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Arvind Varsani - One of the best experts on this subject based on the ideXlab platform.
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Exploring the diversity of Poaceae-infecting Mastreviruses on Reunion Island using a viral metagenomics-based approach
Scientific Reports, 2019Co-Authors: Sohini Claverie, Jean-michel Lett, Arvind Varsani, Darren P Martin, Denis Filloux, Philippe Roumagnac, Alassane Ouattara, Murielle Hoareau, Pierre LefeuvreAbstract:Mostly found in Africa and its surrounding islands, African streak viruses (AfSV) represent the largest group of known Mastreviruses. Of the thirteen AfSV species that are known to infect either cultivated or wild Poaceae plant species, six have been identified on Reunion Island. To better characterize AfSV diversity on this island, we undertook a survey of a small agroecosystem using a new metagenomics-based approach involving rolling circle amplification with random PCR amplification tagging (RCA-RA-PCR), high-throughput sequencing (Illumina HiSeq) and the Mastrevirus reads classification using phylogenetic placement. Mastreviruses that likely belong to three new species were discovered and full genome sequences of these were determined by Sanger sequencing. The geminivirus-focused metagenomics approach we applied in this study was useful in both the detection of known and novel Mastreviruses. The results confirm that Reunion Island is indeed a hotspot of AfSV diversity and that many of the Mastrevirus species have likely been introduced multiple times. Applying a similar approach in other natural and agricultural environments should yield sufficient detail on the composition and diversity of geminivirus communities to precipitate major advances in our understanding of the ecology and the evolutionary history of this important group of viruses.
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discovery of the first maize infecting Mastrevirus in the americas using a vector enabled metagenomics approach
Archives of Virology, 2018Co-Authors: Rafaela S Fontenele, D M T Alvesfreitas, Pedro Italo Tanno Silva, Josemar Foresti, Paulo R Silva, Marcio Tadeu Godinho, Arvind Varsani, S G RibeiroAbstract:The genus Mastrevirus (family Geminiviridae) is composed of single-stranded DNA viruses that infect mono- and dicotyledonous plants and are transmitted by leafhoppers. In South America, there have been only two previous reports of Mastreviruses, both identified in sweet potatoes (from Peru and Uruguay). As part of a general viral surveillance program, we used a vector-enabled metagenomics (VEM) approach and sampled leafhoppers (Dalbulus maidis) in Itumbiara (State of Goias), Brazil. High-throughput sequencing of viral DNA purified from the leafhopper sample revealed Mastrevirus-like contigs. Using a set of abutting primers, a 2746-nt circular genome was recovered. The circular genome has a typical Mastrevirus genome organization and shares 99% pairwise identity with the one from the leafhopper. This is the first report of a maize-infecting Mastrevirus in the Americas, the first identified in a non-vegetatively propagated Mastrevirus host in South America, and the first Mastrevirus to be identified in Brazil.
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occurrence of a novel Mastrevirus in sugarcane germplasm collections in florida guadeloupe and reunion
Virology Journal, 2017Co-Authors: Wardatou Boukari, Jean-michel Lett, Simona Kraberger, Darren P Martin, Ricardo Ivan Alcalabriseno, Emmanuel Fernandez, Denis Filloux, Jeanheinrich Daugrois, Jack C Comstock, Arvind VarsaniAbstract:Background: In Africa and Asia, sugarcane is the host of at least seven different virus species in the genus Mastrevirus of the family Geminiviridae. However, with the exception of Sugarcane white streak virus in Barbados, no other sugarcane-infecting Mastrevirus has been reported in the New World. Conservation and exchange of sugarcane germplasm using stalk cuttings facilitates the spread of sugarcane-infecting viruses. Methods: A virion-associated nucleic acids (VANA)-based metagenomics approach was used to detect Mastrevirus sequences in 717 sugarcane samples from Florida (USA), Guadeloupe (French West Indies), and Reunion (Mascarene Islands). Contig assembly was performed using CAP3 and sequence searches using BLASTn and BLASTx. Mastrevirus full genomes were enriched from total DNA by rolling circle amplification, cloned and sequenced. Nucleotide and amino acid sequence identities were determined using SDT v1.2. Phylogenetic analyses were conducted using MEGA6 and PHYML3. Results: We identified a new sugarcane-infecting Mastrevirus in six plants sampled from germplasm collections in Florida and Guadeloupe. Full genome sequences were determined and analyzed for three virus isolates from Florida, and three from Guadeloupe. These six genomes share > 88% genome-wide pairwise identity with one another and between 89 and 97% identity with a recently identified Mastrevirus (KR150789) from a sugarcane plant sampled in China. Sequences similar to these were also identified in sugarcane plants in Reunion. Conclusions: As these virus isolates share < 64% genome-wide identity with all other known Mastreviruses, we propose classifying them within a new Mastrevirus species named Sugarcane striate virus. This is the first report of sugarcane striate virus (SCStV) in the Western Hemisphere, a virus that most likely originated in Asia. The distribution, vector, and impact of SCStV on sugarcane production remains to be determined.
