Geminivirus strain demarcation and nomenclature
TL;DR: The status of geminivirus species and strain demarcation is reviewed as well as providing updated isolate descriptors for a total of 672 begomovirus isolates, and several others previously classified as “strains” have been upgraded to “species”.
Abstract: Geminivirus taxonomy and nomenclature is growing in complexity with the number of genomic sequences deposited in sequence databases Taxonomic and nomenclatural updates are published at regular intervals (Fauquet et al in Arch Virol 145:1743–1761, 2000, Arch Virol 148:405–421, 2003) A system to standardize virus names, and corresponding guidelines, has been proposed (Fauquet et al in Arch Virol 145:1743–1761, 2000) This system is now followed by a large number of geminivirologists in the world, making geminivirus nomenclature more transparent and useful In 2003, due to difficulties inherent in species identification, the ICTV Geminiviridae Study Group proposed new species demarcation criteria, the most important of which being an 89% nucleotide (nt) identity threshold between full-length DNA-A component nucleotide sequences for begomovirus species This threshold has been utilised since with general satisfaction More recently, an article has been published to clarify the terminology used to describe virus entities below the species level [5] The present publication is proposing demarcation criteria and guidelines to classify and name geminiviruses below the species level Using the Clustal V algorithm (DNAStar MegAlign software), the distribution of pairwise sequence comparisons, for pairs of sequences below the species taxonomic level, identified two peaks: one at 85–94% nt identity that is proposed to correspond to “strain” comparisons and one at 92–100% identity that corresponds to “variant” comparisons Guidelines for descriptors for each of these levels are proposed to standardize nomenclature under the species level In this publication we review the status of geminivirus species and strain demarcation as well as providing updated isolate descriptors for a total of 672 begomovirus isolates As a consequence, we have revised the status of some virus isolates to classify them as “strains”, whereas several others previously classified as “strains” have been upgraded to “species” In all other respects, the classification system has remained robust, and we therefore propose to continue using it An updated list of all geminivirus isolates and a phylogenetic tree with one representative isolate per species are provided
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Texas A&M University1, Agricultural Research Service2, Hebrew University of Jerusalem3, Seoul Women's University4, University of Rennes5, University of Basel6, Norwich Research Park7, University of Bordeaux8, University of Wisconsin-Madison9, North Carolina State University10, University of Bristol11
TL;DR: A short review on each virus of the Top 10 list and its importance is presented, with the intent of initiating discussion and debate amongst the plant virology community, as well as laying down a benchmark, as it will be interesting to see in future years how perceptions change and which viruses enter and leave the Top10.
Abstract: Many scientists, if not all, feel that their particular plant virus should appear in any list of the most important plant viruses. However, to our knowledge, no such list exists. The aim of this review was to survey all plant virologists with an association with Molecular Plant Pathology and ask them to nominate which plant viruses they would place in a 'Top 10' based on scientific/economic importance. The survey generated more than 250 votes from the international community, and allowed the generation of a Top 10 plant virus list for Molecular Plant Pathology. The Top 10 list includes, in rank order, (1) Tobacco mosaic virus, (2) Tomato spotted wilt virus, (3) Tomato yellow leaf curl virus, (4) Cucumber mosaic virus, (5) Potato virus Y, (6) Cauliflower mosaic virus, (7) African cassava mosaic virus, (8) Plum pox virus, (9) Brome mosaic virus and (10) Potato virus X, with honourable mentions for viruses just missing out on the Top 10, including Citrus tristeza virus, Barley yellow dwarf virus, Potato leafroll virus and Tomato bushy stunt virus. This review article presents a short review on each virus of the Top 10 list and its importance, with the intent of initiating discussion and debate amongst the plant virology community, as well as laying down a benchmark, as it will be interesting to see in future years how perceptions change and which viruses enter and leave the Top 10.
