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Thierry Candresse - One of the best experts on this subject based on the ideXlab platform.
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Unravelling the virome in birch: RNA-Seq reveals a complex of known and novel viruses
PLoS ONE, 2020Co-Authors: Artemis Rumbou, Laurence Svanella-dumas, Armelle Marais, Thierry Candresse, Maria Landgraf, Susanne Von Bargen, Carmen BüttnerAbstract:To unravel the virome in birch trees of German and Finnish origin exhibiting symptoms of birch leaf-roll disease (BRLD), high-throughput sequencing (HTS) was employed. In total five viruses, among which three were so far unknown, were detected by RNAseq. One to five virus variants were identified in the transcriptome of individual trees. The novel viruses were genetically-fully or partially-characterized, belonging to the genera Carlavirus, Idaeovirus and Capillovirus and are tentatively named birch carlavirus, birch idaeovirus, and birch Capillovirus, respectively. The recently discovered birch leafroll-associated virus was systematically detected by HTS in symptomatic seedlings but not in symptomless ones. The new carlavirus was detected only in one of the three symptomatic seedlings. The novel puta-tive Capillovirus was detected in all seedlings-irrespective of their BLRD status-while the Idaeovirus was identified in a plant without leaf symptoms at the time of sampling. Further efforts are needed to complete Koch's postulates and to clarify the possible association of the detected viruses with the BLR disease. Our study elucidates the viral population in single birch seedlings and provides a comprehensive overview for the diversities of the viral communities they harbor, to date.
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Unravelling the virome in birch: RNA-Seq reveals a complex of known and novel viruses
2019Co-Authors: Artemis Rumbou, Laurence Svanella-dumas, Armelle Marais, Thierry Candresse, Maria Landgraf, Susanne Von Bargen, Carmen BüttnerAbstract:Abstract High-throughput sequencing (HTS), combined with bioinformatics for de novo discovery and assembly of plant virus or viroid genome reads, has promoted the discovery of abundant novel DNA and RNA viruses and viroids. However, the elucidation of a viral population in a single plant is rarely reported. In five birch trees of German and Finnish origin exhibiting symptoms of birch leaf-roll disease (BRLD), we identified in total five viruses, among which three are novel. The number of identified virus variants in each transcriptome ranged from one to five. The novel species are genetically - fully or partially - characterized, they belong to the genera Carlavirus, Idaeovirus and Capillovirus and they are tentatively named birch carlavirus, birch idaeovirus, and birch Capillovirus, respectively. The only virus systematically detected by HTS in symptomatic trees affected by the BRLD was the recently discovered birch leafroll-associated virus. The role of the new carlavirus in BLRD etiology seems at best weak, as it was detected only in one of three symptomatic trees. Continuing studies have to clarify the impact of the carlavirus to the BLRD. The role of the Capillovirus and the Idaeovirus within the BLRD complex and whether they influence plant vitality need to be investigated. Our study reveals the viral population in single birch trees and provides a comprehensive overview for the diversities of the viral communities they harbor.
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Molecular Characterization of a Novel Species of Capillovirus from Japanese Apricot (Prunus mume).
Viruses, 2018Co-Authors: Armelle Marais, Chantal Faure, Sébastien Theil, Thierry CandresseAbstract:With the increased use of high-throughput sequencing methods, new viruses infecting Prunus spp. are being discovered and characterized, especially in the family Betaflexiviridae. Double-stranded RNAs from symptomatic leaves of a Japanese apricot (Prunus mume) tree from Japan were purified and analyzed by Illumina sequencing. Blast comparisons of reconstructed contigs showed that the P. mume sample was infected by a putative novel virus with homologies to Cherry virus A (CVA) and to the newly described Currant virus A (CuVA), both members of genus Capillovirus. Completion of the genome showed the new agent to have a genomic organization typical of Capilloviruses, with two overlapping open reading frames encoding a large replication-associated protein fused to the coat protein (CP), and a putative movement protein (MP). This virus shares only, respectively, 63.2% and 62.7% CP amino acid identity with the most closely related viruses, CVA and CuVA. Considering the species demarcation criteria in the family and phylogenetic analyses, this virus should be considered as representing a new viral species in the genus Capillovirus, for which the name of Mume virus A is proposed
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First Report of Apricot pseudo-chlorotic leaf spot virus Infecting Plum (Prunus domestica) in the Czech Republic
Plant Disease, 2012Co-Authors: Dana Šafářová, Chantal Faure, Milan Navrátil, Thierry Candresse, Armelle MaraisAbstract:Apricot pseudo-chlorotic leaf spot virus (APCLSV) is a novel, still poorly known Trichovirus in the family Betaflexiviridae. It is most closely related to Apple chlorotic leaf spot virus (ACLSV) (2,4) and infects stone fruit trees of the Prunus genus. Its presence has so far been detected in apricot, plum, Japanese plum, and peach trees in Italy, Spain, France, Hungary, Turkey, Jordan, and Australia (1,2,4). During the summers of 2008 and 2010, leaf samples of old Czech local plum cultivars were obtained from the Holovousy collection and assessed for the presence of viruses belonging to the Capillovirus, Trichovirus, and Foveavirus genera using the polyvalent degenerate oligonucleotides (PDO) nested reverse transcription (RT)-PCR test (3). Following amplification from total RNAs extracts, the amplicons were cloned and several clones were sequenced for each plant sample. In plum (Prunus domestica) cv. Babce, a mixture of amplicons was observed and BlastN and BlastX analyses of the obtained sequences reveal...
