Rhizidiomyces virus

Footnotes The authors declare no conflict of interest. References 1. Stokstad E. Plant pathology. Deadly wheat fungus threatens world's breadbaskets.

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FEBS Lett. Geminiviruses: A tale of a plasmid becoming a virus. BMC Evol Biol. Boland GJ, Hall R. Index of plant hosts of Sclerotinia sclerotiorum. Can J Plant Pathol. Boland GJ. Hypovirulence and double-stranded RNA in Sclerotinia sclerotiorum. Transmissible hypovirulent element in isolate Ep-1PN of Sclerotinia sclerotiorum. Chin Sci Bull. Prog Nat Sci. Xie J, et al. Characterization of debilitation-associated mycovirus infecting the plant-pathogenic fungus Sclerotinia sclerotiorum.

J Gen Virol. Liu H, et al. A novel mycovirus that is related to the human pathogen hepatitis E virus and rubi-like viruses. J Virol.

Heyraud-Nitschke F, et al. Determination of the origin cleavage and joining domain of geminivirus Rep proteins. Nucleic Acids Res. Stanley J, et al. In: Fauquet CM, et al. Virus Taxonomy. Amsterdam: Elsevier; Laufs J, et al. In vitro cleavage and joining at the viral origin of replication by the replication initiator protein of tomato yellow leaf curl virus.

Stanley J, Townsend R. Characterisation of DNA forms associated with cassava latent virus infection. Nahid N, et al. Two dicot-infecting mastreviruses family Geminiviridae occur in Pakistan. Arch Virol. Molecular characterization of a subgroup I geminivirus from a legume in South Africa. The nucleotide sequence of the infectious cloned DNA component of tobacco yellow dwarf virus reveals features of geminiviruses infecting monocotyledonous plants.

Venter JC, et al. Environmental genome shotgun sequencing of the Sargasso Sea. Biella S, et al. Programmed cell death correlates with virus transmission in a filamentous fungus.

Proc Biol Sci. Saupe SJ. Molecular genetics of heterokaryon incompatibility in filamentous ascomycetes. Microbiol Mol Biol Rev. Genetic control of horizontal virus transmission in the chestnut blight fungus, Cryphonectria parasitica. San Diego: Elsevier Academic Press; Use of geminiviral vectors for functional genomics. Curr Opin Plant Biol. Golenberg EM, et al. Development of a gene silencing DNA vector derived from a broad host range geminivirus.

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Maha Mohammed Nahid Khan. Read more. Know all details Read more. What exactly is the metaverse, and how will it function? Until , no hierarchical classification level higher than the family was used, however, the system has recently begun to move in this direction. A first order, Mononegavirales , was accepted in , and another two, Caudovirales and Nidovirales , were adopted in In its nonlinnean structure, the scheme is quite different from that used in the taxonomy of bacteria and other organisms.

Nevertheless, the usefulness of the scheme is being demonstrated by its wide application. It has replaced all competing classification schemes for all viruses and no one would now dispute with the ICTV the international mandate to name and classify viruses. Since its establishment, a total of seven virus taxonomic reports also known by the names of the ICTV Presidents acting as Editors in Chief of the reports have been published by the ICTV: Wildy in ; Fenner in ; Matthews in ; Matthews in ; Francki et al in ; Murphy et al in ; and van Regenmortel et al in At the first meeting in Mexico City in , two families with a corresponding two genera and 24 floating genera were adopted to begin the grouping of the vertebrate, invertebrate and bacterial viruses.

In addition, 16 plant virus groups were designated, as reported by Matthews in The fifth ICTV report, edited by Francki et al in , described one order, 40 families, nine subfamilies, genera, two floating genera and two subgenera for vertebrate, invertebrate, bacterial and fungal viruses, and 32 groups and seven subgroups for plant viruses.

It was only in , as described in the sixth ICTV report, that the ICTV proposed a uniform system for all viruses, with two orders, 50 families, nine subfamilies, genera, 23 floating genera and four subgenera encompassing assigned viruses.

It is a general trend that the number of described taxa and the number of species of viruses is increasing steadily, easily explained by the increasing complexity of the virus classification and by the amount of data available to demarcate viruses.

Therefore, the ICTV classification is not only a taxonomic exercise for virus evolutionists but also a valuable diagnostic tool and educational system for virologists, teachers, medical doctors and epidemiologists. The ICTV is a nonprofit-making organization composed of prominent virologists representing countries from throughout the world who work to designate virus names and taxa through a democratic process.

The ICTV operates through a number of committees, subcommittees and study groups consisting of more than eminent virologists with expertise in viruses infecting humans, animals, insects, protozoa, archaea, bacteria, mycoplasma, fungi, algae, yeasts and plants. Taxonomic proposals are initiated and formulated by individuals or by the study groups. These proposals are revised and accepted by the corresponding subcommittees and presented for executive committee approval. All decisions are then ratified at a plenary session or also now by postal vote held at each Virology Congress where all members of ICTV and more than 50 representatives of national microbiological societies are represented.

At present, there are 47 study groups working in concert with six subcommittees — namely, the vertebrate, invertebrate, plant, bacteria, fungus and virus data subcommittees. The ICTV regularly publishes reports describing all existing virus taxa with a list of classified viruses as well as descriptions of virus families and genera. An Internet web site, where the most important information relative to virus taxonomy is made available, is updated regularly.

