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M J Adams - One of the best experts on this subject based on the ideXlab platform.
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Family Flexiviridae: a case study in virion and genome plasticity.
Annual Review of Phytopathology, 2007Co-Authors: Giovanni P. Martelli, M J Adams, Jan Kreuze, Valerian V. DoljaAbstract:AbstractThe plant virus family Flexiviridae includes the definitive genera Potexvirus, Mandarivirus, Allexivirus, Carlavirus, Foveavirus, Capillovirus, Vitivirus, Trichovirus, the putative genus Citrivirus, and some unassigned species. Its establishment was based on similarities in virion morphology, common features in genome type and organization, and strong phylogenetic relationships between replicational and structural proteins. In this review, we provide a brief account of the main biological and molecular properties of the members of the family, with special emphasis on the relationships within and among the genera. In phylogenetic analyses the potexvirus-like replicases were more closely related to tymoviruses than to carlaviruses. We postulate a common evolutionary ancestor for the family Tymoviridae and the two distinct evolutionary clusters of the Flexiviridae, i.e., a plant virus with a polyadenylated genome, filamentous virions, and a triple gene block of movement proteins. Subsequent recombina...
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The new plant virus family Flexiviridae and assessment of molecular criteria for species demarcation
Archives of Virology, 2004Co-Authors: M J Adams, John F. Antoniw, G. D. Foster, R. G. Milne, Giovanni P. Martelli, A. A. Brunt, M. Joseph, Thierry Candresse, Claude M FauquetAbstract:Summary. The new plant virus family Flexiviridae is described. The family is named because its members have flexuous virions and it includes the existing genera Allexivirus, Capillovirus,Carlavirus,Foveavirus,Potexvirus,Trichovirus andVitivirus, plus the new genus Mandarivirus together with some related viruses not assigned to any genus. The family is justified from phylogenetic analyses of the polymerase and coat protein (CP) sequences. To help to define suitable molecular criteria for demarcation of species, a complete set of pairwise comparisons was made using the nucleotide (nt) and amino acid (aa) sequences of each fullysequenced gene from every available accession in the family. Based on the distributions and on inspection of the data, it was concluded that, as a general rule, distinct species have less than ca. 72% identical nt or 80% identical aa between their entire CP or replication protein genes.
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Virology Division News: The new plant virus family Flexiviridae and assessment of molecular criteria for species demarcation
Archives of Virology, 2004Co-Authors: M J Adams, John F. Antoniw, G. D. Foster, R. G. Milne, G. P. Martelli, A. A. Brunt, M. Joseph, Thierry Candresse, Claude M FauquetAbstract:The new plant virus family Flexiviridae is described. The family is named because its members have flexuous virions and it includes the existing genera Allexivirus , Capillovirus , Carlavirus , Foveavirus , Potexvirus , Trichovirus and Vitivirus , plus the new genus Mandarivirus together with some related viruses not assigned to any genus. The family is justified from phylogenetic analyses of the polymerase and coat protein (CP) sequences. To help to define suitable molecular criteria for demarcation of species, a complete set of pairwise comparisons was made using the nucleotide (nt) and amino acid (aa) sequences of each fully-sequenced gene from every available accession in the family. Based on the distributions and on inspection of the data, it was concluded that, as a general rule, distinct species have less than ca. 72% identical nt or 80% identical aa between their entire CP or replication protein genes.
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Detection and classification of Allexiviruses from garlic in China
Archives of Virology, 2003Co-Authors: John F. Antoniw, M J Adams, H Y Zheng, J. ChenAbstract:Degenerate primers for RT-PCR were designed and used to amplify genome fragments (c. 750 nt in the coat protein-ORF6 region) of Allexiviruses from a total of 28 garlic samples from 24 provinces in China. Many samples contained more than one distinct sequence. A total of 60 different sequences were obtained. Phylogenetic analysis and two-way comparisons were used to assess the status of the sequences and to re-examine the criteria for distinguishing species within the genus. Most of the sequences could be allocated to either Garlic virus D or Garlic virus X on the basis of sequence similarity but some appeared to be intermediate between existing species. There were no sequences of Garlic virus C or Shallot virus X. A comparison with the related genera Carlavirus, Foveavirus and Potexvirus suggests that the published Allexivirus species demarcation criteria may have been drawn too tightly and should be re-examined.
