Access the full text.
Sign up today, get DeepDyve free for 14 days.
T. Melgarejo, A. Alminaite, C. Fribourg, C. Spetz, J. Valkonen (2004)
Strains of Peru tomato virus infecting cocona (Solanum sessiliflorum), tomato and pepper in Peru with reference to genome evolution in genus PotyvirusArchives of Virology, 149
W. Williams (1965)
Evolution of Crop PlantsNature, 206
C. Wallis, A. Stone, D. Sherman, V. Damsteegt, F. Gildow, W. Schneider (2007)
Adaptation of plum pox virus to a herbaceous host (Pisum sativum) following serial passages.The Journal of general virology, 88 Pt 10
K. Katoh, K. Misawa, K. Kuma, T. Miyata (2002)
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.Nucleic acids research, 30 14
M. Fourment, M. Gibbs (2006)
PATRISTIC: a program for calculating patristic distances and graphically comparing the components of genetic changeBMC Evolutionary Biology, 6
T. Hall (1999)
BIOEDIT: A USER-FRIENDLY BIOLOGICAL SEQUENCE ALIGNMENT EDITOR AND ANALYSIS PROGRAM FOR WINDOWS 95/98/ NT
H. Vetten, D. Lesemann, Edgar Maiss (1992)
Serotype A and B strains of bean common mosaic virus are two distinct potyviruses.Archives of virology. Supplementum, 5
A. Beemster, J. Dijkstra (1966)
Viruses of plants.
A. Blakeslee (1921)
A graft-infectious disease of Datura resembling a vegetative mutationJournal of Genetics, 11
A. Hughes (2009)
Small effective population sizes and rare nonsynonymous variants in potyviruses.Virology, 393 1
E. Holmes, Yong‐Zhen Zhang (2009)
The Evolution and Emergence of RNA Viruses
M. Eigen (1996)
On the nature of virus quasispecies.Trends in microbiology, 4 6
N. Simmonds (1977)
Evolution of Crop Plants
Piper Chloranthus, Sarcandra Hedyosmum, Acorus Aechmea, Puya Glomeropit, Cyperus Rhyncospora, Juncus Flagellaria, Oryza Zea, Restio Xyris, Sparganium Calathea, Maranta Costus, Dimerocostus Monocostus, Tapeinochilos Globba, Hedychium Zingiber, Riedelia Orchidantha, Phenakosperm Strelitzia, Ravenala Cannacocc, Helicon Ensete, Musella Musa, Helmholtzia Philydrella, Pontederia Tradescantia, Calectasia Dasypogon, Calamus Metroxylon, Caryota Chamaedorea, Phoenix Iriartea, Podococcus Agave, Behnia Chlorophytum, Bowiea Scilla, Muilla Asparagus, Convallaria Liriope, Ruscus Smilacina, Nolina Luzuriaga, Allium Clivia, Hippeastrum Bulbine, Xanthorrhoea Xeronema, Aristea Gladiolus, Cyanella Tecophilaea, Ixiolirionion Blandfordia, Milligania Rhodohypoxis, Borya Cypripedium, Oncidium Burmannia, Dioscorea Tacca, Bomarea Colchicum, Chamaelirium Trillium, Xerophyllum Clintonia, Lilium Scoliopus, Tricyrtis Smilax, Barbacenia Cyclanthus, Sphaeradenia Freycinetia, Stemona Japonolirion, Petrosavia Aponogeton, Vallisneria Zostera, Pleea Tofieldia, Gymnostachys Spathiphyllum, Austrobaileya Illicium, Schisandra Amborella, Barclaya Brasenia, Cabomba Nuphar, Nymphaea Ephedra, Gnetum Welwitschia, Pinus Podocarpus, Taxus Ginkgo (2009)
Inferring phylogenies with incomplete data sets: a 5-gene, 567-taxon analysis of angiospermsBMC Evolutionary Biology, 9
N. Saitou, M. Nei (1987)
The neighbor-joining method: a new method for reconstructing phylogenetic trees.Molecular biology and evolution, 4 4
K. Smith (1937)
A textbook of plant virus diseases.