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Development of a polyvalent RT-PCR detection assay covering the genetic diversity of Cherry Capillovirus A
Plant Pathology, 2012Co-Authors: Armelle Marais, Laurence Svanella-dumas, Pascal Gentit, Chantal Faure, A. Ragozzino, M. Barone, G. Charlot, Thierry CandresseAbstract:The variability of Cherry Capillovirus A (CVA) was analysed using a short, 275-bp region of the viral RNA-dependent RNA polymerase gene amplified by a polyvalent RT-PCR assay. As for other members of the family Betaflexiviridae, CVA appears to show significant diversity, with an average pairwise nucleotide divergence of 9·4% between isolates in the analysed region. Phylogenetic analyses provide evidence for the existence of at least five clusters of CVA isolates, one of which is associated with noncherry hosts of the virus, providing evidence that transmission of CVA isolates between cherry and noncherry hosts is probably rare. Comparison of existing detection techniques using a panel of CVA isolates representative of the various phylogenetic groups indicated that dot-blot hybridization assays show high polyvalence but may lack the sensitivity to detect CVA in some samples. On the other hand, available detection primers failed to amplify a wide range of CVA isolates. Partial genome sequencing of two divergent isolates allowed the identification of conserved genomic regions and the design of new primer pairs with improved polyvalence. These new primer pairs were used to develop PCR assays allowing the reliable detection of CVA isolates belonging to all phylogenetic clusters.
Claudio Ratti - One of the best experts on this subject based on the ideXlab platform.
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First Report of Apple chlorotic leaf spot virus, Cherry green ring mottle virus, and Cherry necrotic rusty mottle virus on Peach in Montenegro.
Plant Disease, 2014Co-Authors: J. Zindovic, Mattia Dall’ara, C. Rubies Autonell, Claudio RattiAbstract:The sanitary status of peach fruit trees was assessed in central and coastal regions of Montenegro during a survey in September and October of 2011 and 2012. Leaf samples were collected from 58 (2011) and 47 (2012) trees showing chlorotic rings and spots, mosaic, necrosis, leaf distortion, and stunting. Total RNAs was extracted from each sample by RNeasy Plant Mini kit (Qiagen, Germany) and used as a template in PDO (polyvalent degenerate oligonucleotides) nested reverse transcription (RT)-PCR for the detection of fruit tree viruses belonging to the genera Trichovirus, Capillovirus, and Foveavirus (family Betaflexiviridae). PDO primer sets PDO-F1i/PDO-R3i/PDO-R4i and PDO-F2i/PDO-R1i (2) were used in the first RT-PCR and nested PCR, respectively. Total RNAs obtained from Italian Apple chlorotic leaf spot virus (ACLSV)-infected isolate and healthy peach leaves were used as positive and negative controls, respectively. A nested set of primers amplified a 362-bp product from 6 samples collected in 2011 (10.3%...
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First Report of Apple chlorotic leaf spot virus, Cherry green ring mottle virus, and Cherry necrotic rusty mottle virus on Peach in Montenegro.