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Molecular characterisation of a complex mixture of viruses in garlic with mosaic symptoms in China
Archives of Virology, 2001Co-Authors: J. Chen, M J AdamsAbstract:Degenerate primers were used to detect and amplify cDNA of viruses of the genera Carlavirus , Allexivirus and Potyvirus from garlic plants with mosaic symptoms growing in Zhejiang province, China. Plants contained a complex mixture of viruses and strains. Three distinct stains of Garlic latent virus were detected; the most frequent one was completely sequenced and partial sequences were obtained for the other two. The complete sequence (8363 nt) was 76.4% identical to a Korean isolate. Two Allexiviruses were detected and completely sequenced. One (8319 nt) was identified as Garlic virus X and comparisons showed that a published Korean isolate (which had 90.2% identical nucleotides) had an N-terminal deletion in the serine-rich ORF4. The other isolate (8451 nt), tentatively named Garlic virus E , appeared to be a new member of the genus. Phylogenetic analyses of the different viral proteins and distinctive conserved sequence motifs within the genus are discussed. This is the first report of Allexiviruses from China. Using potyvirus primers, three distinct isolates of Onion yellow dwarf virus and one of Leek yellow stripe virus were detected and the 3′-terminal sequences of their genomes were determined. In a coat protein phylogenetic analysis, the new isolates were most closely related to other published isolates from Japan and China.
Milena Leite Oliveira - One of the best experts on this subject based on the ideXlab platform.
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Survey of viruses belonging to different genera and species in noble garlic in Brazil
Scientia Agricola, 2015Co-Authors: Tatiana Mituti, Milena Leite Oliveira, Monika Fecury Moura, Renate Krause Sakate, Julio Massaharu Marubayashi, Vitor Massami Imaizumi, Marcelo Agenor PavanAbstract:Garlic (Allium sativumL.) is a host to several viruses, most commonly those belonging to theAllexivirus,Carlavirus, orPotyvirusgenera. Nine species distributed among these three genera have been reported in Brazil: two species within carlaviruses, two within potyviruses, and five within Allexiviruses. To quantify the prevalence of these viruses, young leaves from 520 plants (plants either symptomatic or asymptomatic) were collected from commercial fields grown in four Brazilian states and analyzed using universal and species-specific primers via the reverse transcription polymerase chain reaction (RT-PCR). Potyvirus presence was positive in 306 samples (81 %), 151 of them (38 %) in mixed infections with other viruses. The most frequent potyviruses wereOnion yellow dwarf virus(OYDV, 56 %) andLeek yellow stripe virus(LYSV, 55 %). 187 samples (49 %) were positive for Allexivirus, with 33 (9 %) showing single infections and 154 (41 %) showing mixed infections withGarlic virus A (GarV-A),Garlic virus B(GarV-B),Garlic virus C(GarV-C),Garlic virus D(GarV-D), and species belonging to theCarlavirus andPotyvirusgenera. The predominant species in which Allexiviruses were found were GarV-A and GarV-D. Only 15 samples (4 %) were infected solely by a carlavirus, and 63 (17 %) showed mixed infections with viruses from different genera. The dominant species of carlavirus wasGarlic commom latent virus(GarCLV). Carlaviruses and Allexiviruses are frequently associated with mixed infections with potyviruses, whereas mixed infections with carlaviruses and Allexiviruses are rare. About 70 % of the plants collected were positive for at least one species of virus.
