The Experts below are selected from a list of 360 Experts worldwide ranked by ideXlab platform
Thierry Candresse - One of the best experts on this subject based on the ideXlab platform.
-
Complete genome sequence of lettuce chordovirus 1 isolated from cultivated lettuce in France.
Archives of Virology, 2018Co-Authors: Laurence Svanella-dumas, Armelle Marais, Sébastien Theil, Jonathan Gaudin, Ιason Τsarmpopoulos, C. Faure, Thierry CandresseAbstract:Double-stranded RNAs purified from cultivated (Lactuca sativa) or wild (L. serriola) lettuce from southwest France were analyzed by high-throughput sequencing. For both samples, BLAST annotation revealed contigs with homology to Betaflexiviridae family members. The full genome sequence of the isolate from cultivated lettuce (JG1) was completed (8,536 nucleotides [nt], excluding the poly(A) tail). The sequence of the 3’ half of the genome (4,800 nt) of a wild lettuce isolate (P22) was determined and found to share 95.1% nt sequence identity with the JG1 isolate. The JG1 genome contains four open reading frames, encoding a replicase, a movement protein, a capsid protein, and a protein of unknown function, respectively. Based on genome organization and phylogenetic relationships, the lettuce virus is most closely related to the recently described carrot chordoviruses 1 and 2 in the family Betaflexiviridae. Considering the species demarcation criteria in this family, the two lettuce viruses represent isolates of a new chordovirus species for which the name “lettuce chordovirus 1” (LeCV1) is proposed.
-
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
-
Determination of the complete genomic sequence of grapevine virus H, a novel vitivirus infecting grapevine.
Archives of Virology, 2018Co-Authors: Thierry Candresse, Chantal Faure, Sébastien Theil, Armelle MaraisAbstract:The present work reports the discovery and the complete genome sequencing of a novel member of the genus Vitivirus in the family Betaflexiviridae (subfamily Trivirinae) from a symptomless grapevine of unknown variety from Portugal. Total RNAs extracted from phloem scrapings were sequenced using Illumina technology. Bioinformatic analysis of the RNA-seq data revealed a mixed infection involving three viruses and two viroids in addition to a novel vitivirus. Completion and analysis of the genome sequence (7446 nt excluding the polyA tail) showed a typical vitivirus genomic organization. Phylogenetic analysis of the various ORFs clearly showed the new virus to belong in the genus Vitivirus, but sequence divergence firmly establishes it as a member of a new species, for which the name "Grapevine virus H" is proposed.
-
Identification by Next Generation Sequencing (NGS) of three novel viral agents infecting lettuce and belonging to the Betaflexiviridae and Secoviridae families
2017Co-Authors: Laurence Svanella-dumas, Chantal Faure, Sébastien Theil, Armelle Marais-colombel, Iason Tsarmpopoulos, Jonathan Gaudin, Thierry CandresseAbstract:Identification by Next Generation Sequencing (NGS) of three novel viral agents infecting lettuce and belonging to the Betaflexiviridae and Secoviridae families. 16. Rencontres de Virologie Végétale (RVV 2017)
-
New Insights into Asian Prunus Viruses in the Light of NGS-Based Full Genome Sequencing.
PLOS ONE, 2016Co-Authors: Armelle Marais, Chantal Faure, Thierry CandresseAbstract:Double stranded RNAs were purified from five Prunus sources of Asian origin and submitted to 454 pyrosequencing after a random, whole genome amplification. Four complete genomes of Asian prunus virus 1 (APV1), APV2 and APV3 were reconstructed from the sequencing reads, as well as four additional, near-complete genome sequences. Phylogenetic analyses confirmed the close relationships of these three viruses and the taxonomical position previously proposed for APV1, the only APV so far completely sequenced. The genetic distances in the respective polymerase and coat protein genes as well as their gene products suggest that APV2 should be considered as a distinct viral species in the genus Foveavirus, even if the amino acid identity levels in the polymerase are very close to the species demarcation criteria for the family Betaflexiviridae. However, the situation is more complex for APV1 and APV3, for which opposite conclusions are obtained depending on the gene (polymerase or coat protein) analyzed. Phylogenetic and recombination analyses suggest that recombination events may have been involved in the evolution of APV. Moreover, genome comparisons show that the unusually long 3’ non-coding region (3' NCR) is highly variable and a hot spot for indel polymorphisms. In particular, two APV3 variants differing only in their 3’ NCR were identified in a single Prunus source, with 3' NCRs of 214–312 nt, a size similar to that observed in other foveaviruses, but 567–850 nt smaller than in other APV3 isolates. Overall, this study provides critical genome information of these viruses, frequently associated with Prunus materials, even though their precise role as pathogens remains to be elucidated.