Plant disease, 2014Co-Authors: J. Zindovic, C. Rubies Autonell, Mattia Dall’ara, Claudio RattiAbstract:The sanitary status of peach fruit trees was assessed in central and coastal regions of Montenegro during a survey in September and October of 2011 and 2012. Leaf samples were collected from 58 (2011) and 47 (2012) trees showing chlorotic rings and spots, mosaic, necrosis, leaf distortion, and stunting. Total RNAs was extracted from each sample by RNeasy Plant Mini kit (Qiagen, Germany) and used as a template in PDO (polyvalent degenerate oligonucleotides) nested reverse transcription (RT)-PCR for the detection of fruit tree viruses belonging to the genera Trichovirus, Capillovirus, and Foveavirus (family Betaflexiviridae). PDO primer sets PDO-F1i/PDO-R3i/PDO-R4i and PDO-F2i/PDO-R1i (2) were used in the first RT-PCR and nested PCR, respectively. Total RNAs obtained from Italian Apple chlorotic leaf spot virus (ACLSV)-infected isolate and healthy peach leaves were used as positive and negative controls, respectively. A nested set of primers amplified a 362-bp product from 6 samples collected in 2011 (10.3%) and 13 samples collected in 2012 (27.7%). Sequence analysis included three isolates (367/11, 133/12, and 168/12) chosen from different peach cultivars (Ritastar, Spring Belle, and Redhaven, respectively). Amplified products of expected size of the partial RNA-dependent RNA polymerase from three positive samples were cloned into p-GEM-T Easy Vector (Promega, Madison, WI) and sequenced (MWG-Biotech AG, Germany). Sequences were deposited in GenBank under accession nos. KF534757, KF534769, and KF534766, respectively. BLAST analysis showed that the sequence of isolate 367/11 (KF534757) shared high nucleotide similarity (78.9 to 87.2%) with ACLSV isolates from GenBank, showing highest identity with isolate PBM1 (AJ243438) from Germany. Sequence analysis of isolate 133/12 (KF534769) proved that it is 90.5 to 93.3% identical to Cherry green ring mottle virus (CGRMV) isolates reported from other parts of the world. In particular, the highest nucleotide similarity was showed with isolate P1C124 (AJ291761) from France. Finally, analysis of sequence from the isolate 168/12 (KF534766) revealed high degree of identity (86.1 to 96.1%) with the corresponding nucleotide sequences of the Cherry necrotic rusty mottle virus (CNRMV) isolates, showing highest similarity with isolate 120/86 (AF237816) from Switzerland. To confirm virus infectivity, according to the FAO/IPGRI Technical Guidelines (1), budwood from 367/11, 133/12, and 168/12 samples were grafted into seedlings of peach (GF305), Prunus serrulata (cv. Shirofugen) and P. avium (cv. Sam) then maintained in a greenhouse with controlled conditions. Six months post inoculation, GF305 indexed with 367/11 sample reacts with a green depressed mottle on leaves typical of ACLSV infection. Cherry tree of cv. Shirofugen indexed with sample 133/12 showed symptoms attributable to CGRMV such as epinasty, twisting and curling of leaves while a tree of cv. Sam indexed with 168/12 sample exhibited classical necrotic shot holes in leaves induced by CNRMV infection (1). Sequence analysis of PCR products obtained from indicator plants by RT-PCR as described above showed full nucleotide identity with KF534757, KF534769, and KF534766 sequences and confirmed the presence of previous described viral agents. To our knowledge, this is the first report of ACLSV, CGRMV, and CNRMV occurrence on peach in Montenegro. Due to the economic importance of this crop, sanitation measures should be adopted to improve the control of imported plants and the use of virus-tested propagation material in order to prevent spreading of these viruses. References: (1) M. Diekmann and C. A. J. Putter. FAO/IPGRI Technical Guidelines for the Safe Movement of Germplasm. No. 16. Stone Fruits, 1996. (2) X. Foissac et al. Phytopathology 95:617, 2005.
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VIRUSES OF KIWIFRUIT (ACTINIDIA SPECIES)
Journal of Plant Pathology, 2013Co-Authors: Arnaud G. Blouin, Claudio Ratti, Michael N. Pearson, Ramesh R. Chavan, E.n.y. Woo, B.s.m. Lebas, S. Veerakone, R. Biccheri, Robin M. Macdiarmid, D. CohenAbstract:Kiwifruit (Actinidia deliciosa) was introduced to New Zealand more than one hundred years ago and the New Zealand-raised cv. Hayward is now the dominant cultivar grown worldwide. Further accessions of kiwifruit seed and scionwood have been sourced from China for research and breeding. In one importation consignment, the first virus naturally infecting kiwifruit, Apple stem grooving virus (ASGV), was identified following symptoms observed in quarantined plants (2003). Since that time a further 12 viruses have been identified in kiwifruit. We classify these 13 viruses into three groups. The first group comprises the non-specialist viruses and includes Alfalfa mosaic virus (AMV) and Cucumber mosaic virus (CMV) both members of the family Bromoviridae. The group also includes a further five viruses that appear to have limited effect on kiwifruit: two tobamoviruses, Ribgrass mosaic virus (RMV) and Turnip vein clearing virus (TVCV); a tombusvirus, Cucumber necrosis virus (CNV); a novel potexvirus; and Apple stem gooving virus (ASGV, genus Capillovirus). Most of the viruses classified in this first group are cosmopolitan and sometimes orchard weeds provide reservoirs for infection. The second group comprises the kiwifruit-adapted viruses. This group includes three novel viruses. i.e. two vitiviruses, Actinidia virus A (AcVA) and Actinidia virus B (AcVB), and a citrivirus closely related to Citrus leaf blotch virus (CLBV). In addition, preliminary evidence of a novel virus belonging to the Closteroviridae family has been obtained. The third group of viruses induces disease in kiwifruit. To date only two viruses have caused significant damage to kiwifruit within commercial orchards. In New Zealand, Cherry leaf roll virus (CLRV) has been detected on kiwifruit associated with symptoms including leaf spots, fruit malformation, reduction in yield, bark cracking and cane wilting. Pelargonium zonate spot virus (PZSV) has been detected in Italy associated with severe symptoms on leaves and fruit.