The sixth report was published by Murphy et al and the seventh by van Regenmortel et al The increasing number of virus species and virus strains being identified, together with the explosion of data on many descriptive aspects of viruses and viral diseases, and particularly sequence data, has led the ICTV to launch an international virus database project. This project, termed ICTVdB, is scheduled to be fully operational and accessible to the scientific community around the year The ICTVdB, in addition to the taxonomic descriptions of all the taxa, will comprise all the information available about each virus species, and later each virus strain, for all the descriptors necessary to identify and recognize all viruses.

There are currently two systems in use for classifying organisms: the linnean and the adansonian systems. The former is the monothetic hierarchical classification applied by Linnaeus to plants and animals, while the adansonian is a polythetic hierarchical system initially proposed by Adanson in In Maurin and collaborators suggested applying the linnean classification system to the viruses.

Although convenient to use, this system has shortcomings when applied to the classification of viruses. Firstly, it is difficult to appreciate the validity of a particular criteria. For example, it may not be appropriate to use the number of genomic components as a hierarchical criteria. Secondly, there are no obvious reasons for prioritizing criteria, and in consequence it is difficult to rank all the available criteria.

The adansonian system considers all available criteria at once and makes several classifications, taking the criteria into consideration successively. The criteria leading to the same classifications are considered as correlated and are therefore not discriminatory.

Subsequently, a subset of criteria are considered, and the process is repeated until all criteria can be ranked to provide the best discrimination of the species. This system has not been used frequently in the past owing to its labor-intensive nature, but this situation has changed as a result of the power and availability of today's computer technology. Furthermore, qualitative and quantitative data can be simultaneously considered when generating such a classification.

In the case of viruses, it was determined by Harrison and collaborators in that at least 60 characters could be used for a complete virus description Table 1. Thus, the limiting factor for applying the adansonian system is now not its labor-intensive nature but the lack of data for many of the viruses. In addition, the increasing number of viral nucleic acid sequences being reported, in combination with the appropriate computer software, allows the comparison of viruses to generate different phylogenetic trees, according to the gene or set of genes used, as for example proposed by Koonin in , Dolja and Koonin in and Dolja et al in However, to date, none of them has satisfactorily provided a clear classification of all viruses.

A multidimensional classification, taking into account all the criteria necessary to describe viruses, would probably be the most appropriate way of representing a virus classification, but again the shortcomings of data for some viruses would prevent the use of this system in the foreseeable future. For almost 25 years, the ICTV has been classifying viruses essentially at the family and genus levels using a nonsystematic polythetic approach.

Viruses were clustered first in genera and then in families. A subset of characters, including physicochemical, structural, genomic and biological criteria, is then used to compare and group viruses. This subset of characters may change from one family to another, according to the availability of the data and the importance of a particular character for a particular family. It is obvious that there is no homogeneity in this respect throughout the virus classification and that virologists weigh the criteria differently in this subjective process, leading to the generation of a nonhomogeneous classification.

Nevertheless, over time we can see stability of the current ICTV classification at the genus and family level. When sequence, genomic organization and replicative cycle data are subsequently used for taxonomic purposes, they usually confirm the actual classification. It is also obvious that hierarchical classifications above the family level will encounter conflicts between phenotypic and genotypic criteria and that virologists will have to consider the entire classification process in order to progress in this direction.

Currently, and for practical reasons only, virus classification is structured according to the presentation indicated in Table 2 , Table 3.

Since a taxonomic structure above the level of family with the exception of the orders Mononegavirales, Caudovirales and Nidovirales has not been developed extensively, any listing must be arbitrary.

The order of presentation of virus families and genera follows four criteria: 1 the nature of the viral nucleic acid; 2 the strandedness of the nucleic acid; 3 the use of a reverse transcription process DNA or RNA ; and 4 the positive or negative sense of gene coding on the encapsidated genome.

These four criteria give rise to six clusters comprising the 86 families and floating genera of viruses. In the past, two other criteria were also taken in account: the presence or absence of a lipid envelope and the segmentation of the genome as mono-, bi-, tri-, tetra- or multipartite.

However, it has become clear that the presence of an envelope was entirely related to the nature of the host and that families could comprise genera having viruses with segmented or nonsegmented genomes, but sharing all other properties, including genome organization and sequence homology.

These criteria have been therefore abandoned. Orders, families and floating genera of viruses according to the seventh ICTV report Viruses are then differentiated in species and tentative species according to this list of criteria and the availability of information to demarcate the species. First, it is intended to define for each genus the criteria demarcating a virus species, and, second, to compare these criteria from one genus to the next, searching for homogeneity throughout the virus classification.

Naturally this list of criteria should follow the polythetic nature of the species definition and more than one criteria should be used to determine a new species. It is obvious that most of the criteria in the list of demarcating criteria are shared amongst the different genera, within and across families; namely, host range, serological relationships, vector transmission type, tissue tropism, genome rearrangement and sequence homology Table 4. However, if the types of criteria are similar, the levels of demarcation clearly differ from one family to another.

This may reflect differences in appreciation from one family to another but also the differential ranking of a particular criterion in different families. The levels of demarcation may even change from one gene to another within the same family. Homogenization of the application of the species definition concept throughout the virus definition will be the next challenge of ICTV for the eighth report to be published by This, in turn, will contribute to homogeneity of the genus and family demarcation criteria Table 4 and will permit creation of new families or merging of existing families.

However, it is important to note that the nature of the demarcating criteria at the genus level will probably not change as these have passed the test of time.