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Análise da presença de vírus em alho semente da segunda e quarta gerações, produzidos por termoterapia e cultura de tecido
Grupo Paulista de Fitopatologia, 2014Co-Authors: Milena Leite Oliveira, Mituti Tatiana, Nardini, João Paulo Calore, Pavan, Marcelo Agenor, Bruno Rossito De ,marchi, Bampi Daiana, Krause-sakate RenateAbstract:The garlic (Allium sativum L.) can be naturally infected by a complex of filamentous viruses belonging to the genera Potyvirus, Carlavirus and Allexivirus. Accumulation of these viruses occurs especially by vegetative propagation through cloves. As the cultivated garlic plant does not produce true seed worldwide, virus-free plants can only be obtained by tissue culture of stem apices and thermotherapy. Using these techniques, garlic seeds were produced at the School of Agricultural Sciences - UNESP, Botucatu, and evaluated by RT-PCR for the presence of potyvirus, carlavirus and Allexivirus. In the second generation of microcloves propagated in a greenhouse, 6.6% infection was detected, only by Allexivirus. In the fourth generation, however, there was 60% incidence by Allexivirus, 35% by potyvirus and all negative by carlavirus. The high rate of infection by Allexivirus may be related to the greater difficulty of removing the species of viruses belonging to this genus, as observed by other authors, and also based on the infection and transmission of the virus by the mite, Aceria tulipae, during the storage of bulbs from one year to the other. The garlic at the fourth generation corresponds to cloves weighed less than 1 gram and not selected for commercial multiplication. Selection for the size of cloves has a positive effect on the choice of cloves with lower rates of viral infection, as the technique of thermotherapy and tissue culture do not eliminate the virus completely. Results also emphasize the need of fumigation for the garlic seed stored from one year to the other in order to prevent the transmission of Allexivirus during storage.O alho (Allium sativum L.) pode estar naturalmente infectado por um complexo de vírus filamentosos pertencentes aos gêneros Potyvirus, Carlavirus e Allexivirus. O acúmulo destes vírus se dá, principalmente, pela sua propagação vegetativa através dos bulbilhos. Como a planta de alho cultivada não produz semente verdadeira em todo o mundo, a única forma de se obter plantas livres de vírus se dá pela cultura de tecidos dos ápices caulinares e termoterapia. Utilizando estas técnicas, alhos sementes foram produzidos na FCA- UNESP de Botucatu e avaliados via RT-PCR para a presença de potyvirus, carlavirus e Allexivirus. Na segunda geração dos microbulbilhos propagados em casa de vegetação, 6,6% de infecção foi verificada por Allexivirus. Já na quarta geração foi observada incidência de 60% com Allexivirus, 35% com potyvirus e todas foram negativas para carlavirus. A alta taxa de infecção por Allexivirus pode estar relacionada à maior dificuldade de remoção de espécies de vírus pertencentes a este gênero, como também já observado por outros autores, pela infecção e transmissão de vírus pelo ácaro, Aceriatulipae, durante o armazenamento dos bulbos de um ano a outro. O alho na quarta geração corresponde a bulbilhos com peso inferior a 1 grama e que não haviam sido selecionados para multiplicação comercial. A seleção para tamanho do bulbilho tem efeito positivo na escolha de bulbilhos com menores taxas de infecção por vírus, já que a técnica de termoterapia e cultura de tecidos não elimina totalmente os vírus. Os resultados também enfatizam a necessidade de se realizar fumigação no alho semente armazenado de um ano a outro a fim de evitar a transmissão de Allexivirus durante o armazenamento
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Bulbilhos aéreos de alho, provenientes de escapes florais, são infectados por vírus