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Novel Mastreviruses identified in Australian wild rice
Virus Research, 2017Co-Authors: Simona Kraberger, Darren P Martin, Andrew D. W. Geering, Matthew Walters, Arvind VarsaniAbstract:Most known Mastreviruses (family Geminiviridae) infect members of the grass family, Poaceae. Although the greatest number of grass-infecting Mastrevirus species have been discovered in Africa, it is apparent that the ten grass-infecting Mastrevirus species that have so far only been discovered in south-east Queensland have a degree of diversity that rivals that observed in Africa. In this study, we have used a deep sequencing approach to identify two new Mastrevirus species, tentatively named rice latent virus 1 and 2 (RLV 1 and 2), from two, undescribed wild rice species (Oryza AA genome group) in Cape York Peninsula, Queensland. The sequences of these new viruses had less than 70% identity with any previously identified Mastrevirus, and therefore their discovery vastly expands the known diversity of monocot-infecting Mastreviruses in Australia. This study also highlights the potential risks of novel crop pathogens emerging from uncultivated grass species, as the wild rice hosts are very closely related to domesticated rice.
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New strains of chickpea chlorotic dwarf virus discovered on diseased papaya and tomato plants in Burkina Faso
Archives of Virology, 2017Co-Authors: Alassane Ouattara, Arvind Varsani, Sohini Claverie, Pierre Lefeuvre, Fidèle Tiendrebeogo, Murielle Hoareau, Edgar Valentin Traoré, Nicolas Barro, Oumar Traoré, Jean-michel LettAbstract:This is the first description of full genome sequences of chickpea chlorotic dwarf virus (CpCDV; genus Mastrevirus; family Geminiviridae) identified in papaya and tomato plants sampled in Burkina Faso. The CpCDV full genome sequences from papaya and tomato share the highest pairwise sequence identity (84% and 93.5%) with Sudanese isolates of the CpCDV-K and CpCDV-M strains, respectively. Based on the strain demarcation threshold (>94% identity) for Mastreviruses, we propose two new strains, CpCDV-Q and CpCDV-R, identified in papaya and tomato, respectively. Phylogenetic analysis confirmed that the sequences belong to a distinct clade of the highly diverse population of CpCDVs. Evidence of inter-strain recombination provided more support for the important role of recombination in CpCDV evolution. The discovery of CpCDV on papaya, a previously unsuspected host, raises many questions about the natural and potential host range of this dicot-infecting Mastrevirus species that is reported to be emerging worldwide.
Darren P Martin - One of the best experts on this subject based on the ideXlab platform.
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Exploring the diversity of Poaceae-infecting Mastreviruses on Reunion Island using a viral metagenomics-based approach
Scientific Reports, 2019Co-Authors: Sohini Claverie, Jean-michel Lett, Arvind Varsani, Darren P Martin, Denis Filloux, Philippe Roumagnac, Alassane Ouattara, Murielle Hoareau, Pierre LefeuvreAbstract:Mostly found in Africa and its surrounding islands, African streak viruses (AfSV) represent the largest group of known Mastreviruses. Of the thirteen AfSV species that are known to infect either cultivated or wild Poaceae plant species, six have been identified on Reunion Island. To better characterize AfSV diversity on this island, we undertook a survey of a small agroecosystem using a new metagenomics-based approach involving rolling circle amplification with random PCR amplification tagging (RCA-RA-PCR), high-throughput sequencing (Illumina HiSeq) and the Mastrevirus reads classification using phylogenetic placement. Mastreviruses that likely belong to three new species were discovered and full genome sequences of these were determined by Sanger sequencing. The geminivirus-focused metagenomics approach we applied in this study was useful in both the detection of known and novel Mastreviruses. The results confirm that Reunion Island is indeed a hotspot of AfSV diversity and that many of the Mastrevirus species have likely been introduced multiple times. Applying a similar approach in other natural and agricultural environments should yield sufficient detail on the composition and diversity of geminivirus communities to precipitate major advances in our understanding of the ecology and the evolutionary history of this important group of viruses.