Armelle Marais - One of the best experts on this subject based on the ideXlab platform.
-
Complete genome sequence of lettuce chordovirus 1 isolated from cultivated lettuce in France.
Archives of Virology, 2018Co-Authors: Laurence Svanella-dumas, Armelle Marais, Sébastien Theil, Jonathan Gaudin, Ιason Τsarmpopoulos, C. Faure, Thierry CandresseAbstract:Double-stranded RNAs purified from cultivated (Lactuca sativa) or wild (L. serriola) lettuce from southwest France were analyzed by high-throughput sequencing. For both samples, BLAST annotation revealed contigs with homology to Betaflexiviridae family members. The full genome sequence of the isolate from cultivated lettuce (JG1) was completed (8,536 nucleotides [nt], excluding the poly(A) tail). The sequence of the 3’ half of the genome (4,800 nt) of a wild lettuce isolate (P22) was determined and found to share 95.1% nt sequence identity with the JG1 isolate. The JG1 genome contains four open reading frames, encoding a replicase, a movement protein, a capsid protein, and a protein of unknown function, respectively. Based on genome organization and phylogenetic relationships, the lettuce virus is most closely related to the recently described carrot chordoviruses 1 and 2 in the family Betaflexiviridae. Considering the species demarcation criteria in this family, the two lettuce viruses represent isolates of a new chordovirus species for which the name “lettuce chordovirus 1” (LeCV1) is proposed.
-
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
-
Determination of the complete genomic sequence of grapevine virus H, a novel vitivirus infecting grapevine.
Archives of Virology, 2018Co-Authors: Thierry Candresse, Chantal Faure, Sébastien Theil, Armelle MaraisAbstract:The present work reports the discovery and the complete genome sequencing of a novel member of the genus Vitivirus in the family Betaflexiviridae (subfamily Trivirinae) from a symptomless grapevine of unknown variety from Portugal. Total RNAs extracted from phloem scrapings were sequenced using Illumina technology. Bioinformatic analysis of the RNA-seq data revealed a mixed infection involving three viruses and two viroids in addition to a novel vitivirus. Completion and analysis of the genome sequence (7446 nt excluding the polyA tail) showed a typical vitivirus genomic organization. Phylogenetic analysis of the various ORFs clearly showed the new virus to belong in the genus Vitivirus, but sequence divergence firmly establishes it as a member of a new species, for which the name "Grapevine virus H" is proposed.
-
RESEARCH ARTICLE New Insights into Asian Prunus Viruses in the Light of NGS-Based Full Genome Sequencing
2016Co-Authors: Armelle Marais, Chantal Faure, Thierry CAbstract:Double stranded RNAs were purified from five Prunus sources of Asian origin and submit-ted to 454 pyrosequencing after a random, whole genome amplification. Four complete genomes of Asian prunus virus 1 (APV1), APV2 and APV3 were reconstructed from the sequencing reads, as well as four additional, near-complete genome sequences. Phyloge-netic analyses confirmed the close relationships of these three viruses and the taxonomi-cal position previously proposed for APV1, the only APV so far completely sequenced. The genetic distances in the respective polymerase and coat protein genes as well as their gene products suggest that APV2 should be considered as a distinct viral species in the genus Foveavirus, even if the amino acid identity levels in the polymerase are very close to the species demarcation criteria for the family Betaflexiviridae. However, the situation is more complex for APV1 and APV3, for which opposite conclusions are obtained depend-ing on the gene (polymerase or coat protein) analyzed. Phylogenetic and recombination analyses suggest that recombination events may have been involved in the evolution of APV. Moreover, genome comparisons show that the unusually long 3 ’ non-coding region (3 ' NCR) is highly variable and a hot spot for indel polymorphisms. In particular, two APV3 variants differing only in their 3 ’ NCR were identified in a single Prunus source, with 3' NCRs of 214–312 nt, a size similar to that observed in other foveaviruses, but 567–850 nt smaller than in other APV3 isolates. Overall, this study provides critical genome informa-tion of these viruses, frequently associated with Prunusmaterials, even though their pre-cise role as pathogens remains to be elucidated
-
New Insights into Asian Prunus Viruses in the Light of NGS-Based Full Genome Sequencing.