Armelle Marais - One of the best experts on this subject based on the ideXlab platform.
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Unravelling the virome in birch: RNA-Seq reveals a complex of known and novel viruses
PLoS ONE, 2020Co-Authors: Artemis Rumbou, Laurence Svanella-dumas, Armelle Marais, Thierry Candresse, Maria Landgraf, Susanne Von Bargen, Carmen BüttnerAbstract:To unravel the virome in birch trees of German and Finnish origin exhibiting symptoms of birch leaf-roll disease (BRLD), high-throughput sequencing (HTS) was employed. In total five viruses, among which three were so far unknown, were detected by RNAseq. One to five virus variants were identified in the transcriptome of individual trees. The novel viruses were genetically-fully or partially-characterized, belonging to the genera Carlavirus, Idaeovirus and Capillovirus and are tentatively named birch carlavirus, birch idaeovirus, and birch Capillovirus, respectively. The recently discovered birch leafroll-associated virus was systematically detected by HTS in symptomatic seedlings but not in symptomless ones. The new carlavirus was detected only in one of the three symptomatic seedlings. The novel puta-tive Capillovirus was detected in all seedlings-irrespective of their BLRD status-while the Idaeovirus was identified in a plant without leaf symptoms at the time of sampling. Further efforts are needed to complete Koch's postulates and to clarify the possible association of the detected viruses with the BLR disease. Our study elucidates the viral population in single birch seedlings and provides a comprehensive overview for the diversities of the viral communities they harbor, to date.
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Unravelling the virome in birch: RNA-Seq reveals a complex of known and novel viruses
2019Co-Authors: Artemis Rumbou, Laurence Svanella-dumas, Armelle Marais, Thierry Candresse, Maria Landgraf, Susanne Von Bargen, Carmen BüttnerAbstract:Abstract High-throughput sequencing (HTS), combined with bioinformatics for de novo discovery and assembly of plant virus or viroid genome reads, has promoted the discovery of abundant novel DNA and RNA viruses and viroids. However, the elucidation of a viral population in a single plant is rarely reported. In five birch trees of German and Finnish origin exhibiting symptoms of birch leaf-roll disease (BRLD), we identified in total five viruses, among which three are novel. The number of identified virus variants in each transcriptome ranged from one to five. The novel species are genetically - fully or partially - characterized, they belong to the genera Carlavirus, Idaeovirus and Capillovirus and they are tentatively named birch carlavirus, birch idaeovirus, and birch Capillovirus, respectively. The only virus systematically detected by HTS in symptomatic trees affected by the BRLD was the recently discovered birch leafroll-associated virus. The role of the new carlavirus in BLRD etiology seems at best weak, as it was detected only in one of three symptomatic trees. Continuing studies have to clarify the impact of the carlavirus to the BLRD. The role of the Capillovirus and the Idaeovirus within the BLRD complex and whether they influence plant vitality need to be investigated. Our study reveals the viral population in single birch trees and provides a comprehensive overview for the diversities of the viral communities they harbor.
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Molecular Characterization of a Novel Species of Capillovirus from Japanese Apricot (Prunus mume).