Grupo Paulista de Fitopatologia, 2014Co-Authors: Tatiana Mituti, Milena Leite Oliveira, João Paulo Calore Nardini, Monika Fecury Moura, Maria Isabel Motta Hoffmann, Leysimar Ribeiro Pitzr Guimarães, Renate Krause Sakate, Marcelo Agenor PavanAbstract:Em campos de produção comercial de alho é comum observar plantas naturalmente infectadas por vírus dos gêneros Allexivirus, Carlavirus e Potyvirus. Os bulbilhos aéreos podem ser uma alternativa para a propagação de plantas de alho livres de vírus. Desta forma, o objetivo deste trabalho foi analisar a taxa de perpetuação dos vírus de plantas infectadas para os bulbilhos aéreos. Os bulbilhos aéreos obtidos de plantas infectadas foram analisados por RT-PCR utilizando oligonucleotídeos universais para os gêneros Allexivirus, Carlavirus e Potyvirus. A taxa de perpetuação foi de 65% para allexivírus, 20% para carlavírus e 82,22% para potyvírus. Os resultados demonstraram que a perpetuação dos diferentes vírus do bulbo para os bulbilhos aéreos é elevada, inviabilizando a utilização direta dos bulbilhos aéreos provenientes de plantas matrizes infectadas por vírus. Esta metodologia deve ser utilizada somente a partir de plantas isentas de vírus
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Análise da presença de vírus em alho semente da segunda e quarta gerações, produzidos por termoterapia e cultura de tecido
Grupo Paulista de Fitopatologia, 2014Co-Authors: Milena Leite Oliveira, Tatiana Mituti, João Paulo Calore Nardini, Marcelo Agenor Pavan, Bruno Rossito De ,marchi, Daiana Bampi, Renate Krause-sakateAbstract:O alho (Allium sativum L.) pode estar naturalmente infectado por um complexo de vírus filamentosos pertencentes aos gêneros Potyvirus, Carlavirus e Allexivirus. O acúmulo destes vírus se dá, principalmente, pela sua propagação vegetativa através dos bulbilhos. Como a planta de alho cultivada não produz semente verdadeira em todo o mundo, a única forma de se obter plantas livres de vírus se dá pela cultura de tecidos dos ápices caulinares e termoterapia. Utilizando estas técnicas, alhos sementes foram produzidos na FCA- UNESP de Botucatu e avaliados via RT-PCR para a presença de potyvirus, carlavirus e Allexivirus. Na segunda geração dos microbulbilhos propagados em casa de vegetação, 6,6% de infecção foi verificada por Allexivirus. Já na quarta geração foi observada incidência de 60% com Allexivirus, 35% com potyvirus e todas foram negativas para carlavirus. A alta taxa de infecção por Allexivirus pode estar relacionada à maior dificuldade de remoção de espécies de vírus pertencentes a este gênero, como também já observado por outros autores, pela infecção e transmissão de vírus pelo ácaro, Aceriatulipae, durante o armazenamento dos bulbos de um ano a outro. O alho na quarta geração corresponde a bulbilhos com peso inferior a 1 grama e que não haviam sido selecionados para multiplicação comercial. A seleção para tamanho do bulbilho tem efeito positivo na escolha de bulbilhos com menores taxas de infecção por vírus, já que a técnica de termoterapia e cultura de tecidos não elimina totalmente os vírus. Os resultados também enfatizam a necessidade de se realizar fumigação no alho semente armazenado de um ano a outro a fim de evitar a transmissão de Allexivirus durante o armazenamento
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Identification and sequence analysis of five Allexiviruses species infecting garlic crops in Brazil
Tropical Plant Pathology, 2014Co-Authors: Milena Leite Oliveira, Tatiana Mituti, Marcelo Agenor Pavan, Bruno Rossitto De Marchi, Renate Krause-sakateAbstract:Garlic plants are naturally infected by a mixture of viruses, including Allexiviruses. Symptomatic garlic plants with mosaic and distorted leaves from garlic producing regions in Brazil were analyzed for the presence of Garlic virus A (GarV-A), Garlic virus B (GarV-B), Garlic virus C (GarV-C), Garlic virus D (GarV-D) and Garlic mite-borne filamentous virus (GarMbFV), five Allexivirus species previously reported in the country. Fifty-nine virus isolates from five distinct Allexivirus species were identified and the complete coat protein region of each genome was sequenced. Mixed infections were very frequent and corresponded to 43% of the positive samples. The nucleotide identity of the coat protein ranged between 75% and 98% for GarV-A isolates, 83% and 90% for GarV-B, 69% and 98% for GarV-C, 87% and 97% for GarV-D, and 72% and 91% for GarMbFV.
Marcelo Agenor Pavan - One of the best experts on this subject based on the ideXlab platform.