Roger Jones (2009)
Plant virus emergence and evolution: origins, new encounter scenarios, factors driving emergence, effects of changing world conditions, and prospects for control.Virus research, 141 2
R. Goldbach (1986)
Molecular evolution of plant RNA viruses.Annual Review of Phytopathology, 24
C. Buchen-Osmond (2003)
The universal virus database ICTVdBComputing in Science and Engineering, 5
S. Moghal, R. Francki (1976)
Towards a system for the identification and classification of potyviruses. I. Serology and amino acid composition of six distinct viruses.Virology, 73 2
J. Dijkstra, J. Khan (1992)
A proposal for a bean common mosaic subgroup of potyviruses.Archives of virology. Supplementum, 5
Peter Bellwood, C. Gamble, S. Blanc, M. Pluciennik, M. Richards, J. Terrell (2007)
First Farmers: the Origins of Agricultural Societies, by Peter Bellwood. Malden (MA): Blackwell, 2005; ISBN 0-631-20565-9 hardback £60; ISBN 0-631-20566-7 paperback £17.99, xix+360 pp., 59 figs., 3 tablesCambridge Archaeological Journal, 17
V. Vance, Ramon Jordan, J. Edwardson, R. Christie, D. Purcifull, T. Turpen, B. Falk (1992)
Evidence that pepper mottle virus and potato virus Y are distinct viruses: analyses of the coat protein and 3' untranslated sequence of a California isolate of pepper mottle virus.Archives of virology. Supplementum, 5
K. Ohshima, Y. Yamaguchi, R. Hirota, T. Hamamoto, K. Tomimura, Zhongyang Tan, T. Sano, F. Azuhata, J. Walsh, J. Fletcher, Jishuang Chen, A. Gera, A. Gibbs (2002)
Molecular evolution of Turnip mosaic virus: evidence of host adaptation, genetic recombination and geographical spread.The Journal of general virology, 83 Pt 6
S. Korkmaz, Y. Tomitaka, S. Onder, K. Ohshima (2008)
Occurrence and molecular characterization of Turkish isolates of Turnip mosaic virusPlant Pathology, 57
D. Shukla, C. Ward (2005)
Identification and classification of potyviruses on the basis of coat protein sequence data and serologyArchives of Virology, 106
C. Desbiez, H. Lecoq (2008)
Evidence for multiple intraspecific recombinants in natural populations of Watermelon mosaic virus (WMV, Potyvirus)Archives of Virology, 153
R. French, D. Stenger (2003)
Evolution of Wheat streak mosaic virus: dynamics of population growth within plants may explain limited variation.Annual review of phytopathology, 41
L. Bos (1992)
Potyviruses, chaos or order?Archives of virology. Supplementum, 5
M. Adams, J. Antoniw, C. Fauquet (2005)
Molecular criteria for genus and species discrimination within the family PotyviridaeArchives of Virology, 150
F. Burnett (1947)
Report on agriculture in Malaya for the year 1946.
C. Spetz, A. Taboada, S. Darwich, J. Ramsell, L. Salazar, J. Valkonen (2003)
Molecular resolution of a complex of potyviruses infecting solanaceous crops at the centre of origin in Peru.The Journal of general virology, 84 Pt 9
M. Regenmortel, B. Mahy (2004)
Emerging Issues in Virus TaxonomyEmerging Infectious Diseases, 10
C. Ward, D. Shukla (1991)
Taxonomy of potyviruses: current problems and some solutions.Intervirology, 32 5
S. Whelan, N. Goldman (2001)
A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach.Molecular biology and evolution, 18 5
K. Tomimura, A. Gibbs, C. Jenner, J. Walsh, K. Ohshima (2003)
The phylogeny of Turnip mosaic virus; comparisons of 38 genomic sequences reveal a Eurasian origin and a recent ‘emergence’ in east AsiaMolecular Ecology, 12
S. Fuji, F. Terami, H. Furuya, H. Naito, F. Fukumoto (2004)
Nucleotide sequence of the coat protein genes of Alstroemeria mosaic virus and Amazon lily mosaic virus, a tentative species of genus PotyvirusArchives of Virology, 149
D. Shukla, C. Ward (1988)
Amino Acid Sequence Homology of Coat Proteins as a Basis for Identification and Classification of the Potyvirus GroupJournal of General Virology, 69
D. Martin, C. Williamson, D. Posada (2005)
RDP2: recombination detection and analysis from sequence alignmentsBioinformatics, 21 2
M. Yu, M. Frenkel, N. Mckern, D. Shukla, P. Strike, C. Ward (1989)
Coat protein of PotyvirusesArchives of Virology, 105
B. Harrison (1981)
Plant virus ecology: ingredients, interactions and environmental influencesAnnals of Applied Biology, 99
B. Janzac, M. Fabre, A. Palloix, B. Moury (2008)
Characterization of a new potyvirus infecting pepper crops in EcuadorArchives of Virology, 153
D. Young, L. Watson (1970)
The classification of dicotyledons: A study of the upper levels of the hierarchyAustralian Journal of Botany, 18