842 citations
TL;DR: Factors driving the emergence and establishment of whitefly-transmitted diseases include genetic changes in the virus through mutation and recombination, changes inThe vector populations coupled with polyphagy of the main vector, Bemisia tabaci, and long distance traffic of plant material or vector insects due to trade of vegetables and ornamental plants.
Abstract: Virus diseases that have emerged in the past two decades limit the production of important vegetable crops in tropical, subtropical, and temperate regions worldwide, and many of the causal viruses are transmitted by whiteflies (order Hemiptera, family Aleyrodidae). Most of these whitefly-transmitted viruses are begomoviruses (family Geminiviridae), although whiteflies are also vectors of criniviruses, ipomoviruses, torradoviruses, and some carlaviruses. Factors driving the emergence and establishment of whitefly-transmitted diseases include genetic changes in the virus through mutation and recombination, changes in the vector populations coupled with polyphagy of the main vector, Bemisia tabaci, and long distance traffic of plant material or vector insects due to trade of vegetables and ornamental plants. The role of humans in increasing the emergence of virus diseases is obvious, and the effect that climate change may have in the future is unclear.
732 citations
TL;DR: Revised guidelines for the classification and nomenclature of begomoviruses are proposed and genome-wide pairwise identities of 91 % and 94 % are proposed as the demarcation threshold for begomviruses belonging to different species and strains, respectively.
Abstract: Viruses of the genus Begomovirus (family Geminiviridae) are emergent pathogens of crops throughout the tropical and subtropical regions of the world. By virtue of having a small DNA genome that is easily cloned, and due to the recent innovations in cloning and low-cost sequencing, there has been a dramatic increase in the number of available begomovirus genome sequences. Even so, most of the available sequences have been obtained from cultivated plants and are likely a small and phylogenetically unrepresentative sample of begomovirus diversity, a factor constraining taxonomic decisions such as the establishment of operationally useful species demarcation criteria. In addition, problems in assigning new viruses to established species have highlighted shortcomings in the previously recommended mechanism of species demarcation. Based on the analysis of 3,123 full-length begomovirus genome (or DNA-A component) sequences available in public databases as of December 2012, a set of revised guidelines for the classification and nomenclature of begomoviruses are proposed. The guidelines primarily consider a) genus-level biological characteristics and b) results obtained using a standardized classification tool, Sequence Demarcation Tool, which performs pairwise sequence alignments and identity calculations. These guidelines are consistent with the recently published recommendations for the genera Mastrevirus and Curtovirus of the family Geminiviridae. Genome-wide pairwise identities of 91 % and 94 % are proposed as the demarcation threshold for begomoviruses belonging to different species and strains, respectively. Procedures and guidelines are outlined for resolving conflicts that may arise when assigning species and strains to categories wherever the pairwise identity falls on or very near the demarcation threshold value.
537 citations
TL;DR: Applications of current molecular tools are facilitating viral diagnosis and the discovery of novel species of geminiviruses and satelliteDNAs and are also advancing the understanding of the global diversity and evolution of satellite DNAs.
Abstract: Begomoviruses are numerous and geographically widespread viruses that cause devastating diseases in many crops. Monopartite begomoviruses are frequently associated with betasatellites or alphasatellites. Both betasatellite and alphasatellite DNA genomes are approximately half the size of begomovirus DNA genomes. Betasatellites are essential for induction of typical disease symptoms. The βC1 genes encoded by the betasatellites have important roles in symptom induction, in suppression of transcriptional and posttranscriptional gene silencing, and they can affect jasmonic acid responsive genes. Host plants of begomoviruses have evolved diverse innate defense mechanisms against the βC1 protein to counter these challenges. Alphasatellites have been identified mainly in monopartite begomoviruses that associate with betasatellites and have no known contributions to pathogenesis of begomovirus-betasatellite disease complexes. Applications of current molecular tools are facilitating viral diagnosis and the discove...
