The Experts below are selected from a list of 24 Experts worldwide ranked by ideXlab platform
Seal S.e. - One of the best experts on this subject based on the ideXlab platform.
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Taxonomy, molecular phylogeny and evolution of plant reverse transcribing viruses (family Caulimoviridae) inferred from full-length genome and reverse transcriptase sequences
'Springer Science and Business Media LLC', 2008Co-Authors: Bousalem M., Douzery Emmanuel, Seal S.e.Abstract:International audienceThis study constitutes the first evaluation and application of quantitative taxonomy to the family Caulimoviridae and the first in-depth phylogenetic study of the family Caulimoviridae that integrates the common origin between LTR retrotransposons and caulimoviruses. The phylogenetic trees and PASC analyses derived from the full genome and from the corresponding partial RT concurred, providing strong support for the current genus classification based mainly on genome organisation and use of partial RT sequence as a molecular marker. The PASC distributions obtained are multimodal, making it possible to distinguish between genus, species and strain. The taxonomy of badnaviruses infecting banana (Musa spp.) was clarified, and the consequence of endogenous badnaviruses on the genetic diversity and evolution of caulimoviruses is discussed. The use of LTR retrotransposons as outgroups reveals a structured bipolar topology separating the genus Badnavirus from the other genera. Badnaviruses appear to be the most recent genus, with the genus Tungrovirus in an intermediary position. This structuring intersects the one established by genomic and biological properties and allows us to make a correlation between phylogeny and biogeography. The variability shown between members of the family Caulimoviridae is in a similiar range to that reported within other DNA and RNA plant virus families
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Taxonomy, molecular phylogeny and evolution of plant reverse transcribing viruses (family Caulimoviridae) inferred from full-length genome and reverse transcriptase sequences
'Springer Science and Business Media LLC', 2008Co-Authors: Bousalem M., Douzery E.j.p., Seal S.e.Abstract:This study constitutes the first evaluation and application of quantitative taxonomy to the family Caulimoviridae and the first in-depth phylogenetic study of the family Caulimoviridae that integrates the common origin between LTR retrotransposons and caulimoviruses. The phylogenetic trees and PASC analyses derived from the full genome and from the corresponding partial RT concurred, providing strong support for the current genus classification based mainly on genome organisation and use of partial RT sequence as a molecular marker. The PASC distributions obtained are multimodal, making it possible to distinguish between genus, species and strain. The taxonomy of badnaviruses infecting banana (Musa spp.) was clarified, and the consequence of endogenous badnaviruses on the genetic diversity and evolution of caulimoviruses is discussed. The use of LTR retrotransposons as outgroups reveals a structured bipolar topology separating the genus Badnavirus from the other genera. Badnaviruses appear to be the most recent genus, with the genus Tungrovirus in an intermediary position. This structuring intersects the one established by genomic and biological properties and allows us to make a correlation between phylogeny and biogeography. The variability shown between members of the family Caulimoviridae is in a similiar range to that reported within other DNA and RNA plant virus families
Emmanuelle Muller - One of the best experts on this subject based on the ideXlab platform.
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approches phylogenetiques de la taxonomie du genre badnavirus
12èmes Rencontres de virologie végétale Aussois du 18 au 22 janvier 2009, 2009Co-Authors: Emmanuelle MullerAbstract:De nouvelles sequences entieres ou partielles de badnavirus sont produites regulierement et mises a disposition sur Genbank, certaines remettant en cause la classification liee au type de plante hote. La variabilite importante des badnavirus rend peu aise le choix de la partie du genome a etudier qui "resumerait" la variabilite globale. En effet, il existe environ 47% identite entre une espece de badnavirus et le Rice tungro bacilliform virus (RTBV) representant le genre des Tungrovirus et il existe seulement autour de 50% entre deux badnavirus eloignes. L'existence de motifs consensus sur la 3eme partie de l'ORF3 et sur le site d'accrochage au tRNAmet a permis le design de differents couples d'amorces badnavirus "universelles" badna 2/badnaT (1993), Badna2.1/3.1 (1996), Badna1/4 (2002), BadnaF/R (2003). Les motifs de type RTase et RNaseH, correspondant aux sites d'accrochage de la plupart de ces amorces, sont, malheureusement, egalement presents sur des sequences de retrotransposons. Les sequences amplifiees par ces amorces ont neanmoins permis de generer de nombreuses sequences de badnavirus libres ou integrees qui ont abouti a la construction de nombreuses phylogenies de badnavirus. Ces phylogenies ne sont cependant pas toujours coherentes avec les phylogenies obtenues d'apres l'alignement des sequences entieres. Il n'y a en fait pas eu de reflexion sur le choix d'une zone adaptee a la classification taxonomique du genre badnavirus puisque la region du genome utilisee pour la classification correspond par defaut a la region du genome des badnavirus disponible majoritairement sur Genbank et il est impossible d'obtenir systematiquement des sequences entieres pour classifier ce genre de virus. Afin de mieux comprendre la diversite des badnavirus voire proposer des reamenagements de leur taxonomie, il est necessaire de se baser sur des phylogenies utilisant des regions du genome representatives du genome complet. Des etudes phylogenetiques plus poussees qui permettent d'implementer des taux d'evolution differents selon les groupes de sequences ont egalement besoin de ce type de resultat. Pour remedier a ce manque d'informations phylogenetiques pertinentes, le genome des badnavirus entierement sequences (20 sequences) a ete decoupe en morceaux et des phylogenies ont ete construites en alignant les differentes zones obtenues. Les phylogenies construites avec le logiciel Phyml (maximum de vraisemblance) sont presentees et discutees; une portion du genome ne produisant que peu de distorsions par rapport aux phylogenies basees sur les sequences entieres est proposee. (Texte integral)
Muller Emmanuelle - One of the best experts on this subject based on the ideXlab platform.
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Approches phylogénétiques de la taxonomie du genre badnavirus
'INIST-CNRS', 2009Co-Authors: Muller EmmanuelleAbstract:De nouvelles séquences entières ou partielles de badnavirus sont produites régulièrement et mises à disposition sur Genbank, certaines remettant en cause la classification liée au type de plante hôte. La variabilité importante des badnavirus rend peu aisé le choix de la partie du génome à étudier qui "résumerait" la variabilité globale. En effet, il existe environ 47% identité entre une espèce de badnavirus et le Rice tungro bacilliform virus (RTBV) représentant le genre des Tungrovirus et il existe seulement autour de 50% entre deux badnavirus éloignés. L'existence de motifs consensus sur la 3ème partie de l'ORF3 et sur le site d'accrochage au tRNAmet a permis le design de différents couples d'amorces badnavirus "universelles" badna 2/badnaT (1993), Badna2.1/3.1 (1996), Badna1/4 (2002), BadnaF/R (2003). Les motifs de type RTase et RNaseH, correspondant aux sites d'accrochage de la plupart de ces amorces, sont, malheureusement, également présents sur des séquences de rétrotransposons. Les séquences amplifiées par ces amorces ont néanmoins permis de générer de nombreuses séquences de badnavirus libres ou intégrées qui ont abouti à la construction de nombreuses phylogénies de badnavirus. Ces phylogénies ne sont cependant pas toujours cohérentes avec les phylogénies obtenues d'après l'alignement des séquences entières. Il n'y a en fait pas eu de réflexion sur le choix d'une zone adaptée à la classification taxonomique du genre badnavirus puisque la région du génome utilisée pour la classification correspond par défaut à la région du génome des badnavirus disponible majoritairement sur Genbank et il est impossible d'obtenir systématiquement des séquences entières pour classifier ce genre de virus. Afin de mieux comprendre la diversité des badnavirus voire proposer des réaménagements de leur taxonomie, il est nécessaire de se baser sur des phylogénies utilisant des régions du génome représentatives du génome complet. Des études phylogénétiques plus poussées qui permettent d'implémenter des taux d'évolution différents selon les groupes de séquences ont également besoin de ce type de résultat. Pour remédier à ce manque d'informations phylogénétiques pertinentes, le génome des badnavirus entièrement séquencés (20 séquences) a été découpé en morceaux et des phylogénies ont été construites en alignant les différentes zones obtenues. Les phylogénies construites avec le logiciel Phyml (maximum de vraisemblance) sont présentées et discutées; une portion du génome ne produisant que peu de distorsions par rapport aux phylogénies basées sur les séquences entières est proposée. (Texte intégral
Bousalem M. - One of the best experts on this subject based on the ideXlab platform.
