Plant Viruses Online
Plant Viruses Online
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These pages contain information on most species of virus known to infect plants, not only those whose virions have been described, but also those like umbraviruses that have no virion protein genes of their own, and use the virion proteins of their symbiotic helper viruses instead. We include data on host range; transmission and control; geographical distribution; physical, chemical and genomic properties; taxonomy and relationships; and selected literature references. We also include the database accession numbers (up to Gb[90] and Em[44]) of the genomic sequences of viruses and of satellite RNAs, and provide links to the NCBI taxonomy database to facilitate searchs for these and for more current accessions. These pages also contain generic-level summaries of data for viruses that are definitive or tentative members of genera or `groups'.
These pages are a product of the VIDE (Virus Identification Data Exchange) project (Boswell and Gibbs, 1983; Boswell and Gibbs, 1986; Boswell, Dallwitz, Gibbs and Watson, 1986; Brunt, Crabtree and Gibbs, 1990; Búchen-Osmond, Crabtree, Gibbs and McLean, 1988; Watson, Dallwitz, Gibbs and Pankhurst,1988; Brunt et al., 1996). The project has used the DELTA (DEscription Language for TAxonomy) system (Dallwitz, 1980; Dallwitz, Paine and Zurcher, 1993; also URL http://www.keil.ukans.edu/delta/) for formatting, storing and manipulating data on all plant viruses. The data to be stored were defined in the character list, which also served as a questionnaire for each virus. The data were then encoded, and manipulated using the DELTA software and associated programs to automatically generate a printed version (Brunt et al., 1996).
The data for experimental infections, natural hosts and host ranges were then collated at the plant species and family level and used to produce an interactive key (INTKEY) version and finally this HTML version, available on InterNet from the BioWeb server (URL http://biology.anu.edu.au). Although these three forms of presentation each represent substantially the same data, they offer rather different means of accessing that data, and users may prefer one presentation to another, depending on their needs and circumstances. The editors would be grateful for comments from users as to which of these presentations they find most useful, and the reasons for their preference.
Each virus species description is headed by a formal vernacular name which, in most instances, is the most commonly used name for that virus, or is that used in ICTV publications (Murphy et al., 1995), or that listed in Steadman's ICTV Words (Calisher and Fauquet, 1992). The order of words in some names has been changed so that host names appear first.
Many of the viruses described are definitive members of genera, whose names have been approved by the ICTV. The names of such viruses include their generic names, in italics, in the style introduced by Fenner (1976). Thus `American plum line pattern virus', for example, appears as `Plum American line pattern ilarvirus'.
Some virus clusterings, although generally recognized by virologists, have not yet been given generic status with ICTV-approved names. For these we have used the most commonly used euphonious name, but without italics. However for those that have no generally agreed name we have coined one for use in these pages. New names of this type are:
Some viruses are only tentatively associated with particular genera or groups. The descriptions of these viruses include `(?)' placed before the generic component of their names. In addition there are several viruses with virions characteristic of the families Potyviridae or Rhabdoviridae, which have not yet been assigned to particular genera in these families. Their formal vernacular names contain `(?) potyvirus' or `(?) rhabdovirus' (N.B. no italics) respectively.
The data for each virus description were mostly collated by the person named at the start of each description, however the editors have added some key references to some descriptions. The references given for each virus are indicative, certainly not exhaustive, and some are unfortunately incomplete; they are included to assist those wishing to find the major areas of published work on each species.
Where possible the data have been encoded numerically (i.e. as a series of characters and states). Viruses are, however, a particularly disparate group of pathogens, and this has made it impossible to define a set of genuinely homologous characters that apply to all plant viruses. As a result much information has been stored as `comments', associated with appropriate characters, and this is responsible for the many differences between the character list and the translated description of each species.
Summaries of viral genera were generated automatically from the species descriptions via the program INTKEY. Comments in the data are removed during the conversion to INTKEY format; hence all comments are missing from the summaries. Also omitted from these summaries are data that are clearly specific to individual species, such as their geographic distribution and host range. The summaries give a list of the definitive and tentative species in the genus, and also the ranges and means for numerical characters, and the frequency of occurrence of each state of multistate characters. This frequency information is placed within parentheses following each state. For example, you might read: "Virus retained when the vector moults (9/14), or lost by the vector when it moults (5/14)." This indicates that the virus was reported as being retained by a moulting vector for 9 species within the genus, and as being lost for 5 species. The number 14 in the "denominator" indicates the number of species within the genus for which data on this character has been recorded.