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Survey of viruses belonging to different genera and species in noble garlic in Brazil
Scientia Agricola, 2015Co-Authors: Tatiana Mituti, Milena Leite Oliveira, Monika Fecury Moura, Renate Krause Sakate, Julio Massaharu Marubayashi, Vitor Massami Imaizumi, Marcelo Agenor PavanAbstract:Garlic (Allium sativumL.) is a host to several viruses, most commonly those belonging to theAllexivirus,Carlavirus, orPotyvirusgenera. Nine species distributed among these three genera have been reported in Brazil: two species within carlaviruses, two within potyviruses, and five within Allexiviruses. To quantify the prevalence of these viruses, young leaves from 520 plants (plants either symptomatic or asymptomatic) were collected from commercial fields grown in four Brazilian states and analyzed using universal and species-specific primers via the reverse transcription polymerase chain reaction (RT-PCR). Potyvirus presence was positive in 306 samples (81 %), 151 of them (38 %) in mixed infections with other viruses. The most frequent potyviruses wereOnion yellow dwarf virus(OYDV, 56 %) andLeek yellow stripe virus(LYSV, 55 %). 187 samples (49 %) were positive for Allexivirus, with 33 (9 %) showing single infections and 154 (41 %) showing mixed infections withGarlic virus A (GarV-A),Garlic virus B(GarV-B),Garlic virus C(GarV-C),Garlic virus D(GarV-D), and species belonging to theCarlavirus andPotyvirusgenera. The predominant species in which Allexiviruses were found were GarV-A and GarV-D. Only 15 samples (4 %) were infected solely by a carlavirus, and 63 (17 %) showed mixed infections with viruses from different genera. The dominant species of carlavirus wasGarlic commom latent virus(GarCLV). Carlaviruses and Allexiviruses are frequently associated with mixed infections with potyviruses, whereas mixed infections with carlaviruses and Allexiviruses are rare. About 70 % of the plants collected were positive for at least one species of virus.
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Bulbilhos aéreos de alho, provenientes de escapes florais, são infectados por vírus
Grupo Paulista de Fitopatologia, 2014Co-Authors: Tatiana Mituti, Milena Leite Oliveira, João Paulo Calore Nardini, Monika Fecury Moura, Maria Isabel Motta Hoffmann, Leysimar Ribeiro Pitzr Guimarães, Renate Krause Sakate, Marcelo Agenor PavanAbstract:Em campos de produção comercial de alho é comum observar plantas naturalmente infectadas por vírus dos gêneros Allexivirus, Carlavirus e Potyvirus. Os bulbilhos aéreos podem ser uma alternativa para a propagação de plantas de alho livres de vírus. Desta forma, o objetivo deste trabalho foi analisar a taxa de perpetuação dos vírus de plantas infectadas para os bulbilhos aéreos. Os bulbilhos aéreos obtidos de plantas infectadas foram analisados por RT-PCR utilizando oligonucleotídeos universais para os gêneros Allexivirus, Carlavirus e Potyvirus. A taxa de perpetuação foi de 65% para allexivírus, 20% para carlavírus e 82,22% para potyvírus. Os resultados demonstraram que a perpetuação dos diferentes vírus do bulbo para os bulbilhos aéreos é elevada, inviabilizando a utilização direta dos bulbilhos aéreos provenientes de plantas matrizes infectadas por vírus. Esta metodologia deve ser utilizada somente a partir de plantas isentas de vírus
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Análise da presença de vírus em alho semente da segunda e quarta gerações, produzidos por termoterapia e cultura de tecido
Grupo Paulista de Fitopatologia, 2014Co-Authors: Milena Leite Oliveira, Tatiana Mituti, João Paulo Calore Nardini, Marcelo Agenor Pavan, Bruno Rossito De ,marchi, Daiana Bampi, Renate Krause-sakateAbstract:O alho (Allium sativum L.) pode estar naturalmente infectado por um complexo de vírus filamentosos pertencentes aos gêneros Potyvirus, Carlavirus e Allexivirus. O acúmulo destes vírus se dá, principalmente, pela sua propagação vegetativa através dos bulbilhos. Como a planta de alho cultivada não produz semente verdadeira em todo o mundo, a única forma de se obter plantas livres de vírus se dá pela cultura de tecidos dos ápices caulinares e termoterapia. Utilizando estas técnicas, alhos sementes foram produzidos na FCA- UNESP de Botucatu e avaliados via RT-PCR para a presença de potyvirus, carlavirus e Allexivirus. Na segunda geração dos microbulbilhos propagados em casa de vegetação, 6,6% de infecção foi verificada por Allexivirus. Já na quarta geração foi observada incidência de 60% com Allexivirus, 35% com potyvirus e todas foram negativas para carlavirus. A alta taxa de infecção