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occurrence of a novel Mastrevirus in sugarcane germplasm collections in florida guadeloupe and reunion
Virology Journal, 2017Co-Authors: Wardatou Boukari, Jean-michel Lett, Simona Kraberger, Darren P Martin, Ricardo Ivan Alcalabriseno, Emmanuel Fernandez, Denis Filloux, Jeanheinrich Daugrois, Jack C Comstock, Arvind VarsaniAbstract:Background: In Africa and Asia, sugarcane is the host of at least seven different virus species in the genus Mastrevirus of the family Geminiviridae. However, with the exception of Sugarcane white streak virus in Barbados, no other sugarcane-infecting Mastrevirus has been reported in the New World. Conservation and exchange of sugarcane germplasm using stalk cuttings facilitates the spread of sugarcane-infecting viruses. Methods: A virion-associated nucleic acids (VANA)-based metagenomics approach was used to detect Mastrevirus sequences in 717 sugarcane samples from Florida (USA), Guadeloupe (French West Indies), and Reunion (Mascarene Islands). Contig assembly was performed using CAP3 and sequence searches using BLASTn and BLASTx. Mastrevirus full genomes were enriched from total DNA by rolling circle amplification, cloned and sequenced. Nucleotide and amino acid sequence identities were determined using SDT v1.2. Phylogenetic analyses were conducted using MEGA6 and PHYML3. Results: We identified a new sugarcane-infecting Mastrevirus in six plants sampled from germplasm collections in Florida and Guadeloupe. Full genome sequences were determined and analyzed for three virus isolates from Florida, and three from Guadeloupe. These six genomes share > 88% genome-wide pairwise identity with one another and between 89 and 97% identity with a recently identified Mastrevirus (KR150789) from a sugarcane plant sampled in China. Sequences similar to these were also identified in sugarcane plants in Reunion. Conclusions: As these virus isolates share < 64% genome-wide identity with all other known Mastreviruses, we propose classifying them within a new Mastrevirus species named Sugarcane striate virus. This is the first report of sugarcane striate virus (SCStV) in the Western Hemisphere, a virus that most likely originated in Asia. The distribution, vector, and impact of SCStV on sugarcane production remains to be determined.
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Novel Mastreviruses identified in Australian wild rice
Virus Research, 2017Co-Authors: Simona Kraberger, Darren P Martin, Andrew D. W. Geering, Matthew Walters, Arvind VarsaniAbstract:Most known Mastreviruses (family Geminiviridae) infect members of the grass family, Poaceae. Although the greatest number of grass-infecting Mastrevirus species have been discovered in Africa, it is apparent that the ten grass-infecting Mastrevirus species that have so far only been discovered in south-east Queensland have a degree of diversity that rivals that observed in Africa. In this study, we have used a deep sequencing approach to identify two new Mastrevirus species, tentatively named rice latent virus 1 and 2 (RLV 1 and 2), from two, undescribed wild rice species (Oryza AA genome group) in Cape York Peninsula, Queensland. The sequences of these new viruses had less than 70% identity with any previously identified Mastrevirus, and therefore their discovery vastly expands the known diversity of monocot-infecting Mastreviruses in Australia. This study also highlights the potential risks of novel crop pathogens emerging from uncultivated grass species, as the wild rice hosts are very closely related to domesticated rice.
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ICTV Virus Taxonomy Profile: Geminiviridae
Journal of General Virology, 2017Co-Authors: F. Murilo Zerbini, Rob W. Briddon, Darren P Martin, Philippe Roumagnac, Enrique Moriones, Ali M. Idris, Jesús Navas-castillo, Rafael F. Rivera-bustamante, Arvind VarsaniAbstract:The geminiviruses are a family of small, non-enveloped viruses with single-stranded, circular DNA genomes of 2500–5200 bases. Geminiviruses are transmitted by various types of insect (whiteflies, leafhoppers, treehoppers and aphids). Members of the genus Begomovirus are transmitted by whiteflies, those in the genera Becurtovirus, Curtovirus, Grablovirus, Mastrevirus and Turncurtovirus are transmitted by specific leafhoppers, the single member of the genus Topocuvirus is transmitted by a treehopper and one member of the genus Capulavirus is transmitted by an aphid. Geminiviruses are plant pathogens causing economically important diseases in most tropical and subtropical regions of the world. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the Geminiviridae which is available at www.ictv.global/report/geminiviridae.