A. Gibbs, M. Gibbs (2006)
A broader definition of ‘the virus species’Archives of Virology, 151
E. Koonin, Y. Wolf, K. Nagasaki, V. Dolja (2008)
The Big Bang of picorna-like virus evolution antedates the radiation of eukaryotic supergroupsNature Reviews Microbiology, 6
C. Desbiez, H. Lecoq (2004)
The nucleotide sequence of Watermelon mosaic virus (WMV, Potyvirus) reveals interspecific recombination between two related potyviruses in the 5′ part of the genomeArchives of Virology, 149
I. Cooper, Roger Jones (2006)
Wild plants and viruses: under-investigated ecosystems.Advances in virus research, 67
M. Regenmortel (2005)
Applying the species concept to plant virusesArchives of Virology, 104
F. García-Arenal, A. Fraile, J. Malpica (2001)
Variability and genetic structure of plant virus populations.Annual review of phytopathology, 39
Y. Tomitaka, K. Ohshima (2006)
A phylogeographical study of the Turnip mosaic virus population in East Asia reveals an ‘emergent’ lineage in JapanMolecular Ecology, 15
F. Schneider, K. Mundry (1956)
Die elektronenmikroskopische Darstellung des Mosaikvirus der ZuckerrübenZeitschrift für Naturforschung B, 11
P. Lemey, M. Salemi, A. Vandamme (2009)
The Phylogenetic Handbook: List of contributors
J. Riechmann, S. Laín, J. García (1992)
Highlights and prospects of potyvirus molecular biology.The Journal of general virology, 73 ( Pt 1)
F. Revers, O. Gall, T. Candresse, A. Maule (1999)
New Advances in Understanding the Molecular Biology of Plant/Potyvirus InteractionsMolecular Plant-microbe Interactions, 12
R. Murray, E. Stackebrandt (1995)
Taxonomic note: implementation of the provisional status Candidatus for incompletely described procaryotes.International journal of systematic bacteriology, 45 1
C. Ward, N. Mckern, M. Frenkel, D. Shukla (1992)
Sequence data as the major criterion for potyvirus classification.Archives of virology. Supplementum, 5
S. Le, O. Gascuel (2008)
An improved general amino acid replacement matrix.Molecular biology and evolution, 25 7
T. Ogawa, Y. Tomitaka, A. Nakagawa, K. Ohshima (2008)
Genetic structure of a population of Potato virus Y inducing potato tuber necrotic ringspot disease in Japan; comparison with North American and European populations.Virus research, 131 2
David Jones, W. Taylor, J. Thornton (1994)
A mutation data matrix for transmembrane proteinsFEBS Letters, 339
A. Gibbs, B. Harrison (1976)
Plant Virology: The Principles
Adrian Gibbs, Denis Fargette, F. García-Arenal, Mark Gibbs (2010)
Time--the emerging dimension of plant virus studies.The Journal of general virology, 91 Pt 1
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
E. Domingo, C. Escarmís, L. Menéndez-Arias, C. Perales, M. Herrera, I. Novella, J. Holland (2008)
Viral Quasispecies: Dynamics, Interactions, and Pathogenesis*Origin and Evolution of Viruses
R. Vlugt (1992)
Is pepper mottle virus a strain of potato virus YArchives of virology. Supplementum, 5
Adrian Gibbs, J. Trueman, M. Gibbs (2008)
The bean common mosaic virus lineage of potyviruses: where did it arise and when?Archives of Virology, 153
K. Petrzik, J. Fránová (2006)
Complete genome sequence of Daphne mosaic virus – a potyvirus from an ornamental shrub related to papaya leaf distortion mosaic virusArchives of Virology, 151
Adrian Gibbs, A. Mackenzie, Ke-jun Wei, Mark Gibbs (2008)
The potyviruses of AustraliaArchives of Virology, 153
Xiaojun Hu, T. Meacham, Lorie Ewing, S. Gray, A. Karasev (2009)
A novel recombinant strain of Potato virus Y suggests a new viral genetic determinant of vein necrosis in tobacco.Virus research, 143 1
Shawn Krosnick, J. Freudenstein (2005)
Monophyly and Floral Character Homology of Old World Passiflora (Subgenus Decaloba: Supersection Disemma), 30
E. Hiebert, D. Purcifull (1992)
A comparison of pepper mottle virus with potato virus Y and evidence for their distinction.Archives of virology. Supplementum, 5
G. Mink, M. Silbernagel (1992)
Serological and biological relationships among viruses in the bean common mosaic virus subgroup.Archives of virology. Supplementum, 5
A. Gibbs, K. Ohshima, M. Phillips, M. Gibbs (2008)
The Prehistory of Potyviruses: Their Initial Radiation Was during the Dawn of AgriculturePLoS ONE, 3
B. Harrison, J. Finch, A. Gibbs, M. Hollings, R. Shepherd, V. Valenta, C. Wetter (1971)
Sixteen groups of plant viruses.Virology, 45 2
A. Gibbs, M. Gibbs, K. Ohshima, F. García-Arenal (2008)
More About Plant Virus Evolution: Past, Present, and Future