318 citations
TL;DR: Fine-mapped the widely used Solanum chilense–derived Ty-1 and Ty-3 genes by screening nearly 12,000 plants for recombination events and generating recombinant inbred lines and identified the resistance gene, which unveils a completely new class of resistance gene.
Abstract: Tomato Yellow Leaf Curl Virus Disease incited by Tomato yellow leaf curl virus (TYLCV) causes huge losses in tomato production worldwide and is caused by different related begomovirus species. Breeding for TYLCV resistance has been based on the introgression of multiple resistance genes originating from several wild tomato species. In this study we have fine-mapped the widely used Solanum chilense–derived Ty-1 and Ty-3 genes by screening nearly 12,000 plants for recombination events and generating recombinant inbred lines. Multiple molecular markers were developed and used in combination with disease tests to fine-map the genes to a small genomic region (approximately 70 kb). Using a Tobacco Rattle Virus–Virus Induced Gene Silencing approach, the resistance gene was identified. It is shown that Ty-1 and Ty-3 are allelic and that they code for a RNA–dependent RNA polymerase (RDR) belonging to the RDRγ type, which has an atypical DFDGD motif in the catalytic domain. In contrast to the RDRα type, characterized by a catalytic DLDGD motif, no clear function has yet been described for the RDRγ type, and thus the Ty-1/Ty-3 gene unveils a completely new class of resistance gene. Although speculative, the resistance mechanism of Ty-1/Ty-3 and its specificity towards TYLCV are discussed in light of the function of the related RDRα class in the amplification of the RNAi response in plants and transcriptional silencing of geminiviruses in plants.
260 citations
Cites background from "Geminivirus strain demarcation and ..."
...The whitefly transmitted tomato yellow leaf curl disease (TYLCD) is one of the most devastating diseases of tomato (Solanum lycopersicum) and is caused by several species of the Begomovirus genus (Geminiviridae) [15]....
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TL;DR: Geminiviruses are a group of plant viruses characterized by a genome of circular single-stranded DNA encapsidated in twinned quasi-isometric particles and recombination is very frequent and occurs between species and within and across genera.
1,432 citations
TL;DR: Members of the family Geminiviridae characteristically have circular single-stranded DNAgenomes packaged within twinned (so-called geminate) particles that cause yield losses to many crop plants throughout the world.
Abstract: Members of the family Geminiviridae characteristically have circular single-stranded DNAgenomes packaged within twinned (so-called geminate) particles. Geminiviruses are currentlydivided into four genera on the basis of their genome organizations and biological properties[2,20].Thosethathaveamonopartitegenomeandaretransmittedbyleafhoppervectors,primarilyto monocotyledonous plants, are included in the genus Mastrevirus, of which Maize streak virus isthe type species. Viruses that have monopartite genomes distinct from those of the mastrevirusesand that are transmitted by leafhopper vectors to dicotyledonous plants are included in thegenus Curtovirus, with Beet curly top virus as the type species. The genus Topocuvirus, recentlyrecognized by the International Committee on Taxonomy of Viruses (ICTV) [18], has only onemember (also the type species), Tomato pseudo-curly top virus, which has a monopartite genomeandistransmittedbyatreehoppervectortodicotyledonousplants.ThegenusBegomoviruscontainsviruses that are transmitted by the whitefly Bemisia tabaci (Gennadius) to dicotyledonous plants,with Bean golden yellow mosaic virus (originally Bean golden mosaic virus – Puerto Rico)asthetype species. Many begomoviruses have bipartite genomes (DNA A and DNA B components),although numerous begomoviruses with a monopartite genome occur in the Old World, and thereare some for which a single component is not infectious yet no DNA B component has been found.Geminiviruses cause significant yield losses to many crop plants throughout the world [5, 7].Because of their economic importance and the relative ease with which their DNA genomescan be cloned, many geminiviruses have been isolated and characterized. Guidelines for naming
367 citations
"Geminivirus strain demarcation and ..." refers methods in this paper
...In 2003, following guidelines established by the International Committee on Taxonomy of Viruses (ICTV) [11], we published a comprehensive list of species and isolates of geminiviruses [7]....