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identification of an australian like dicot infecting Mastrevirus in pakistan
Archives of Virology, 2015Co-Authors: Simona Kraberger, Rob W. Briddon, Arvind Varsani, Darren P Martin, Sohini Claverie, Huma MumtazAbstract:Although members of five distinct viral species in the genus Mastrevirus (family Geminiviridae) infect dicotyledonous plants in Australia, in the remainder of the world, only a single dicot-infecting Mastrevirus, chickpea chlorotic dwarf virus (CpCDV) has ever been identified. This virus has been found infecting leguminous hosts in Africa, the Middle East and the Indian subcontinent. To further explore the diversity of CpCDV in Pakistan, ten full Mastrevirus genome sequences from chickpea and lentil plants were determined. Eight of these genomes were from previously described CpCDV strains and included the first reported strain D and H isolates in Pakistan. Two other genomes derived from infected chickpea plants are more closely related to dicot-infecting Mastreviruses found in Australia than they are to CpCDV. These two divergent genomes shared less than 75 % genome-wide nucleotide sequence identity with other characterised Mastreviruses and therefore are likely to belong to a second species of dicot-infecting Mastreviruses outside of Australia. We propose naming this species Chickpea yellow dwarf virus. We discuss how the presence of chickpea yellow dwarf virus (CpYDV) in Pakistan weakens the hypothesis that Australia is the geographical origin of the dicot-infecting Mastreviruses.
Rob W. Briddon - One of the best experts on this subject based on the ideXlab platform.
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Molecular characterization of Chickpea chlorotic dwarf virus strain D in Chickpea (Cicer arietinum) from District Dera Ismail Khan Khyber Pakhtunkhwa, Pakistan
Cellular and Molecular Biology, 2019Co-Authors: Kamran Rashid, Nazia Nahid, Faiqah Ramzan, Muhammad Asaf Khan, Shabnum Shaheen, Ammara Nasim, Nazish Masood, Rob W. Briddon, Khadim HussainAbstract:Chickpea chlorotic dwarf virus (CpCDV), a member of genus Mastrevirus (family Geminiviridae) is an important viral pathogen of chickpea and other legume crops in Middle East, North Africa, India and Pakistan. Among sixteen known strains of CpCDV three are known to infect legume crops in Punjab province of Pakistan. In this study diversity of CpCDV was explored in Khyber Pakhtunkhwa (KP) province of Pakistan. In year 2016, during a survey in the chickpea growing areas of district Dera Ismail Khan, CpCDV infected plants were identified. Leaf samples were collected, and a diagnostic PCR confirmed mastreivrus infection in 4 out of 100 samples. From these samples full-length genome of CpCDV was amplified using specific back-to-back primers. Virus molecules were sequenced to their entirety and sequence analysis of a molecule KRF4 (GenBank accession # KY952837) showed the highest pair wise sequence identity of 97% with a CpCDV molecule (KM229787) isolated from chickpea plant. An SDT analysis revealed it to be the D strain of CpCDV and a recombination detection program (RDP) showed it to be a recombinant between C (KM229780) and L (KT634301) strains of CpCDV. Thus, further supporting the intra-species recombination for CpCDV and presence of the same strain in chickpea growing areas of Pakistan other than Punjab province. This is the first identification of CpCDV (genus Mastrevirus family Geminiviridae) from chickpea (Cicer arietinum) plants in District Dera Ismail Khan, KP province, Pakistan.
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ICTV Virus Taxonomy Profile: Geminiviridae
Journal of General Virology, 2017Co-Authors: F. Murilo Zerbini, Rob W. Briddon, Darren P Martin, Philippe Roumagnac, Enrique Moriones, Ali M. Idris, Jesús Navas-castillo, Rafael F. Rivera-bustamante, Arvind VarsaniAbstract:The geminiviruses are a family of small, non-enveloped viruses with single-stranded, circular DNA genomes of 2500–5200 bases. Geminiviruses are transmitted by various types of insect (whiteflies, leafhoppers, treehoppers and aphids). Members of the genus Begomovirus are transmitted by whiteflies, those in the genera Becurtovirus, Curtovirus, Grablovirus, Mastrevirus and Turncurtovirus are transmitted by specific leafhoppers, the single member of the genus Topocuvirus is transmitted by a treehopper and one member of the genus Capulavirus is transmitted by an aphid. Geminiviruses are plant pathogens causing economically important diseases in most tropical and subtropical regions of the world. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the Geminiviridae which is available at www.ictv.global/report/geminiviridae.