por Allexivirus pode estar relacionada à maior dificuldade de remoção de espécies de vírus pertencentes a este gênero, como também já observado por outros autores, pela infecção e transmissão de vírus pelo ácaro, Aceriatulipae, durante o armazenamento dos bulbos de um ano a outro. O alho na quarta geração corresponde a bulbilhos com peso inferior a 1 grama e que não haviam sido selecionados para multiplicação comercial. A seleção para tamanho do bulbilho tem efeito positivo na escolha de bulbilhos com menores taxas de infecção por vírus, já que a técnica de termoterapia e cultura de tecidos não elimina totalmente os vírus. Os resultados também enfatizam a necessidade de se realizar fumigação no alho semente armazenado de um ano a outro a fim de evitar a transmissão de Allexivirus durante o armazenamento
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Identification and sequence analysis of five Allexiviruses species infecting garlic crops in Brazil
Tropical Plant Pathology, 2014Co-Authors: Milena Leite Oliveira, Tatiana Mituti, Marcelo Agenor Pavan, Bruno Rossitto De Marchi, Renate Krause-sakateAbstract:Garlic plants are naturally infected by a mixture of viruses, including Allexiviruses. Symptomatic garlic plants with mosaic and distorted leaves from garlic producing regions in Brazil were analyzed for the presence of Garlic virus A (GarV-A), Garlic virus B (GarV-B), Garlic virus C (GarV-C), Garlic virus D (GarV-D) and Garlic mite-borne filamentous virus (GarMbFV), five Allexivirus species previously reported in the country. Fifty-nine virus isolates from five distinct Allexivirus species were identified and the complete coat protein region of each genome was sequenced. Mixed infections were very frequent and corresponded to 43% of the positive samples. The nucleotide identity of the coat protein ranged between 75% and 98% for GarV-A isolates, 83% and 90% for GarV-B, 69% and 98% for GarV-C, 87% and 97% for GarV-D, and 72% and 91% for GarMbFV.
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First Report of Garlic virus X in Garlic Plants in Brazil
Plant disease, 2014Co-Authors: Milena Leite Oliveira, Tatiana Mituti, Maria Isabel Motta Hoffmann, Marcelo Agenor Pavan, Renate Krause-sakateAbstract:Garlic is the fifth most economically important vegetable in Brazil and is frequently infected by a complex of different viruses that cause significant degeneration of the crop under field conditions. The species of the genus Allexivirus that infect garlic are: Garlic virus A (GarV-A), Garlic virus B (GarV-B), Garlic virus C (GarV-C), Garlic virus D (GarV-D), Garlic virus E (GarV-E), Garlic virus X (GarV-X), Garlic mite-borne filamentous viru s (GarMbFV), and Shallot virus X (ShVX). So far, only GarV-A, GarV-B, GarV-C, GarV-D, and GarMbFV have been reported in Brazil (3). During the 2010 through 2013 seasons, between April and October, 302 garlic plants with yellow mosaic strips and distorted leaves from the cultivars Cacador, Quiteria, Tropical Bergamota, and Tropical Shangai were collected in the states of Parana, Minas Gerais, Sao Paulo, and Goias and analyzed for the presence of Allexiviruses. Total plant RNA was extracted with the Total RNA Purification kit (Norgen Biotek Corp., Canada) according to ...
Claude M Fauquet - One of the best experts on this subject based on the ideXlab platform.
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The new plant virus family Flexiviridae and assessment of molecular criteria for species demarcation
Archives of Virology, 2004Co-Authors: M J Adams, John F. Antoniw, G. D. Foster, R. G. Milne, Giovanni P. Martelli, A. A. Brunt, M. Joseph, Thierry Candresse, Claude M FauquetAbstract:Summary. The new plant virus family Flexiviridae is described. The family is named because its members have flexuous virions and it includes the existing genera Allexivirus, Capillovirus,Carlavirus,Foveavirus,Potexvirus,Trichovirus andVitivirus, plus the new genus Mandarivirus together with some related viruses not assigned to any genus. The family is justified from phylogenetic analyses of the polymerase and coat protein (CP) sequences. To help to define suitable molecular criteria for demarcation of species, a complete set of pairwise comparisons was made using the nucleotide (nt) and amino acid (aa) sequences of each fullysequenced gene from every available accession in the family. Based on the distributions and on inspection of the data, it was concluded that, as a general rule, distinct species have less than ca. 72% identical nt or 80% identical aa between their entire CP or replication protein genes.