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TL;DR: The status of geminivirus species demarcation and nomenclature is reviewed for a total of 389 isolates and the need for a better description of virus isolates is recognized to elevate them to “strains”.
Abstract: Geminivirus taxonomy and nomenclature is increasing in complexity with time, and the growing number of geminivirus sequences deposited in gene banks requires regular taxonomic updates and calls for new descriptors to identify virus isolates unambiguously. Fauquet et al. [1] proposed a system to standardize the names of the viruses, and corresponding guidelines have been followed since, rendering nomenclature much easier. Recently, due to difficulties inherent in species identification, the ICTV Geminiviridae Study Group proposed new species demarcation criteria, the most important of which being an 89% identity threshold between complete DNA-A component nucleotide sequences of begomoviruses. This threshold has been utilised since with general satisfaction. In this paper, we review the status of geminivirus species demarcation and nomenclature for a total of 389 isolates. A small number of corrections have been made to comply with the adopted demarcation criteria but otherwise the classification system has remained robust and therefore we propose to continue using it. However, the large numbers of geminivirus sequences that have become available have led us to recognize the need for a better description of virus isolates. The pairwise comparison distribution below the taxonomic level of species identified two peaks, one at 90-91% identity that may correspond to "strains" and one at 96-98% identity that may correspond to "variants". Guidelines for descriptors for each of these levels are proposed to standardize nomenclature. As a consequence, we have revisited the status of some virus isolates to elevate them to "strains". An updated list of all geminivirus isolates currently available is provided.
171 citations
"Geminivirus strain demarcation and ..." refers background or methods in this paper
...In order to classify viruses and to avoid further confusion, we published in 2005 a paper [5] describing the nomenclature used by virologists below the species level, and we proposed, for the time being, to restrict the number of categories to ‘‘strains’’ and ‘‘variants’’....
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...More recently, an article has been published to clarify the terminology used to describe virus entities below the species level [5]....
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...On this basis, reviewing geminivirus information compiled in sequence databases and the last update of geminivirus isolates that we have done [5], the following begomoviruses would gain the status of strain:...
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TL;DR: This research attacked the mode of action of the immune system by targeting the “spatially aggregating immune checkpoints” in response to the presence of E.coli.
Abstract: 1 UPR 9021-Immunochimie des Peptides et des Virus, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, France 20xford University, St. Cross College, St. Giles, Oxford, U.K. 30RSTOM/ILTAB, The Scripps Research Institute, Division of Plant Biology, La Jolla, California, U.S.A. 4 Scottish Crop Research lnstitute, Invergowrie, Dundee, U.K. 'Department of Microbiology and Immunology, University of Rochester, Rochester, New Y ark. U.S.A. 6 Arthropod Borne & Infectious Disease Labaratory, Department of Microbiology, Colorado State University, Ft. Collins, Colorado, U.S.A.
132 citations
"Geminivirus strain demarcation and ..." refers methods in this paper
...In 2003, due to difficulties inherent in species identification, the ICTV Geminiviridae Study Group proposed new species demarcation criteria, the most important of which being an 89% nucleotide (nt) identity threshold between full-length DNA-A component nucleotide sequences for begomovirus species....
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...In 2003, following guidelines established by the International Committee on Taxonomy of Viruses (ICTV) [11], we published a comprehensive list of species and isolates of geminiviruses [7]....
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...Certainly, the mandate of the ICTV does not include any consideration under the species level, and, hence, the decision has been left to the initiative of speciality groups like the Geminiviridae Study Group....
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97 citations
"Geminivirus strain demarcation and ..." refers background in this paper
...The names of geminiviruses have been standardised, and a set of rules to derive names for newly identified species were laid down several years ago [6]....
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