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identification of an australian like dicot infecting Mastrevirus in pakistan
Archives of Virology, 2015Co-Authors: Simona Kraberger, Rob W. Briddon, Arvind Varsani, Darren P Martin, Sohini Claverie, Huma MumtazAbstract:Although members of five distinct viral species in the genus Mastrevirus (family Geminiviridae) infect dicotyledonous plants in Australia, in the remainder of the world, only a single dicot-infecting Mastrevirus, chickpea chlorotic dwarf virus (CpCDV) has ever been identified. This virus has been found infecting leguminous hosts in Africa, the Middle East and the Indian subcontinent. To further explore the diversity of CpCDV in Pakistan, ten full Mastrevirus genome sequences from chickpea and lentil plants were determined. Eight of these genomes were from previously described CpCDV strains and included the first reported strain D and H isolates in Pakistan. Two other genomes derived from infected chickpea plants are more closely related to dicot-infecting Mastreviruses found in Australia than they are to CpCDV. These two divergent genomes shared less than 75 % genome-wide nucleotide sequence identity with other characterised Mastreviruses and therefore are likely to belong to a second species of dicot-infecting Mastreviruses outside of Australia. We propose naming this species Chickpea yellow dwarf virus. We discuss how the presence of chickpea yellow dwarf virus (CpYDV) in Pakistan weakens the hypothesis that Australia is the geographical origin of the dicot-infecting Mastreviruses.
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a distinct strain of chickpea chlorotic dwarf virus genus Mastrevirus family geminiviridae identified in cotton plants affected by leaf curl disease
Archives of Virology, 2014Co-Authors: Muhammad Tariq Manzoor, Muhammad Saleem Haider, Muhammad Ilyas, Muhammad Shafiq, Ahmad Ali Shahid, Rob W. BriddonAbstract:As part of a study to determine the diversity of whitefly-transmitted viruses (genus Begomovirus, family Geminiviridae) associated with cotton leaf curl disease in Pakistan, leaf samples from cotton plants showing typical leaf curl disease symptoms were collected in various locations of Punjab province. Sequence analysis of full-length virus clones (~2.7 kb) showed plants to be infected with the begomovirus cotton leaf curl Burewala virus, the only virus identified in cotton in the Punjab since 2001. Surprisingly, a second virus, the leafhopper-transmitted chickpea chlorotic dwarf virus (CpCDV) of the genus Mastrevirus (family Geminiviridae), was identified in a small number of plants. The sequences of four CpCDV isolates from cotton originating from geographically distinct areas in Punjab were obtained. Analysis of the sequences showed them to represent a distinct, newly identified strain of CpCDV with the highest levels of nucleotide sequence identity to isolates of CpCDV strains C and D that have been identified previously in Pakistan. CpCDV has not been identified previously in cotton. The significance of this finding is discussed.
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A Distinct Strain of Chickpea chlorotic dwarf virus Infecting Pepper in Oman
Plant Disease, 2014Co-Authors: Sohail Akhtar, A. J. Khan, Rob W. BriddonAbstract:During a field survey in 2011, pepper (Capsicum annum) plants showing symptoms suggestive of geminivirus infection were observed in three fields in the Al-Sharqiya region of Oman. Symptoms observed included upward leaf curling leading to cupping and stunting with 15 to 25% disease incidence in surveyed fields. Total DNA was extracted from the leaves of seven symptomatic plants and subjected to rolling circle amplification (RCA). The RCA product was digested with several restriction endonucleases to obtain unit length of ~2.6 to 2.8, typical of geminivirus. Out of seven samples, only four yielded a product of ~2.6 kb in size by KpnI digestion. The fragments were cloned in pUC19 and sequenced. The partial sequences of four isolates were >95% identical to each other at the nucleotide (nt) level and thus only one isolate (P-25) was fully sequenced, determined to be 2,572 nt in length, and its sequence deposited in GenBank (KF111683). The P-25 sequence showed a genome organization typical of a Mastrevirus, wit...
Simona Kraberger - One of the best experts on this subject based on the ideXlab platform.