PLOS ONE, 2016Co-Authors: Armelle Marais, Chantal Faure, Thierry CandresseAbstract:Double stranded RNAs were purified from five Prunus sources of Asian origin and submitted to 454 pyrosequencing after a random, whole genome amplification. Four complete genomes of Asian prunus virus 1 (APV1), APV2 and APV3 were reconstructed from the sequencing reads, as well as four additional, near-complete genome sequences. Phylogenetic analyses confirmed the close relationships of these three viruses and the taxonomical position previously proposed for APV1, the only APV so far completely sequenced. The genetic distances in the respective polymerase and coat protein genes as well as their gene products suggest that APV2 should be considered as a distinct viral species in the genus Foveavirus, even if the amino acid identity levels in the polymerase are very close to the species demarcation criteria for the family Betaflexiviridae. However, the situation is more complex for APV1 and APV3, for which opposite conclusions are obtained depending on the gene (polymerase or coat protein) analyzed. Phylogenetic and recombination analyses suggest that recombination events may have been involved in the evolution of APV. Moreover, genome comparisons show that the unusually long 3’ non-coding region (3' NCR) is highly variable and a hot spot for indel polymorphisms. In particular, two APV3 variants differing only in their 3’ NCR were identified in a single Prunus source, with 3' NCRs of 214–312 nt, a size similar to that observed in other foveaviruses, but 567–850 nt smaller than in other APV3 isolates. Overall, this study provides critical genome information of these viruses, frequently associated with Prunus materials, even though their precise role as pathogens remains to be elucidated.
Chantal Faure - One of the best experts on this subject based on the ideXlab platform.
-
Determination of the complete genomic sequence of grapevine virus H, a novel vitivirus infecting grapevine.
Archives of Virology, 2018Co-Authors: Thierry Candresse, Chantal Faure, Sébastien Theil, Armelle MaraisAbstract:The present work reports the discovery and the complete genome sequencing of a novel member of the genus Vitivirus in the family Betaflexiviridae (subfamily Trivirinae) from a symptomless grapevine of unknown variety from Portugal. Total RNAs extracted from phloem scrapings were sequenced using Illumina technology. Bioinformatic analysis of the RNA-seq data revealed a mixed infection involving three viruses and two viroids in addition to a novel vitivirus. Completion and analysis of the genome sequence (7446 nt excluding the polyA tail) showed a typical vitivirus genomic organization. Phylogenetic analysis of the various ORFs clearly showed the new virus to belong in the genus Vitivirus, but sequence divergence firmly establishes it as a member of a new species, for which the name "Grapevine virus H" is proposed.