Viruses, 2018Co-Authors: Armelle Marais, Chantal Faure, Sébastien Theil, Thierry CandresseAbstract:With the increased use of high-throughput sequencing methods, new viruses infecting Prunus spp. are being discovered and characterized, especially in the family Betaflexiviridae. Double-stranded RNAs from symptomatic leaves of a Japanese apricot (Prunus mume) tree from Japan were purified and analyzed by Illumina sequencing. Blast comparisons of reconstructed contigs showed that the P. mume sample was infected by a putative novel virus with homologies to Cherry virus A (CVA) and to the newly described Currant virus A (CuVA), both members of genus Capillovirus. Completion of the genome showed the new agent to have a genomic organization typical of Capilloviruses, with two overlapping open reading frames encoding a large replication-associated protein fused to the coat protein (CP), and a putative movement protein (MP). This virus shares only, respectively, 63.2% and 62.7% CP amino acid identity with the most closely related viruses, CVA and CuVA. Considering the species demarcation criteria in the family and phylogenetic analyses, this virus should be considered as representing a new viral species in the genus Capillovirus, for which the name of Mume virus A is proposed
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First Report of Apricot pseudo-chlorotic leaf spot virus Infecting Plum (Prunus domestica) in the Czech Republic
Plant Disease, 2012Co-Authors: Dana Šafářová, Chantal Faure, Milan Navrátil, Thierry Candresse, Armelle MaraisAbstract:Apricot pseudo-chlorotic leaf spot virus (APCLSV) is a novel, still poorly known Trichovirus in the family Betaflexiviridae. It is most closely related to Apple chlorotic leaf spot virus (ACLSV) (2,4) and infects stone fruit trees of the Prunus genus. Its presence has so far been detected in apricot, plum, Japanese plum, and peach trees in Italy, Spain, France, Hungary, Turkey, Jordan, and Australia (1,2,4). During the summers of 2008 and 2010, leaf samples of old Czech local plum cultivars were obtained from the Holovousy collection and assessed for the presence of viruses belonging to the Capillovirus, Trichovirus, and Foveavirus genera using the polyvalent degenerate oligonucleotides (PDO) nested reverse transcription (RT)-PCR test (3). Following amplification from total RNAs extracts, the amplicons were cloned and several clones were sequenced for each plant sample. In plum (Prunus domestica) cv. Babce, a mixture of amplicons was observed and BlastN and BlastX analyses of the obtained sequences reveal...
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Development of a polyvalent RT-PCR detection assay covering the genetic diversity of Cherry Capillovirus A
Plant Pathology, 2012Co-Authors: Armelle Marais, Laurence Svanella-dumas, Pascal Gentit, Chantal Faure, A. Ragozzino, M. Barone, G. Charlot, Thierry CandresseAbstract:The variability of Cherry Capillovirus A (CVA) was analysed using a short, 275-bp region of the viral RNA-dependent RNA polymerase gene amplified by a polyvalent RT-PCR assay. As for other members of the family Betaflexiviridae, CVA appears to show significant diversity, with an average pairwise nucleotide divergence of 9·4% between isolates in the analysed region. Phylogenetic analyses provide evidence for the existence of at least five clusters of CVA isolates, one of which is associated with noncherry hosts of the virus, providing evidence that transmission of CVA isolates between cherry and noncherry hosts is probably rare. Comparison of existing detection techniques using a panel of CVA isolates representative of the various phylogenetic groups indicated that dot-blot hybridization assays show high polyvalence but may lack the sensitivity to detect CVA in some samples. On the other hand, available detection primers failed to amplify a wide range of CVA isolates. Partial genome sequencing of two divergent isolates allowed the identification of conserved genomic regions and the design of new primer pairs with improved polyvalence. These new primer pairs were used to develop PCR assays allowing the reliable detection of CVA isolates belonging to all phylogenetic clusters.
Tsuyoshi Takahashi - One of the best experts on this subject based on the ideXlab platform.
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Single-strand conformation polymorphism analysis of apple stem grooving Capillovirus sequence variants.
Phytopathology, 1999Co-Authors: H. Magome, N Yoshikawa, Tsuyoshi TakahashiAbstract:ABSTRACT In an earlier study, we demonstrated that isolates of apple stem grooving Capillovirus (ASGV) from fruit trees comprise at least two to four sequence variants that differ considerably from each other in nucleotide sequence. In order to characterize the population of sequence variants within a single tree, we applied a combination of an immunocapture reverse transcription-polymerase chain reaction (IC-RT-PCR) and a single-strand conformation polymorphism (SSCP) analysis of a nested asymmetric PCR product. In the SSCP analysis of the PCR products from ASGV-infected apple, Japanese pear, or European pear trees, two to four bands were detected in samples from all trees, indicating that ASGV exists as a mixture of sequence variants. The composition of sequence variants (the number of bands and their relative quantity) differed among leaf samples from different branches, showing that each sequence variant is distributed unevenly within an individual tree. The SSCP analysis of isolates after serial pass...