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occurrence of a novel Mastrevirus in sugarcane germplasm collections in florida guadeloupe and reunion
Virology Journal, 2017Co-Authors: Wardatou Boukari, Jean-michel Lett, Simona Kraberger, Darren P Martin, Ricardo Ivan Alcalabriseno, Emmanuel Fernandez, Denis Filloux, Jeanheinrich Daugrois, Jack C Comstock, Arvind VarsaniAbstract:Background: In Africa and Asia, sugarcane is the host of at least seven different virus species in the genus Mastrevirus of the family Geminiviridae. However, with the exception of Sugarcane white streak virus in Barbados, no other sugarcane-infecting Mastrevirus has been reported in the New World. Conservation and exchange of sugarcane germplasm using stalk cuttings facilitates the spread of sugarcane-infecting viruses. Methods: A virion-associated nucleic acids (VANA)-based metagenomics approach was used to detect Mastrevirus sequences in 717 sugarcane samples from Florida (USA), Guadeloupe (French West Indies), and Reunion (Mascarene Islands). Contig assembly was performed using CAP3 and sequence searches using BLASTn and BLASTx. Mastrevirus full genomes were enriched from total DNA by rolling circle amplification, cloned and sequenced. Nucleotide and amino acid sequence identities were determined using SDT v1.2. Phylogenetic analyses were conducted using MEGA6 and PHYML3. Results: We identified a new sugarcane-infecting Mastrevirus in six plants sampled from germplasm collections in Florida and Guadeloupe. Full genome sequences were determined and analyzed for three virus isolates from Florida, and three from Guadeloupe. These six genomes share > 88% genome-wide pairwise identity with one another and between 89 and 97% identity with a recently identified Mastrevirus (KR150789) from a sugarcane plant sampled in China. Sequences similar to these were also identified in sugarcane plants in Reunion. Conclusions: As these virus isolates share < 64% genome-wide identity with all other known Mastreviruses, we propose classifying them within a new Mastrevirus species named Sugarcane striate virus. This is the first report of sugarcane striate virus (SCStV) in the Western Hemisphere, a virus that most likely originated in Asia. The distribution, vector, and impact of SCStV on sugarcane production remains to be determined.
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Novel Mastreviruses identified in Australian wild rice
Virus Research, 2017Co-Authors: Simona Kraberger, Darren P Martin, Andrew D. W. Geering, Matthew Walters, Arvind VarsaniAbstract:Most known Mastreviruses (family Geminiviridae) infect members of the grass family, Poaceae. Although the greatest number of grass-infecting Mastrevirus species have been discovered in Africa, it is apparent that the ten grass-infecting Mastrevirus species that have so far only been discovered in south-east Queensland have a degree of diversity that rivals that observed in Africa. In this study, we have used a deep sequencing approach to identify two new Mastrevirus species, tentatively named rice latent virus 1 and 2 (RLV 1 and 2), from two, undescribed wild rice species (Oryza AA genome group) in Cape York Peninsula, Queensland. The sequences of these new viruses had less than 70% identity with any previously identified Mastrevirus, and therefore their discovery vastly expands the known diversity of monocot-infecting Mastreviruses in Australia. This study also highlights the potential risks of novel crop pathogens emerging from uncultivated grass species, as the wild rice hosts are very closely related to domesticated rice.
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Molecular diversity, geographic distribution and host range of monocot-infecting Mastreviruses in Africa and surrounding islands
Virus Research, 2017Co-Authors: Simona Kraberger, Daniel Pande, Salem Saumtally, Michel H.r. Khoodoo, Sonalall Dhayan, Asha Dookun-saumtally, Dionne N. Shepherd, Penelope Hartnady, Richard Atkinson, Francisco LakayAbstract:Abstract Maize streak virus (MSV), an important pathogen of maize in Africa, is the most extensively studied member of the Mastrevirus genus in the family Geminiviridae. Comparatively little is known about other monocot-infecting African Mastreviruses, most of which infect uncultivated grasses. Here we determine the complete sequences of 134 full African Mastrevirus genomes from predominantly uncultivated Poaceae species. Based on established taxonomic guidelines for the genus Mastrevirus, these genomes could be classified as belonging to the species Maize streak virus, Eragrostis minor streak virus, Maize streak Reunion virus, Panicum streak virus, Sugarcane streak Reunion virus and Sugarcane streak virus. Together with all other publicly available African monocot-infecting Mastreviruses, the 134 new isolates extend the known geographical distributions of many of these species, including MSV which we found infecting Digitaria sp. on the island of Grand Canaria: the first definitive discovery of any African monocot-infecting Mastreviruses north-west of the Saharan desert. These new isolates also extend the known host ranges of both African Mastrevirus species and the strains within these. Most notable was the discovery of MSV-C isolates infecting maize which suggests that this MSV strain, which had previously only ever been found infecting uncultivated species, may be in the process of becoming adapted to this important staple crop.