We have generated summary tables for over 1500 different vascular plant species listing all virus species reported to (or reported not to) infect them. Note that these host summaries include reports of susceptibility to experimental infections as well as to natural infections, and does not distinguish between the two. However, detailed information on reported natural host ranges is available as part of the individual virus species descriptions.
We provide lists of synonyms and common names for many of the host species; these appear in the various host family indexes. These synonyms and common names were obtained from the GRIN database on 20 June 1996. (GRIN is the Germplasm Resources Information Network, managed by the Database Management Unit of the National Germplasm Resources Laboratory, Agricultural Research Service, U.S. Department of Agriculture.) In those cases where a host name used in VIDE is regarded by GRIN as a synonym of an `accepted' name, the name which is regarded by GRIN as the accepted name is presented in bold at the start of the list of synonyms.
Assignment of plant genera to families follows Watson and Dallwitz, 1991; and Watson and Dallwitz, 1992 onwards. In particular, note the use of `traditional' names, such as Graminae rather than Poaceae, and Cruciferae rather than Brassicaceae. Devotees of Cronquistian classification should note that rather "narrow" definitions of families (i.e., a tendency for splitting rather than lumping) are used herein, particularly within the Liliaceae sensu lato. Also note that within the Leguminosae, the three major sub-families (Caesalpinioideae, Mimosoideae and Papilionoideae) are treated as if they are separate families.
Information on the susceptibility of plant families was derived automatically from the data on the susceptibility of host species. Within the viral species descriptions, the family susceptibility is typically followed by a pair of numbers, so that the information appears, for example, as "Chenopodiaceae (3/5)". The notation in this example indicates that 5 plant species within the family Chenopodiaceae are known to have been tested against the virus, and 3 of these proved to be susceptible (or insusceptible, depending on the section in which this line appears). The same notation, when occurring within the generic summaries carries a quite different meaning. In this context, our example indicates that 5 species within the viral genus have at least some data on host susceptibility; of these, 3 species are known to be capable of infecting at least one member of the Chenopodiaceae.
The illustrations currently attached to this data set are a series of
electron micrographs, primarily of the type species of ICTV-approved viral
genera. These illustrations are provided courtesy of the
Rothamsted Experimental Station, U.K.,
and are available at URL
http://www.res.bbscr.ac.uk/plantpath/virusems/.
The following copyright notice applies: This notice must accompany any
copy of the images. The images must not be used for commercial purpose without
the consent of the copyright owners. The images are not in the public domain.
The images can be freely used for educational purposes.
(Copyright) 1994 Rothamsted Experimental Station.
HOW YOU CAN HELP US ! ! !
The VIDEdB would be greatly improved if it included colour pictures of symptoms. We want to assemble a set of picture of characteristic symptoms (primary host and diagnostic test plants) - 2 or 3 photos per virus. Do you or any of your colleagues have any suitable pictures we could use? Photos (transparencies and/or prints) could be sent airmail for us to scan here, and returned immediately, or, if you have already scanned them, transferred to us electronically. Please send E-mail to vide-manager@biology.anu.edu.au or write to:
Adrian Gibbs
Research School of Biological Sciences
Australian National University
GPO Box 475
Canberra ACT 2601
Australia.
The VIDE (Virus Identification Data Exchange) project started in the early 1980s and, with support from the Rural Credit Development Fund of the Reserve Bank of Australia, produced and published an experimental database of viruses of legumes in 1983. Legumes were chosen, not just because of their economic importance, and that they are hosts to a large and representative collection of viruses, but also because the International Working Group on Legume Viruses comprised a group of experts willing to collate the information. The database was extended, with further support from the Fund, to produce the book `Viruses of Plants in Australia' in 1988.
Since 1983 the project has also been generously supported by the Australian Centre for International Agricultural Research (ACIAR), and this work resulted in the publication of `Viruses of Tropical Crops' in 1990 and, in 1996 the book `Viruses of Plants'. Further funding from ACIAR allowed this data to be converted into an INTKEY dataset and HTML format.