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Virology Division News: The new plant virus family Flexiviridae and assessment of molecular criteria for species demarcation
Archives of Virology, 2004Co-Authors: M J Adams, John F. Antoniw, G. D. Foster, R. G. Milne, G. P. Martelli, A. A. Brunt, M. Joseph, Thierry Candresse, Claude M FauquetAbstract:The new plant virus family Flexiviridae is described. The family is named because its members have flexuous virions and it includes the existing genera Allexivirus , Capillovirus , Carlavirus , Foveavirus , Potexvirus , Trichovirus and Vitivirus , plus the new genus Mandarivirus together with some related viruses not assigned to any genus. The family is justified from phylogenetic analyses of the polymerase and coat protein (CP) sequences. To help to define suitable molecular criteria for demarcation of species, a complete set of pairwise comparisons was made using the nucleotide (nt) and amino acid (aa) sequences of each fully-sequenced gene from every available accession in the family. Based on the distributions and on inspection of the data, it was concluded that, as a general rule, distinct species have less than ca. 72% identical nt or 80% identical aa between their entire CP or replication protein genes.
S. Majumder - One of the best experts on this subject based on the ideXlab platform.
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FIRST REPORT OF ONION YELLOW DWARF VIRUS IN GARLIC FROM NIGERIA
Journal of Plant Pathology, 2017Co-Authors: S. Majumder, V. Yadav, M.a. Yakasai, J.y. MuhammadAbstract:Garlic (Allium sativum L.) is one of the most important culinary herbs in the world. Several viruses belonging to genera Potyvirus, Carlavirus, and Allexivirus are known to infect garlic (Dijk, 1994; Walkey and Antill, 1989). This study was undertaken to investigate the status of viral infection in Nigerian garlic. Ten garlic bulbs showing mild to severe mosaic symptoms each were collected in March of 2015 from two fields in Kano and Sokoto region of Nigeria. Direct antigen coated (DAC)-ELISA was performed with antisera to Onion yellow dwarf virus (OYDV) (Bioreba, Reinach, Switzerland). All the samples were positive for OYDV. To confirm the presence of OYDV, reverse transcription (RT)-PCR was performed using primers published earlier (Majumder and Baranwal, 2014) and total RNA extracted from 100 mg of leaves with the RNeasy Plant Mini kit (Qiagen, Germany) according to the manufacturer’s instructions. Expected amplicons of ca. 320 bp for OYDV were obtained from all the samples tested, indicating infection by OYDV. Direct sequencing of the PCR products produced 276 bp long nucleotide sequences with 87% identity with sequence of an OYDV isolate from leek in Vietnam (GenBank accession No. DQ925454.1). Sequence obtained from the Nigerian isolate was deposited in GenBank under accession number KU854388. To our knowledge, this is the first report of OYDV in garlic from Nigeria.
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FIRST REPORT OF GARLIC COMMON LATENT VIRUS IN GARLIC FROM NIGERIA
Journal of Plant Pathology, 2016Co-Authors: S. Majumder, V. Yadav, M.a. Yakasai, J.y. MuhammadAbstract:Garlic (Allium sativum L.) is one of the oldest known horticultural crops of the world. Several viruses belonging to the genera Potyvirus, Carlavirus, and Allexivirus are known to infect garlic and reduce their yield worldwide (Dijk, 1994; Walkey and Antill, 1989). This study was undertaken to investigate the status of viral infection in Nigerian garlic. Ten garlic bulbs collected in March of 2015 from two fields in Kano and Sokoto region of Nigeria were tested by direct antigen coated (DAC)-ELISA with antisera to Garlic common latent virus (GarCLV) (Bioreba, Reinach, Switzerland). All the samples were positive for GarCLV. To confirm the presence of GarCLV, reverse transcription (RT)-PCR was performed using primers published earlier (Majumder and Baranwal, 2014) and total RNA extracted from 100 mg of leaves with the RNeasy Plant Mini kit (Qiagen, GmbH, Hilden, Germany) according to the manufacturer's instructions. Expected amplicons of ca. 450 bp were obtained from all the samples tested. Direct sequencing of the PCR products from one sample produced a 418-bp long nucleotide sequence. It showed 95% identity with a garlic isolate from The Netherlands (GenBank accession No. AB004804). To our knowledge, this is the first report of GarCLV on garlic in Nigeria.