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metagenomics based discovery and molecular characterization of a novel sugarcane Mastrevirus p13
Livre des résumés des 16 ème Rencontres de virologie végétale, 2017Co-Authors: Emmanuel Fernandez, Jean-michel Lett, Simona Kraberger, Wardatou Boukari, Ricardo Ivan Alcalabriseno, Denis Filloux, Jeanheinrich Daugrois, Jack C Comstock, Pierre Lefeuvre, Arvind VarsaniAbstract:A viral metagenomics-based study of the viromes of Saccharum species from Florida, Reunion, Guadeloupe, and Cirad's sugarcane quarantine in Montpellier, France, was carried out using the virion-associated nucleic acid (VANA) approach. The goal of this study was to identify known and potentially new sugarcane viruses. This study revealed the presence of a potential new Mastrevirus species infecting Saccharum species in Florida, Guadeloupe and Reunion. Seventeen full genome sequences (2738-2749 nt long) were obtained using either rolling circle amplification followed by enzymatic restriction, or PCR using back-to-back primers, followed by cloning of full length restricted fragment or full length amplicon and Sanger sequencing. Three full genome sequences were obtained from S. barberi (Florida), five from S. officinarum (Florida and Guadeloupe), four from S. spontaneum (Florida) and five from sugarcane hybrids (Guadeloupe). BLASTn and BLASTx comparisons between these 17 genome sequences and all sequences in GenBank resulted in the highest identity score with a recently deposited geminivirus genome isolated from sugarcane in China (KR150789, highest percentage identity = 89%, e-value = 0.0). Based on the distribution of pairwise identity scores yielded by the species demarcation tool (SDTv1.2), and using Mastrevirus species demarcation threshold of >78 %, we propose that all 18 genomic sequences (17 from our study and KR150789 from China) belong to the same species of Mastrevirus. ,Because this novel Mastrevirus species has never been tested in routine quarantine detection assays, it most likely occurs in several countries of Africa, America, Asia and the Caribbean Islands. In order to develop a new molecular diagnostic assay, we designed specific detection primers using the alignment of the 18 full available genomes. This assay will be used to screen the 2016 variety collection of Cirad's sugarcane quarantine for the presence of the new Mastrevirus species. Results of this screening and analysis of the genetic diversity of the produced amplicons will be presented. (Resume d'auteur)
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identification of a new Mastrevirus of saccharum barberi saccharum officinarum and saccharum spontaneum in florida
2016Co-Authors: Wardatou Boukari, Arvind Varsani, Simona Kraberger, Ricardo Ivan Alcalabriseno, Emmanuel Fernandez, Denis Filloux, Jack C Comstock, Philippe Roumagnac, Jane E Polston, Philippe RottAbstract:A metagenomic study was conducted to identify viruses present in 180 leaf samples of Saccharum species collected in 2013/2014 from plants in commercial fields in the Everglades Agricultural Area and the germplasm collection of the USDA-ARS Sugarcane Field station at Canal Point, FL. The objective of this study was to identify known and potentially new sugarcane viruses. In addition to previously reported sugarcane viruses in Florida, we identified the presence of a potential new Mastrevirus species. Since there are no Mastrevirus species reported from Florida, and species in this genus such as Sugarcane streak virus and Maize streak virus are known to cause diseases in sugarcane, efforts were made to obtain full length viral genome sequences from individual plants of Saccharum spp. Rolling circle amplification followed by enzymatic restriction and cloning was used to obtain nine full genome length sequences (each approximately 2.8 kb): three from S. barberi, two from S. officinarum and four from S. spontaneum, all from the germplasm collection. All nine genome sequences appeared to represent a new species of Mastrevirus after their pairwise comparison using the species demarcation tool (SDTversion1.2). Sequence similarity among sequences also suggested the presence of two strains of this new virus. This new species was found in plants that were introduced to Florida more than six decades ago. (Texte integral)
Rakesh Tuli - One of the best experts on this subject based on the ideXlab platform.