-
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
-
Identification by Next Generation Sequencing (NGS) of three novel viral agents infecting lettuce and belonging to the Betaflexiviridae and Secoviridae families
2017Co-Authors: Laurence Svanella-dumas, Chantal Faure, Sébastien Theil, Armelle Marais-colombel, Iason Tsarmpopoulos, Jonathan Gaudin, Thierry CandresseAbstract:Identification by Next Generation Sequencing (NGS) of three novel viral agents infecting lettuce and belonging to the Betaflexiviridae and Secoviridae families. 16. Rencontres de Virologie Végétale (RVV 2017)
-
RESEARCH ARTICLE New Insights into Asian Prunus Viruses in the Light of NGS-Based Full Genome Sequencing
2016Co-Authors: Armelle Marais, Chantal Faure, Thierry CAbstract:Double stranded RNAs were purified from five Prunus sources of Asian origin and submit-ted to 454 pyrosequencing after a random, whole genome amplification. Four complete genomes of Asian prunus virus 1 (APV1), APV2 and APV3 were reconstructed from the sequencing reads, as well as four additional, near-complete genome sequences. Phyloge-netic analyses confirmed the close relationships of these three viruses and the taxonomi-cal position previously proposed for APV1, the only APV so far completely sequenced. The genetic distances in the respective polymerase and coat protein genes as well as their gene products suggest that APV2 should be considered as a distinct viral species in the genus Foveavirus, even if the amino acid identity levels in the polymerase are very close to the species demarcation criteria for the family Betaflexiviridae. However, the situation is more complex for APV1 and APV3, for which opposite conclusions are obtained depend-ing on the gene (polymerase or coat protein) analyzed. Phylogenetic and recombination analyses suggest that recombination events may have been involved in the evolution of APV. Moreover, genome comparisons show that the unusually long 3 ’ non-coding region (3 ' NCR) is highly variable and a hot spot for indel polymorphisms. In particular, two APV3 variants differing only in their 3 ’ NCR were identified in a single Prunus source, with 3' NCRs of 214–312 nt, a size similar to that observed in other foveaviruses, but 567–850 nt smaller than in other APV3 isolates. Overall, this study provides critical genome informa-tion of these viruses, frequently associated with Prunusmaterials, even though their pre-cise role as pathogens remains to be elucidated
-
New Insights into Asian Prunus Viruses in the Light of NGS-Based Full Genome Sequencing.
PLOS ONE, 2016Co-Authors: Armelle Marais, Chantal Faure, Thierry CandresseAbstract:Double stranded RNAs were purified from five Prunus sources of Asian origin and submitted to 454 pyrosequencing after a random, whole genome amplification. Four complete genomes of Asian prunus virus 1 (APV1), APV2 and APV3 were reconstructed from the sequencing reads, as well as four additional, near-complete genome sequences. Phylogenetic analyses confirmed the close relationships of these three viruses and the taxonomical position previously proposed for APV1, the only APV so far completely sequenced. The genetic distances in the respective polymerase and coat protein genes as well as their gene products suggest that APV2 should be considered as a distinct viral species in the genus Foveavirus, even if the amino acid identity levels in the polymerase are very close to the species demarcation criteria for the family Betaflexiviridae. However, the situation is more complex for APV1 and APV3, for which opposite conclusions are obtained depending on the gene (polymerase or coat protein) analyzed. Phylogenetic and recombination analyses suggest that recombination events may have been involved in the evolution of APV. Moreover, genome comparisons show that the unusually long 3’ non-coding region (3' NCR) is highly variable and a hot spot for indel polymorphisms. In particular, two APV3 variants differing only in their 3’ NCR were identified in a single Prunus source, with 3' NCRs of 214–312 nt, a size similar to that observed in other foveaviruses, but 567–850 nt smaller than in other APV3 isolates. Overall, this study provides critical genome information of these viruses, frequently associated with Prunus materials, even though their precise role as pathogens remains to be elucidated.
Kenneth C. Eastwell - One of the best experts on this subject based on the ideXlab platform.
-
genomic analyses of cherry rusty mottle group and cherry twisted leaf associated viruses reveal a possible new genus within the family Betaflexiviridae
Phytopathology, 2015Co-Authors: D E V Villamor, James Susaimuthu, Kenneth C. EastwellAbstract:It is demonstrated that closely related viruses within the family Betaflexiviridae are associated with a number of diseases that affect sweet cherry (Prunus avium) and other Prunus spp. Cherry rusty mottle-associated virus (CRMaV) is correlated with the appearance of cherry rusty mottle disease (CRMD), and Cherry twisted leaf-associated virus (CTLaV) is linked to cherry twisted leaf disease (CTLD) and apricot ringpox disease (ARPD). Comprehensive analysis of previously reported full genomic sequences plus those determined in this study representing isolates of CTLaV, CRMaV, Cherry green ring mottle virus, and Cherry necrotic rusty mottle virus revealed segregation of sequences into four clades corresponding to distinct virus species. High-throughput sequencing of RNA from representative source trees for CRMD, CTLD, and ARPD did not reveal additional unique virus sequences that might be associated with these diseases, thereby further substantiating the association of CRMaV and CTLaV with CRMD and CTLD or ARPD, respectively. Based on comparison of the nucleotide and amino acid sequence identity values, phylogenetic relationships with other triple-gene block-coding viruses within the family Betaflexiviridae, genome organization, and natural host range, a new genus (Robigovirus) is suggested.