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Analysis of Double-stranded RNA in Tissues Infected with Apple Stem Grooving Capillovirus
Japanese Journal of Phytopathology, 1997Co-Authors: H. Magome, Nobuyuki Yoshikawa, Hidetaka Terauchi, Tsuyoshi TakahashiAbstract:Northern hybridization analyses using an RNA probe corresponding to the 3'-terminal region of apple stem grooving virus (ASGV) genome indicated that all dsRNA preparations from tissues infected with 10 ASGV isolates contained three virus-specific dsRNAs (6.5, 2.0 and 1.0 kbp). Using additional RNA probes corresponding to different parts of the genome, a dsRNA preparation from ASGV (isolate P-209)-infected tissues was found to contain five virus-specific dsRNAs of 6.5 kbp (G-ds), 5.5 kbp (ds1), 4.5 kbp (ds2), 2.0 kbp (SG-ds1) and 1.0 kbp (SG-ds2). G-ds was probably the replicative form of the ASGV-genome. Ds1 and ds2 were thought to be 5'-coterminal with the ASGV genome. In contrast, SG-ds1 and SG-ds2 were thought to be 3'-coterminal with the genome. Both the positions of these RNAs relative to the genome and their sizes suggest that SG-ds1 and SG-ds2 are ds forms of subgenomic RNAs for the ORF2-encoded protein and the coat protein (CP), respectively. The C-terminal regions of the ORF1-encoded protein including the CP were expressed in Escherichia coli. The size of the expressed protein, which starts with methionine (Met) at amino acid position 1869 agreed with that of ASGV-CP, suggesting this Met is the starting amino acid of the CP.
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Construction of an Infectious cDNA Clone of the Apple Stem Grooving Capillovirus (Isolate Li-23) Genome Containing a Cauliflower Mosaic Virus 35S RNA Promoter
Japanese Journal of Phytopathology, 1997Co-Authors: Hidetaka Terauchi, H. Magome, Nobuyuki Yoshikawa, Tsuyoshi Takahashi, Narinobu InouyeAbstract:The complete nucleotide sequence of the genome of apple stem grooving Capillovirus (ASGV) isolate Li-23 from lily was determined. The isolate Li-23 genome consists of 6496 nucleotides excluding poly(A) tail and contains two overlapping open reading frames (ORFs 1 and 2). ORF1 encodes a protein with a Mr 241, 768 (242K) and ORF2, in a different frame within ORF1, encodes a Mr 36, 179 (36K) protein. The number of nucleotides and the arrangement of ORFs of the isolate Li-23 genome are in perfect agreement with those of isolate P-209 from apple and isolate L from lily. Identities of the nucleotide sequences were 98.4% (Li-23/L) and 83.0% (Li-23/P-209) in whole genomes excluding poly(A) tail. A full-length cDNA clone (pCT35SF) of the isolate Li-23 genome was cloned into a plasmid vector containing cauliflower mosaic virus 35S RNA promoter which was designed to transcribe the isolate Li-23 genome from its first nucleotide. Mechanical inoculation of pCT35SF onto Chenopodium quinoa induced symptoms typical of isolate Li-23 infection. Virus particles, viral RNA and coat protein could be detected in pCT35SF-inoculated plants, demonstrating that pCT35SF is infectious.
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Apple stem grooving and citrus tatter leaf Capilloviruses obtained from a single shoot of Japanese pear (Pyrus serotina)
Japanese Journal of Phytopathology, 1996Co-Authors: Nobuyuki Yoshikawa, Tsuyoshi Takahashi, Kazutoshi Sasamoto, Manabu Sakurada, Haruo YanaseAbstract:By means of polymerase chain reactions, nucleotide sequence analyses of the 3'-terminal regions, and amino acid sequence analyses, two Capillovirus isolates, apple stem grooving (ASGV) and citrus tatter leaf virus (CTLV) were found from virus culture V3 obtained from a single shoot of Japanese pear (Pyrus serotina). V3 was originally presumed to be a pure culture of ASGV. The two isolates that were eventually determined to be different Capilloviruses were designated V3-1 and V3-2, respectively. V3-1 differed from ASGV reference isolate P-209 from apple by only 3 base substitutions in the 3'-terminal 2611 nucleotides. V3-2 was closer to CTLV reference isolates Li-23 (95.9% homology) and L (95.6% homology) from lilies in the sequence of its 3'-terminal 1669 nucleotides than it was to that of ASGV isolate P-209 (89.1% homology). In the comparison of ORF2 proteins (313 amino acids, aa) the similarity between as sequences of V3-2 and P-209 was 94.8%, while that between V3-2 and CTLV isolates (Li-23 and L) was 97.4%. In the case of the as sequence homology of the putative coat protein regions (237 aa), equivalent to the C-terminal region of ORF1 protein, the similarity between V3-2 and P-209 was 97.5% and was 99.2% between V3-2 and CTLV isolates (Li-23 and L). The most striking difference in aa sequence homologies was found in the ORF1 protein (277 aa) encoding ORF2 in the other frame. The similarity between V3-1 and P-209 was 99.3%, while that between V3-2 and P-209 was 61.0%. Isolate V3-2 shared 85.6% and 93.8% aa sequence homologies with Li-23 and L, respectively. Solely on the basis of comparison of nucleotide and amino acid sequences of Japanese pear isolates V3-1 and V3-2 with reference isolates, we conclude that V3-1 is almost identical to an ASGV reference isolate from apple, while V3-2 is similar to CTLV reference isolates from lilies. We recommend that CTLV be considered as a strain of ASGV.
