8 results on '"Caulimoviridae"'
Search Results
2. A novel badnavirus discovered from Betula sp. affected by birch leaf-roll disease.
- Author
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Rumbou, Artemis, Candresse, Thierry, Marais, Armelle, Theil, Sebastien, Langer, Juliane, Jalkanen, Risto, and Büttner, Carmen
- Subjects
- *
BIRCH diseases & pests , *CAULIMOVIRIDAE , *LEAFROLLERS , *NUCLEOTIDE sequence , *HAPLOTYPES - Abstract
In declining birches (Betula sp.) from different European stands affected by the “birch leaf-roll disease” (BLRD) a novel virus is identified by means of RNA-Seq virome analysis. The virus represents a new member in the genus Badnavirus, family Caulimoviridae, tentatively named Birch leaf roll-associated virus (BLRaV) and it is the first badnavirus found to infect birch. Complete genome sequences (7,862–7,864 nucleotides) of three viral isolates of Finnish and German origin have been determined. The virus sequences show a typical badnavirus organization with three major open reading frames (ORFs) and a fourth potential ORF overlapping with the end of ORF3. ORFs 1-2-3 show low level of amino acid identity to the corresponding proteins encoded by other badnaviruses, reaching a maximum of 44% identity (ORF3). Grapevine vein-clearing virus appears as the closest badnavirus when considering the polymerase region. So far, we can exclude evidence for presence of endogenous BLRaV elements in the birch genome, while evidence for the episomal activity of BLRaV is provided. The viral population holds significant haplotype diversity, while co-infection by different BLRaV variants are observed in single hosts. BLRaV presence is associated with the BLRD in both silver (B. pendula) and downy birch (B. pubescens). These results challenge the earlier hypothesis of a causal role of Cherry leaf roll virus in BLRD. Further work is now needed to finally prove that BLRaV is the causal agent for the BLRD. [ABSTRACT FROM AUTHOR]
- Published
- 2018
- Full Text
- View/download PDF
3. Characterization by Small RNA Sequencing of Taro Bacilliform CH Virus (TaBCHV), a Novel Badnavirus.
- Author
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Kazmi, Syeda Amber, Yang, Zuokun, Hong, Ni, Wang, Guoping, and Wang, Yanfen
- Subjects
- *
RNA sequencing , *ANTIVIRAL agents , *GENE silencing , *GENETIC regulation , *OPEN reading frames (Genetics) , *CAULIMOVIRIDAE , *VIRUSES - Abstract
RNA silencing is an antiviral immunity that regulates gene expression through the production of small RNAs (sRNAs). In this study, deep sequencing of small RNAs was used to identify viruses infecting two taro plants. Blast searching identified five and nine contigs assembled from small RNAs of samples T1 and T2 matched onto the genome sequences of badnaviruses in the family Caulimoviridae. Complete genome sequences of two isolates of the badnavirus determined by sequence specific amplification comprised of 7,641 nucleotides and shared overall nucleotide similarities of 44.1%‒55.8% with other badnaviruses. Six open reading frames (ORFs) were identified on the plus strand, showed amino acid similarities ranging from 59.8% (ORF3) to 10.2% (ORF6) to the corresponding proteins encoded by other badnaviruses. Phylogenetic analysis also supports that the virus is a new member in the genus Badnavirus. The virus is tentatively named as Taro bacilliform CH virus (TaBCHV), and it is the second badnavirus infecting taro plants, following Taro bacilliform virus (TaBV). In addition, analyzes of viral derived small RNAs (vsRNAs) from TaBCHV showed that almost equivalent number of vsRNAs were generated from both strands and the most abundant vsRNAs were 21 nt, with uracil bias at 5' terminal. Furthermore, TaBCHV vsRNAs were asymmetrically distributed on its entire circular genome at both orientations with the hotspots mainly generated in the ORF5 region. [ABSTRACT FROM AUTHOR]