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Taxonomy, molecular phylogeny and evolution of plant reverse transcribing viruses (family Caulimoviridae) inferred from full-length genome and reverse transcriptase sequences
'Springer Science and Business Media LLC', 2008Co-Authors: Bousalem M., Douzery Emmanuel, Seal S.e.Abstract:International audienceThis study constitutes the first evaluation and application of quantitative taxonomy to the family Caulimoviridae and the first in-depth phylogenetic study of the family Caulimoviridae that integrates the common origin between LTR retrotransposons and caulimoviruses. The phylogenetic trees and PASC analyses derived from the full genome and from the corresponding partial RT concurred, providing strong support for the current genus classification based mainly on genome organisation and use of partial RT sequence as a molecular marker. The PASC distributions obtained are multimodal, making it possible to distinguish between genus, species and strain. The taxonomy of badnaviruses infecting banana (Musa spp.) was clarified, and the consequence of endogenous badnaviruses on the genetic diversity and evolution of caulimoviruses is discussed. The use of LTR retrotransposons as outgroups reveals a structured bipolar topology separating the genus Badnavirus from the other genera. Badnaviruses appear to be the most recent genus, with the genus Tungrovirus in an intermediary position. This structuring intersects the one established by genomic and biological properties and allows us to make a correlation between phylogeny and biogeography. The variability shown between members of the family Caulimoviridae is in a similiar range to that reported within other DNA and RNA plant virus families
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Taxonomy, molecular phylogeny and evolution of plant reverse transcribing viruses (family Caulimoviridae) inferred from full-length genome and reverse transcriptase sequences
'Springer Science and Business Media LLC', 2008Co-Authors: Bousalem M., Douzery E.j.p., Seal S.e.Abstract:This study constitutes the first evaluation and application of quantitative taxonomy to the family Caulimoviridae and the first in-depth phylogenetic study of the family Caulimoviridae that integrates the common origin between LTR retrotransposons and caulimoviruses. The phylogenetic trees and PASC analyses derived from the full genome and from the corresponding partial RT concurred, providing strong support for the current genus classification based mainly on genome organisation and use of partial RT sequence as a molecular marker. The PASC distributions obtained are multimodal, making it possible to distinguish between genus, species and strain. The taxonomy of badnaviruses infecting banana (Musa spp.) was clarified, and the consequence of endogenous badnaviruses on the genetic diversity and evolution of caulimoviruses is discussed. The use of LTR retrotransposons as outgroups reveals a structured bipolar topology separating the genus Badnavirus from the other genera. Badnaviruses appear to be the most recent genus, with the genus Tungrovirus in an intermediary position. This structuring intersects the one established by genomic and biological properties and allows us to make a correlation between phylogeny and biogeography. The variability shown between members of the family Caulimoviridae is in a similiar range to that reported within other DNA and RNA plant virus families
Indranil Dasgupta - One of the best experts on this subject based on the ideXlab platform.
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bacilliform dna containing plant viruses in the tropics commonalities within a genetically diverse group
Molecular Plant Pathology, 2013Co-Authors: Basanta K Borah, Shweta Sharma, Ravi Kant, A Anthony M Johnson, Divi Venkata Ramana Saigopal, Indranil DasguptaAbstract:Summary Plant viruses, possessing a bacilliform shape and containing double-stranded DNA, are emerging as important pathogens in a number of agricultural and horticultural crops in the tropics. They have been reported from a large number of countries in African and Asian continents, as well as from islands from the Pacific region. The viruses, belonging to two genera, Badnavirus and Tungrovirus, within the family Caulimoviridae, have genomes displaying a common plan, yet are highly variable, sometimes even between isolates of the same virus. In this article, we summarize the current knowledge with a view to revealing the common features embedded within the genetic diversity of this group of viruses. Taxonomy Virus; order Unassigned; family Caulimoviridae; genera Badnavirus and Tungrovirus; species Banana streak viruses, Bougainvillea spectabilis chlorotic vein banding virus, Cacao swollen shoot virus, Citrus yellow mosaic badnavirus, Dioscorea bacilliform viruses, Rice tungro bacilliform virus, Sugarcane bacilliform viruses and Taro bacilliform virus. Microbiological properties Bacilliform in shape; length, 60–900 nm; width, 35–50 nm; circular double-stranded DNA of approximately 7.5 kbp with one or more single-stranded discontinuities. Host range Each virus generally limited to its own host, including banana, bougainvillea, black pepper, cacao, citrus species, Dioscorea alata, rice, sugarcane and taro. Disease symptoms Foliar streaking in banana and sugarcane, swelling of shoots in cacao, yellow mosaic in leaves and stems in citrus, brown spot in the tubers in yam and yellow–orange discoloration and stunting in rice. Useful websites http://www.dpvweb.net.