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Striking similarities between the nucleotide sequence and genome organization of citrus tatter leaf and apple stem grooving Capilloviruses.
Journal of General Virology, 1993Co-Authors: N Yoshikawa, Tsuyoshi Takahashi, M. Imaizumi, N. InouyeAbstract:The sequence of the 3′-terminal 2956 nucleotides, excluding the poly(A) tail, of the citrus tatter leaf virus (CTLV) genome was determined and compared with that of the apple stem grooving virus (ASGV) genome. The sequence of the 3′-terminal region of CTLV contains two overlapping open reading frames (ORFs) and a 3′-terminal non-coding region of 142 nucleotides. The long, incomplete ORF1 ends at UAG (position 2812) and encodes a protein with at least 938 amino acids (M r > 108 703). This protein contains the GDD motif associated with the RNA polymerase. ORF2, in a different frame within ORF1, starts at AUG (position 1248) and stops at UGA (position 2208) encoding a protein with an M r of 36179 (36K). Partial homologies were found among the 36K protein of CTLV, the 50K protein of apple chlorotic leaf spot closterovirus, the 40K protein of potato virus T and the gene 1 products of caulimoviruses. The arrangement of ORFs in the 3′-terminal region of the CTLV genome is in perfect agreement with that of the ASGV genome. The sequence of the 3′-terminal 2956 nucleotides, excluding the poly(A) tail, of the CTLV genome shows 86.1% identity to that of the ASGV genome. Similarities of amino acid sequences encoded by ORF1 and ORF2 of CTLV with the corresponding regions of ASGV are 86.1% and 97.3%, respectively. These results indicate that CTLV is a Capillovirus closely related to ASGV.
N Yoshikawa - One of the best experts on this subject based on the ideXlab platform.
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Evidence for translation of apple stem grooving capiHovirus genomic RNA
2014Co-Authors: N Yoshikawa, T. TakahashiAbstract:Apple stem grooving virus (ASGV) RNA was trans-lated in a rabbit reticulocyte lysate system and shown to direct the synthesis of several polypeptides of Mr ranging from 200K to 43K. A polypeptide of 200K was a major product, but no polypeptide with electropho-retic mobility the same as that of the ASGV coat protein was synthesized. Immunoprecipitation experi-ments showed that a polypeptide of 200K was selectively precipitated by antiserum against purified ASGV. These results indicate that ASGV coat protein is translated as part of a 200K polyprotein. Apple stem grooving virus (ASGV) is distributed world-wide in apple trees (Lister, 1970; N6meth, 1986). The virus is one of the causative agents of apple topworking disease in Japan (Yanase, 1974, 1981) and induces decline syndrome in Mitsuba Kaido (Malus sieboldii) plants, which are used as rootstocks of apple trees in Japan (Yanase, 1981). ASGV is also reported to infect pear and apricot trees (N6meth, 1986; Motoshima et al., 1983; Sawamura et al., 1988; Takahashi et al., 1990). ASGV is the type member of the Capillovirus group
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Capillovirus foveavirus trichovirus vitivirus
Encyclopedia of Virology (Third Edition), 2008Co-Authors: N YoshikawaAbstract:Capillovirus , Foveavirus , Trichovirus , and Vitivirus are genera of plant viruses in the family Flexiviridae , and they have flexuous filamentous particles 12–13 nm in diameter composed of a monopartite, positive sense, single-stranded RNA genome with a 3′-poly A-tail and a single coat protein. The viruses occur throughout the world in Rosaceae fruit trees including apple, pear, peach, plum, cherry, apricot, and prune, and also citrus trees and grapevines. Although the genome organization of viruses seems to be different among each genus, that is, the number of open reading frames (ORFs) in their genomes is two ( Capillovirus ), three or four ( Trichovirus ) and five ( Foveavirus and Vitivirus ), all viral genomes have an ORF encoding an ‘alphavirus-like’ replication protein containing the consensus motifs of methyltransferase, papain-like protease, nucleotide triphosphate-binding helicase, and RNA-dependent RNA polymerase, and ORF(s) encoding a movement protein of the ‘30K’ superfamily or a triple gene block. The viruses in these genera also make use of similar gene expression strategies based on proteolytic processing of ORF1 protein and production of subgenomic RNAs to enable the 3′ORFs on genomic RNA to be translated.