- Published
- 2015
- Full Text
- View/download PDF
4. The Temporal Evolution and Global Spread of Cauliflower mosaic virus, a Plant Pararetrovirus.
- Author
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Yasaka, Ryosuke, Nguyen, Huy D., Ho, Simon Y. W., Duchêne, Sebastián, Korkmaz, Savas, Katis, Nikolaos, Takahashi, Hideki, Gibbs, Adrian J., and Ohshima, Kazusato
- Subjects
- *
CAULIFLOWER mosaic virus , *VIRUS diseases of plants , *PLANT evolution , *CAULIMOVIRIDAE , *DNA viruses , *REPRODUCTIVE isolation in plants , *PLANT phylogeny , *RECOMBINANT DNA - Abstract
Cauliflower mosaic virus (CaMV) is a plant pararetrovirus with a double-stranded DNA genome. It is the type member of the genus Caulimovirus in the family Caulimoviridae. CaMV is transmitted by sap inoculation and in nature by aphids in a semi-persistent manner. To investigate the patterns and timescale of CaMV migration and evolution, we sequenced and analyzed the genomes of 67 isolates of CaMV collected mostly in Greece, Iran, Turkey, and Japan together with nine published sequences. We identified the open-reading frames (ORFs) in the genomes and inferred their phylogeny. After removing recombinant sequences, we estimated the substitution rates, divergence times, and phylogeographic patterns of the virus populations. We found that recombination has been a common feature of CaMV evolution, and that ORFs I–V have a different evolutionary history from ORF VI. The ORFs have evolved at rates between 1.71 and 5.81×10−4 substitutions/site/year, similar to those of viruses with RNA or ssDNA genomes. We found four geographically confined lineages. CaMV probably spread from a single population to other parts of the world around 400–500 years ago, and is now widely distributed among Eurasian countries. Our results revealed evidence of frequent gene flow between populations in Turkey and those of its neighboring countries, with similar patterns observed for Japan and the USA. Our study represents the first report on the spatial and temporal spread of a plant pararetrovirus. [ABSTRACT FROM AUTHOR]
- Published
- 2014
- Full Text
- View/download PDF
5. Characterization of a novel member of the family Caulimoviridae infecting Dioscorea nummularia in the Pacific, which may represent a new genus of dsDNA plant viruses
- Author
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Robert M. Harding, Amit C. Sukal, James L. Dale, Anthony P. James, and Dawit B. Kidanemariam
- Subjects
0301 basic medicine ,viruses ,lcsh:Medicine ,Caulimoviridae ,Genome ,03 medical and health sciences ,Open Reading Frames ,Viral Proteins ,Plant virus ,Amino Acid Sequence ,ORFS ,Movement protein ,lcsh:Science ,Genome size ,Phylogeny ,Genetics ,Multidisciplinary ,Pacific Ocean ,biology ,Dioscorea ,lcsh:R ,Nucleic acid sequence ,DNA virus ,Genomics ,biology.organism_classification ,030104 developmental biology ,lcsh:Q - Abstract
We have characterized the complete genome of a novel circular double-stranded DNA virus, tentatively named Dioscorea nummularia-associated virus (DNUaV), infecting Dioscorea nummularia originating from Samoa. The genome of DNUaV comprised 8139 bp and contained four putative open reading frames (ORFs). ORFs 1 and 2 had no identifiable conserved domains, while ORF 3 had conserved motifs typical of viruses within the family Caulimoviridae including coat protein, movement protein, aspartic protease, reverse transcriptase and ribonuclease H. A transactivator domain, similar to that present in members of several caulimoviridae genera, was also identified in the putative ORF 4. The genome size, organization, and presence of conserved amino acid domains are similar to other viruses in the family Caulimoviridae. However, based on nucleotide sequence similarity and phylogenetic analysis, DNUaV appears to be a distinct novel member of the family and may represent a new genus.
- Published
- 2018
6. Extension of the viral ecology in humans using viral profile hidden Markov models
- Author
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Joakim Dillner, Emilie Hultin, and Zurab Bzhalava
- Subjects
0301 basic medicine ,Markov models ,lcsh:Medicine ,Database and Informatics Methods ,Contig Mapping ,0302 clinical medicine ,Anelloviridae ,Hidden Markov models ,Database Searching ,lcsh:Science ,Databases, Protein ,Phylogeny ,Multidisciplinary ,Microbiota ,Genomics ,Genomic Databases ,Markov Chains ,Physical sciences ,030220 oncology & carcinogenesis ,Viruses ,Caulimoviridae ,Sequence Analysis ,Algorithms ,Research Article ,Multiple Alignment Calculation ,Bioinformatics ,Sequence Databases ,Sequence alignment ,Computational biology ,Biology ,Research and Analysis Methods ,03 medical and health sciences ,Viral Proteins ,Computational Techniques ,Genetics ,Humans ,Mimiviridae ,Geminiviridae ,Sequence Similarity Searching ,Virus classification ,BLAST algorithm ,lcsh:R ,Marseillevirus ,Biology and Life Sciences ,Computational Biology ,Probability theory ,biology.organism_classification ,Genome Analysis ,Split-Decomposition Method ,030104 developmental biology ,Biological Databases ,lcsh:Q ,Metagenomics ,Phycodnaviridae ,Sequence Alignment ,Mathematics - Abstract
When human samples are sequenced, many assembled contigs are “unknown”, as conventional alignments find no similarity to known sequences. Hidden Markov models (HMM) exploit the positions of specific nucleotides in protein-encoding codons in various microbes. The algorithm HMMER3 implements HMM using a reference set of sequences encoding viral proteins, “vFam”. We used HMMER3 analysis of “unknown” human sample-derived sequences and identified 510 contigs distantly related to viruses (Anelloviridae (n = 1), Baculoviridae (n = 34), Circoviridae (n = 35), Caulimoviridae (n = 3), Closteroviridae (n = 5), Geminiviridae (n = 21), Herpesviridae (n = 10), Iridoviridae (n = 12), Marseillevirus (n = 26), Mimiviridae (n = 80), Phycodnaviridae (n = 165), Poxviridae (n = 23), Retroviridae (n = 6) and 89 contigs related to described viruses not yet assigned to any taxonomic family). In summary, we find that analysis using the HMMER3 algorithm and the “vFam” database greatly extended the detection of viruses in biospecimens from humans.