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correction for kumar et al association of satellites with a Mastrevirus in natural infection complexity of wheat dwarf india virus disease
Journal of Virology, 2014Co-Authors: Jitendra Kumar, Sudhir P Singh, Jitesh Kumar, Rakesh TuliAbstract:Volume 88, no. 12, p. [7093–7104][1], 2014. Page 7100: [Fig 6][2]. and its legend should appear as shown below. ![FIG 6][3] FIG 6 Accumulation of virus and virus-derived siRNA in different tissues of wheat plants infected with WDIV or WDIV with the satellites. (A) Agroinoculated wheat
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βc1 is a pathogenicity determinant not only for begomoviruses but also for a Mastrevirus
Archives of Virology, 2014Co-Authors: Jitendra Kumar, Sudhir P Singh, Jitesh Kumar, Rakesh TuliAbstract:βC1 proteins, encoded by betasatellites, are known to be pathogenicity determinants, and they are responsible for symptom expression in many devastating diseases caused by begomoviruses. We report the involvement of βC1 in pathogenicity determination of a Mastrevirus. Analysis of field samples of wheat plants containing wheat dwarf India virus (WDIV) revealed the presence of a full-length and several defective betasatellite molecules. The detected betasatellite was identified as ageratum yellow leaf curl betasatellite (AYLCB). No begomovirus was detected in any of the samples. The full-length AYLCB contained an intact βC1 gene, whereas the defective molecules contained complete or partial deletions of βC1. Agroinoculation of wheat with the full-length AYLCB and WDIV or of tobacco with ageratum enation virus enhanced the pathogenicity and accumulation of the respective viruses, whereas the defective molecules could not. This study indicates that βC1 is a pathogenicity determinant for WDIV and can interact functionally not only with begomoviruses but also with a Mastrevirus.
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association of satellites with a Mastrevirus in natural infection complexity of wheat dwarf india virus disease
Journal of Virology, 2014Co-Authors: Jitesh Kumar, Sudhir P Singh, Rakesh TuliAbstract:In contrast to begomoviruses, Mastreviruses have not previously been shown to interact with satellites. This study reports the first identification of the association of satellites with a Mastrevirus in field-grown plants. Two alphasatellite species were detected in different field samples of wheat infected with Wheat Dwarf India Virus (WDIV), a Cotton leaf curl Multan alphasatellite (CLCuMA) and a Guar leaf curl alphasatellite (GLCuA). In addition to the alphasatellites, a betasatellite, Ageratum yellow leaf curl betasatellite (AYLCB), was also identified in the wheat samples. No begomovirus was detected in the wheat samples, thus establishing association of the above-named satellites with WDIV. Agrobacterium-mediated inoculation of WDIV in wheat, in the presence of either of the alphasatellites or the betasatellite, resulted in infections inducing more severe symptoms. WDIV efficiently maintained each of the alphasatellites and the betasatellite in wheat. The satellites enhanced the level of WDIV DNA in wheat. Inoculation of the satellites isolated from wheat with various begomoviruses into Nicotiana tabacum demonstrated that these remain capable of interacting with the viruses with which they were first identified. Virus-specific small RNAs accumulated in wheat upon infection with WDIV but were lower in abundance in plants coinfected with the satellites, suggesting that both the alphasatellites and the betasatellite suppress RNA silencing. These results suggest that the selective advantage for the maintenance of the alphasatellites and the betasatellite by WDIV in the field is in overcoming RNA silencing-mediated host defense. IMPORTANCE Wheat is the most widely cultivated cereal crop in the world. A number of viruses are important pathogens of wheat, including the viruses of the genus Mastrevirus, family Geminiviridae. This study reports the association of subgenomic components, called satellites (alpha- and betasatellites), with a Mastrevirus, Wheat Dwarf India Virus (WDIV), isolated from two distant locations in India. This study reports the first identification of the satellites in a monocot plant. The satellites enhanced accumulation of WDIV and severity of disease symptoms. The satellites lowered the concentration of virus-specific small RNAs in wheat plants, indicating their silencing suppressor activity. The involvement of the satellites in symptom severity of the Mastrevirus can have implications in the form of economic impact of the virus on crop yield. Understanding the role of the satellites in disease severity is important for developing disease management strategies.
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a novel Mastrevirus infecting wheat in india
Archives of Virology, 2012Co-Authors: Jitendra Kumar, Sudhir P Singh, Jitesh Kumar, Rakesh TuliAbstract:A new Mastrevirus (family Geminivridae) infecting wheat in India was detected by rolling-circle amplification (RCA). The complete nucleotide sequence of the virus was determined to be 2783 bp long. Analysis of the nucleotide sequence revealed identity and a genome organisation typical of a Mastrevirus. An identical virus was detected in the candidate insect vector (leafhopper) collected from the field. Agroinoculation of young wheat plants with an infectious clone of the virus resulted in dwarfing of plants, identical to what was observed in the field, confirming that this novel virus was the causative agent of the disease. Considering the low degree of sequence identity to any known Mastrevirus, the virus described here is suggested to be a member of a new species. Based on symptoms, we propose the name “wheat dwarf India virus”.