-
Complete nucleotide sequence of a strain of cherry mottle leaf virus associated with peach wart disease in peach
Archives of Virology, 2013Co-Authors: Tefera A. Mekuria, James Susaimuthu, Keri L. Druffel, Kenneth C. EastwellAbstract:The complete nucleotide sequence and genome organization of a peach virus isolate from a naturally infected peach tree showing typical peach wart-like symptoms on the fruit surface was determined and compared to sequences of members of the family Betaflexiviridae . The genome consists of 7,987 nucleotides, excluding the poly-A tail, and has four open reading frames (ORFs). Analysis of the whole genome and putative proteins encoded by each ORF revealed greatest sequence similarity to a cherry isolate of cherry mottle leaf virus (CMLV). The two isolates have similar genome organizations and share 88 and 93 % homology in their corresponding products of the replicase and coat protein genes, respectively. CMLV has been reported from several Prunus spp. and may be associated with peach wart-like disease symptoms on peach fruit.
Claudine M. Carvalho - One of the best experts on this subject based on the ideXlab platform.
-
Cowpea mild mottle virus (Carlavirus, Betaflexiviridae): a review
Tropical Plant Pathology, 2017Co-Authors: Larissa G. Zanardo, Claudine M. CarvalhoAbstract:In this review we describe and discuss the biology and aspects of infection of a pathogen, the RNA virus Cowpea mild mottle virus (CPMMV), that emerged as a problem in soybean and is re-emerging in common bean. The review takes a global perspective but has an emphasis on Brazilian soybean in which CPMMV causes stem necrosis. Since its first description in Ghana in 1973, CPMMV has spread across the world and, although it principally infects Fabaceae, it is also able to infect hosts from Solanaceae and Lamiaceae. While the problem in soybean is being tackled with resistant varieties, CPMMV is re-emerging in genetically modified common bean. To limit the impact of CPMMV and combat future outbreaks, it is necessary to understand the ecological and evolutionary factors that influence its emergence. We identify surveillance as a key defense against CPMMV, as CPMMV is transmitted non-persistently by the whitefly Bemisia tabaci , there is the possibility of seed transmission and the virus is able to cause asymptomatic infections. We discuss the potential for development of resistant crop lines and identify key areas for future research.
-
molecular variability of cowpea mild mottle virus infecting soybean in brazil
Archives of Virology, 2014Co-Authors: Larissa G. Zanardo, Fabio Nascimiento Silva, Alison T M Lima, D F Milanesi, G P Castilhourquiza, A M R Almeida, F M Zerbini, Claudine M. CarvalhoAbstract:Molecular variability was assessed for 18 isolates of cowpea mild mottle virus (CPMMV, genus Carlavirus, family Betaflexiviridae) found infecting soybean in various Brazilian states (Bahia, Goias, Maranhao, Mato Grosso, Minas Gerais, Para) in 2001 and 2010. A variety of symptoms was expressed in soybean cv. CD206, ranging from mild (crinkle/blistering leaves, mosaic and vein clearing) to severe (bud blight, dwarfing, leaf and stem necrosis). Recombination analysis revealed only one CPMMV isolate to be recombinant. Pairwise comparisons and phylogenetic analysis were performed for partial genomes (ORF 2 to the 3’ terminus) and for each ORF individually (ORFs 2 to 6), showing the isolates to be distinct. The topology of the phylogenetic tree could be related to symptoms, but not to the year of collection or geographical origin. Additionally, the phylogenetic analysis supported the existence of two distinct strains of the virus, designated CPMMV-BR1 and CPMMV-BR2, with molecular variations between them.