabenstein, J. Schubert (2005)
Molecular cloning and nucleotide sequencing of the partial genomes of Agropyron and Hordeum mosaic viruses, two members of theRymovirus genus in the taxonomic familyPotyviridaeArchives of Virology, 141
J. Huelsenbeck, F. Ronquist (2001)
MRBAYES : Bayesian inference of phylogenyBioinformatics, 17
J. Felsenstein (1978)
Cases in which Parsimony or Compatibility Methods will be Positively MisleadingSystematic Biology, 27
A. Mackenzie, D. Webster, M. Gibbs, B. Thomas, A. Gibbs (1999)
Australian isolates of ryegrass mosaic rymovirus and their relationshipsArchives of Virology, 144
Hidetoshi Shimodaira, M. Hasegawa (1999)
Multiple Comparisons of Log-Likelihoods with Applications to Phylogenetic InferenceMolecular Biology and Evolution, 16
D. Swofford, D. Swofford, D. Swofford (2002)
PAUP*: Phylogenetic analysis using parsimony (*and other methods), Version 4.0b10
W. Dougherty, S. Cary, T. Parks (1989)
Molecular genetic analysis of a plant virus polyprotein cleavage site: a model.Virology, 171 2
Sudhir Kumar, K. Tamura, I. Jakobsen, M. Nei (2001)
MEGA2: molecular evolutionary genetics analysis softwareBioinformatics, 17 12
J. Farris, M. Källersjö, A. Kluge, C. Bult (1995)
Constructing a Significance Test for IncongruenceSystematic Biology, 44
M. Regenmortel (2000)
Virus taxonomy: classification and nomenclature of viruses. Seventh report of the International Committee on Taxonomy of Viruses.
J. Verchot, E. Koonin, J. Carrington (1991)
The 35-kDa protein from the N-terminus of the potyviral polyprotein functions as a third virus-encoded proteinase.Virology, 185 2
M. Cummings (2000)
PAUP* Phylogenetic analysis using parsimony (*and other methods) Version 4
K. Zagula, C. Niblett, N. Robertson, R. French, S. Lommel (1992)
Potyviridae: genus Rymovirus.Archives of virology. Supplementum, 5
Jeffrey Hall, Byron Adams, Thomas Parsons, Roy French, Leslie Lane, Stanley Jensen (1998)
Molecular cloning, sequencing, and phylogenetic relationships of a new potyvirus: sugarcane streak mosaic virus, and a reevaluation of the classification of the potyviridae.Molecular phylogenetics and evolution, 10 3
S. Salm, M. Rey, E. Rybicki (2005)
Phylogenetic justification for splitting theRymovirus genus of the taxonomic familyPotyviridaeArchives of Virology, 141
O. Gascuel (1997)
BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data.Molecular biology and evolution, 14 7
Summary.Assignment of mite-transmitted species to the genus Rymovirus (family Potyviridae) has changed several times, and the status of the genus has been questioned. To address this issue, complete genome sequences of the rymoviruses Agropyron mosaic virus (AgMV) and Hordeum mosaic virus (HoMV) were determined. AgMV (9540 nucleotides) and HoMV (9463 nucleotides) each encode a single polyprotein with proteinase cleavage sites demarcating protein products characteristic of monopartite species of the family Potyviridae. Of the described species of Potyviridae, AgMV and HoMV are most closely related to each other (68.5% nucleotide and 71.6% amino acid sequence identity) and equidistant (about 53% nucleotide and about 49% amino acid sequence identity) from a third rymovirus, Ryegrass mosaic virus (RGMV). Phylogenetic analyses by neighbor joining, maximum parsimony, and Bayesian inference each grouped the three Rymovirus species in an exclusive clade distinct from a clade containing 34 species of the genus Potyvirus. Because AgMV, HoMV, and RGMV share a reciprocal monophyletic relationship with species of the genus Potyvirus and are divergent in sequence and type of vector, the genus Rymovirus should be retained as a taxonomic unit within the family Potyviridae.
Archives of Virology – Springer Journals
Published: Feb 1, 2005
Keywords: Nucleotide; Phylogenetic Analysis; Genome Sequence; Protein Product; Mosaic Virus
Read and print from thousands of top scholarly journals.
Already have an account? Log in
Bookmark this article. You can see your Bookmarks on your DeepDyve Library.
To save an article, log in first, or sign up for a DeepDyve account if you don’t already have one.
Copy and paste the desired citation format or use the link below to download a file formatted for EndNote
Access the full text.
Sign up today, get DeepDyve free for 14 days.
All DeepDyve websites use cookies to improve your online experience. They were placed on your computer when you launched this website. You can change your cookie settings through your browser.