C. Ward, G. Weiller, D. Shukla, A. Gibbs (1995)
Molecular Basis of Virus Evolution: Molecular systematics of the Potyviridae, the largest plant virus family
K. Ohshima, Y. Tomitaka, J. Wood, Yoshiteru Minematsu, Hiromi Kajiyama, K. Tomimura, A. Gibbs (2007)
Patterns of recombination in turnip mosaic virus genomic sequences indicate hotspots of recombination.The Journal of general virology, 88 Pt 1
W. Schneider, M. Roossinck (2001)
Genetic Diversity in RNA Virus Quasispecies Is Controlled by Host-Virus InteractionsJournal of Virology, 75
M. Beckner (1959)
The biological way of thought
C. Webster, B. Coutts, Roger Jones, Michael Jones, S. Wylie (2007)
Virus impact at the interface of an ancient ecosystem and a recent agroecosystem: studies on three legume‐infecting potyviruses in the southwest Australian floristic regionPlant Pathology, 56
H. Simmons, E. Holmes, A. Stephenson (2008)
Rapid evolutionary dynamics of zucchini yellow mosaic virus.The Journal of general virology, 89 Pt 4
R. Goldbach (1992)
The recombinative nature of potyviruses: implications for setting up true phylogenetic taxonomy.Archives of virology. Supplementum, 5
Y.-H. Shi, X.-Y. Hong, J. Chen, M. Adams, H.-Y. Zheng, L. Lin, B. Qin, J.‐P. Chen (2004)
Further molecular characterisation of potyviruses infecting aroid plants for medicinal use in ChinaArchives of Virology, 150
R. Milne (1985)
Alternatives to the species concept for virus taxonomy.Intervirology, 24 2
Jang-Kyun Seo, K. Ohshima, Hyeok-Geun Lee, Moonil Son, Hongsoo Choi, Su-Heon Lee, Seong-Han Sohn, Kook Kim (2009)
Molecular variability and genetic structure of the population of soybean mosaic virus based on the analysis of complete genome sequences.Virology, 393 1
K. Smith (1931)
On the composite nature of certain potato virus diseases of the mosaic group as revealed by the use of plant indicators.Proceedings of The Royal Society B: Biological Sciences, 189
M. Dallwitz (1980)
A General System for Coding Taxonomic DescriptionsTaxon, 29
S. Kwon, Misoon Kim, Hongsoo Choi, Kook Kim (2005)
Biological characteristics and nucleotide sequences of three Korean isolates of Zucchini yellow mosaic virusJournal of General Plant Pathology, 71
S. Farzadfar, Y. Tomitaka, Mutsumi Ikematsu, A. Golnaraghi, R. Pourrahim, K. Ohshima (2009)
Molecular characterisation of Turnip mosaic virus isolates from Brassicaceae weedsEuropean Journal of Plant Pathology, 124
K. Tomimura, J. Špak, N. Katis, C. Jenner, J. Walsh, A. Gibbs, K. Ohshima (2004)
Comparisons of the genetic structure of populations of Turnip mosaic virus in West and East Eurasia.Virology, 330 2
N. Mckern, C. Ward, D. Shukla (1992)
Strains of bean common mosaic virus consist of at least two distinct potyviruses.Archives of virology. Supplementum, 5
D. Jensen (1949)
Papaya virus diseases with special reference to Papaya ringspot.Phytopathology, 39
L. Bos (2005)
The identification of three new viruses isolated from Wisteria and Pisum in The Netherlands, and the problem of variation within the potato virus Y groupNetherlands Journal of Plant Pathology, 76
J. Randles, C. Davies, J. Gibbs, T. Hatta (1980)
Amino acid composition of capsid protein as a taxonomic criterion for classifying the atypical S strain of bean yellow mosaic virus.Australian Journal of Biological Sciences, 33
Stéphane Guindon, O. Gascuel (2003)
A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood.Systematic biology, 52 5
S. Urcuqui-Inchima, A. Haenni, F. Bernardi (2001)
Potyvirus proteins: a wealth of functions.Virus research, 74 1-2
The potyviruses are one of the two most speciose taxa of plant viruses. Our expanded knowledge of the breadth and depth of their diversity and its origins has depended greatly on the use of computing and the Internet in biological research and is reviewed here. We report a fully supported phylogeny based on gene sequence data for approximately half the named species. The phylogeny shows that the genus probably originated from a virus of monocotyledonous plants and that it first diverged approximately 7250 years ago in Southwest Eurasia or North Africa. The use of computer programs to better understand the structure and evolutionary trajectory of potyvirus populations is illustrated. The review concludes with recommendations for improving potyvirus nomenclature and the databasing of potyvirus information.
Annual Review of Phytopathology – Annual Reviews
Published: Sep 8, 2010
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.