The VIDE project has relied on the help and encouragement of a very large number of colleagues around the world. Those who collated most of the data of each virus are specifically named in the description of that virus. Very large contributions were made by past members of the editorial team: K.F. Boswell, C. Büchen-Osmond and G.D. McLean. T.A. Paine of the CSIRO Division of Entomology provided invaluable help with the theory and practical use of the DELTA system. J.F. Antoniw of Rothamsted Experimental Station, U.K. very kindly provided the sequence database accession codes.
We are pleased to receive comments on all aspects of the VIDE project, to discuss additional applications of the database, to learn of errors in the data and to have offers of assistance in revising or adding new information. Send your comments, corrections and suggestions to: vide-manager@biology.anu.edu.au.
Boswell, K.F. and Gibbs, A.J. (eds) (1983). Viruses of Legumes 1983 - Descriptions and Keys from VIDE. 139 pp. Australian National University, Canberra.
Boswell, K. and Gibbs, A. (1986). The VIDE data bank for plant viruses. In Developments and Applications in Virus Testing (ed. R.A.C. Jones). pp. 283-287. Assoc. Applied Biologists, U.K.
Boswell, K.F., Dallwitz, M.J., Gibbs, A.J. and Watson, L. (1986). The VIDE (Virus Identification Data Exchange) project: a database for plant viruses. Rev. Plant Path. 65: 221-231.
Büchen-Osmond, C., Crabtree, K., Gibbs, A. and McLean, G. (1988). Viruses of Plants in Australia. 590 pp. Australian National University, Canberra. (Also available as URL http://life.anu.edu.au/viruses/Aussi/aussi.html.)
Brunt, A., Crabtree, K., Dallwitz, M., Gibbs, A. and Watson, L. (1996). Viruses of Plants: Descriptions and Lists from the VIDE Database. 1484 pp. C.A.B. International, U.K.
Brunt, A., Crabtree, K. and Gibbs, A. (1990). Viruses of Tropical Plants: Descriptions and Lists from the VIDE Database. 707 pp. C.A.B. International, U.K.
Calisher, C.H. and Fauquet, C.M. (1992). Steadman's ICTV Virus Words. 271 pp. Williams and Wilkins, Baltimore.
Dallwitz, M.J. (1980). A general system for coding taxonomic descriptions. Taxon 29: 41-46.
Dallwitz, M. J., Paine, T. A., and Zurcher, E. J. (1993). User's Guide to the DELTA System: a general system for processing taxonomic descriptions. 4th edition. 136 pp. (CSIRO Division of Entomology: Canberra).
Fenner, F. (1976). Classification and Nomenclature of Viruses; 2nd Report of the International Committee on Taxonomy of Viruses. Intervirology 7: 1-116.
Howarth, A.J. and Vandemark, G.J. (1989). Phylogeny of geminiviruses. J. gen. Virol. 70: 2717-2727.
Murphy, F.A., Fauquet, C.M., Mayo, M.A., Jarvis, A.W., Ghabrial, S.A., Summers, M.D., Martelli, G.P. and Bishop, D.H.L. (1995). 6th Report of the International Committee on Taxonomy of Virusus. Archiv. Virol. Suppl. 10, Springer-Verlag, Wein, New York.
Padidam, M. Beachy, R.N. and Fauquet, C.M. (1995). Classification and identification of geminiviruses using sequence comparisons. J. gen. Virol. 76: 249-263.
Watson, L. and Dallwitz, M.J. (1991). The Families of Angiosperms: automated descriptions, with interactive identification and information retrieval. Aust. Sys. Bot. 4: 601-695.
Watson, L. and Dallwitz, M.J. (1992 onwards). `The Families of Flowering Plants: Descriptions, Illustrations, Identification and Information Retrieval.' URL ftp://www.keil.ukans.edu/pub/delta/
Watson, L., Dallwitz, M.J., Gibbs, A.J. and Pankhurst, R.J. (1988). Automated taxonomic descriptions. In Prospects in Systematics (ed D.L. Hawksworth). pp 292-304. Clarendon Press, Oxford.
Cite this publication as: Brunt, A.A., Crabtree, K., Dallwitz, M.J., Gibbs, A.J., Watson, L. and Zurcher, E.J. (eds.) (1996 onwards). `Plant Viruses Online: Descriptions and Lists from the VIDE Database. Version: 20th August 1996.' URL http://biology.anu.edu.au/Groups/MES/vide/
Dallwitz (1980) and Dallwitz, Paine and Zurcher (1993) should also be cited.
Please send comments, corrections and suggestions to: vide-manager@biology.anu.edu.au