- Published
- 2018
7. A novel badnavirus discovered from Betula sp. affected by birch leaf-roll disease
- Author
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Rumbou, Artemis, Candresse, Thierry, Marais, Armelle, Theil, Sebastien, Langer, Juliane, Jalkanen, Risto, Büttner, Carmen, Humboldt University of Berlin, Biologie du fruit et pathologie (BFP), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1, and Natural Resources Institute Finland (LUKE)
- Subjects
Leaves ,Virologie ,Birch leaf roll-associated virus ,lcsh:Medicine ,Plant Science ,Trees ,santé des plantes ,lcsh:Science ,pathologie végétale ,Betula ,Phylogeny ,Data Management ,Viral Genomics ,Database and informatics methods ,Plant Anatomy ,Sequence analysis ,Eukaryota ,Phylogenetic Analysis ,Genomics ,Plants ,Phylogenetics ,[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,Research Article ,Computer and Information Sciences ,Bioinformatics ,birch leaf-roll disease ,Microbial Genomics ,Genome, Viral ,Microbiology ,Open Reading Frames ,Viral Proteins ,Amino Acid Sequence Analysis ,Virology ,Genetics ,Evolutionary Systematics ,Birches ,Badnavirus ,DNA sequence analysis ,Taxonomy ,Plant Diseases ,caulimoviridae ,virus phytopathogène ,Evolutionary Biology ,lcsh:R ,Organisms ,Biology and Life Sciences ,Genetic Variation ,Correction ,Sequence Analysis, DNA ,BLRD ,Research and analysis methods ,Plant Leaves ,Seedlings ,DNA, Viral ,identification ,lcsh:Q - Abstract
UMR BFP - Equipe Virologie; International audience; In declining birches (Betula sp.) from different European stands affected by the "birch leaf-roll disease" (BLRD) a novel virus is identified by means of RNA-Seq virome analysis. The virus represents a new member in the genus Badnavirus, family Caulimoviridae, tentatively named Birch leaf roll-associated virus (BLRaV) and it is the first badnavirus found to infect birch. Complete genome sequences (7,862-7,864 nucleotides) of three viral isolates of Finnish and German origin have been determined. The virus sequences show a typical badnavirus organization with three major open reading frames (ORFs) and a fourth potential ORF overlapping with the end of ORF3. ORFs 1-2-3 show low level of amino acid identity to the corresponding proteins encoded by other badnaviruses, reaching a maximum of 44% identity (ORF3). Grapevine vein-clearing virus appears as the closest badnavirus when considering the polymerase region. So far, we can exclude evidence for presence of endogenous BLRaV elements in the birch genome, while evidence for the episomal activity of BLRaV is provided. The viral population holds significant haplotype diversity, while co-infection by different BLRaV variants are observed in single hosts. BLRaV presence is associated with the BLRD in both silver (B. pendula) and downy birch (B. pubescens). These results challenge the earlier hypothesis of a causal role of Cherry leaf roll virus in BLRD. Further work is now needed to finally prove that BLRaV is the causal agent for the BLRD.
- Published
- 2017
8. Correction: A novel badnavirus discovered from Betula sp. affected by birch leaf-roll disease.
- Subjects
- *
BIRCH diseases & pests , *CAULIMOVIRIDAE - Published
- 2018
- Full Text
- View/download PDF
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