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Single-strand conformation polymorphism analysis of apple stem grooving Capillovirus sequence variants.
Phytopathology, 1999Co-Authors: H. Magome, N Yoshikawa, Tsuyoshi TakahashiAbstract:ABSTRACT In an earlier study, we demonstrated that isolates of apple stem grooving Capillovirus (ASGV) from fruit trees comprise at least two to four sequence variants that differ considerably from each other in nucleotide sequence. In order to characterize the population of sequence variants within a single tree, we applied a combination of an immunocapture reverse transcription-polymerase chain reaction (IC-RT-PCR) and a single-strand conformation polymorphism (SSCP) analysis of a nested asymmetric PCR product. In the SSCP analysis of the PCR products from ASGV-infected apple, Japanese pear, or European pear trees, two to four bands were detected in samples from all trees, indicating that ASGV exists as a mixture of sequence variants. The composition of sequence variants (the number of bands and their relative quantity) differed among leaf samples from different branches, showing that each sequence variant is distributed unevenly within an individual tree. The SSCP analysis of isolates after serial pass...
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Grapevine berry inner necrosis, a new trichovirus: comparative studies with several known trichoviruses
Archives of Virology, 1997Co-Authors: N Yoshikawa, H. Iida, S. Goto, H. Magome, T. Takahashi, Y. TeraiAbstract:Biological, morphological and serological properties of grapevine berry inner necrosis virus (GINV), the causal virus of grapevine berry inner necrosis disease occurring in Japan, were compared with those of several known trichoviruses. Host range and particle length of GINV were quite similar to those of apple chlorotic leaf spot trichovirus (ACLSV). In ultrathin sections of the infected tissues, GINV particles existed in aggregated masses in the cytoplasm of vascular parenchyma and mesophyll cells. No virus specific inclusion bodies, such as pinwheels, viroplasmas or vesicles were observed. Serological relationships were not found between GINV and ACLSV, grapevine virus A or grapevine virus B. The cDNAs of the 3′-terminal region of the GINV genome were synthesized from poly (A)^+RNAs extracted from infected tissues by PCR-selected cDNA subtraction and 3′-RACE PCR. The sequence of the 3′-terminal 2 469 nucleotides contained three open reading frames (ORF) encoding a protein with the conserved motifs of RNA polymerase (ORF1), a 39 kDa putative movement protein (ORF2) and a 22 kDa protein (ORF3). The 22 kDa protein expressed in Escherichia coli reacted with antiserum against GINV, indicating that it is the coat protein of GINV. Polymerase and coat protein amino acid sequence comparisons and phylogenetic analyses with nine species of the genera Trichovirus and Capillovirus indicated that GINV is a new trichovirus relatively close to ACLSV.
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Striking similarities between the nucleotide sequence and genome organization of citrus tatter leaf and apple stem grooving Capilloviruses.
Journal of General Virology, 1993Co-Authors: N Yoshikawa, Tsuyoshi Takahashi, M. Imaizumi, N. InouyeAbstract:The sequence of the 3′-terminal 2956 nucleotides, excluding the poly(A) tail, of the citrus tatter leaf virus (CTLV) genome was determined and compared with that of the apple stem grooving virus (ASGV) genome. The sequence of the 3′-terminal region of CTLV contains two overlapping open reading frames (ORFs) and a 3′-terminal non-coding region of 142 nucleotides. The long, incomplete ORF1 ends at UAG (position 2812) and encodes a protein with at least 938 amino acids (M r > 108 703). This protein contains the GDD motif associated with the RNA polymerase. ORF2, in a different frame within ORF1, starts at AUG (position 1248) and stops at UGA (position 2208) encoding a protein with an M r of 36179 (36K). Partial homologies were found among the 36K protein of CTLV, the 50K protein of apple chlorotic leaf spot closterovirus, the 40K protein of potato virus T and the gene 1 products of caulimoviruses. The arrangement of ORFs in the 3′-terminal region of the CTLV genome is in perfect agreement with that of the ASGV genome. The sequence of the 3′-terminal 2956 nucleotides, excluding the poly(A) tail, of the CTLV genome shows 86.1% identity to that of the ASGV genome. Similarities of amino acid sequences encoded by ORF1 and ORF2 of CTLV with the corresponding regions of ASGV are 86.1% and 97.3%, respectively. These results indicate that CTLV is a Capillovirus closely related to ASGV.