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FIRST REPORT OF ONION YELLOW DWARF VIRUS AND GARLIC COMMON LATENT VIRUS INFECTION IN GARLIC FROM NEPAL
Journal of Plant Pathology, 2014Co-Authors: S. Majumder, Shivangi JohariAbstract:Garlic (Allium sativum L.) is one of the most important culinary herbs in the Indian subcontinent. Several viruses belonging to the genera Potyvirus, Carlavirus and Allexivirus are known to infect garlic worldwide (Dijk, 1994; Walkey and Antill, 1989). Leaves from 20 different samples of cultivar ‘Sauntha lasoon’ showing mild to severe mosaic symptoms were collected in April of 2013 from two fields of Dharchula, Nepal. Direct antigen coated (DAC)-ELISA was performed with antisera to Onion yellow dwarf virus (OYDV), Shallot latent virus (SLV) and Garlic common latent virus (GarCLV) (Bioreba, Reinach, Switzerland). All the samples were positive for OYDV and 16 were positive for GarCLV. These results were confirmed by reverse transcription (RT)- PCR using specific primers (Majumder and Baranwal, 2014) and total RNA extracted from 100 mg of leaves with the RNeasy Plant Mini kit (Qiagen, USA) according to the manufacturer's protocol. Expected amplicons of ca. 320 bp for OYDV and ca. 450 bp for GarCLV were obtained from all the samples tested, indicating mixed infections. Direct sequencing of the PCR products produced 276 bp and 461 bp long nucleotide sequences with 78% and 91% identity with sequences of an OYDV isolate from garlic in India (GenBank accession No. DQ519034 ) and a GarCLV isolate from garlic in India (GenBank accession No. FJ154841), respectively. SLV was not found by ELISA or RT-PCR in any of the samples tested. To our knowledge, this is the first report of OYDV and GarCLV in garlic in Nepal.
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Simultaneous detection of four garlic viruses by multiplex reverse transcription PCR and their distribution in Indian garlic accessions
Journal of virological methods, 2014Co-Authors: S. Majumder, Virendra Kumar BaranwalAbstract:Indian garlic is infected with Onion yellow dwarf virus (OYDV), Shallot latent virus (SLV), Garlic common latent virus (GarCLV) and Allexiviruses. Identity and distribution of garlic viruses in various garlic accessions from different geographical regions of India were investigated. OYDV and Allexiviruses were observed in all the garlic accessions, while SLV and GarCLV were observed only in a few accessions. A multiplex reverse transcription (RT)-PCR method was developed for the simultaneous detection and identification of OYDV, SLV, GarCLV and Allexivirus infecting garlic accessions in India. This multiplex protocol standardized in this study will be useful in indexing of garlic viruses and production of virus free seed material.
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Sequence Comparison and Phylogeny of Nucleotide Sequence of Coat Protein and Nucleic Acid Binding Protein of a Distinct Isolate of Shallot virus X from India
Indian Journal of Virology, 2011Co-Authors: S. Majumder, V. K. BaranwalAbstract:Shallot virus X (ShVX), a type species in the genus Allexivirus of the family Alfaflexiviridae has been associated with shallot plants in India and other shallot growing countries like Russia, Germany, Netherland, and New Zealand. Coat protein (CP) and nucleic acid binding protein (NB) region of the virus was obtained by reverse transcriptase polymerase chain reaction from scales leaves of shallot bulbs. The partial cDNA contained two open reading frames encoding proteins of molecular weights of 28.66 and 14.18 kDa belonging to Flexi_CP super-family and viral NB super-family, respectively. The percent identity and phylogenetic analysis of amino acid sequences of CP and NB region of the virus associated with shallot indicated that it was a distinct isolate of ShVX.
