Phylogenetic and Molecular Variability Studies Reveal a New Genetic Clade of Citrus leprosis virus C
Identifieur interne : 000088 ( Main/Exploration ); précédent : 000087; suivant : 000089Phylogenetic and Molecular Variability Studies Reveal a New Genetic Clade of Citrus leprosis virus C
Auteurs : Pedro Luis Ramos-González ; Camila Chabi-Jesus [Brésil] ; Orlene Guerra-Peraza ; Michèle Claire Breton ; Gabriella Dias Arena [Brésil] ; Maria Andreia Nunes ; Elliot Watanabe Kitajima ; Marcos Antonio Machado ; Juliana Freitas-Astúa [Brésil]Source :
- Viruses [ 1999-4915 ] ; 2016.
Abstract
Url:
DOI: 10.3390/v8060153
PubMed: 27275832
PubMed Central: 4926173
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Phylogenetic and Molecular Variability Studies Reveal a New Genetic Clade of <italic>Citrus leprosis virus C</italic></title><author><name sortKey="Ramos Gonzalez, Pedro Luis" sort="Ramos Gonzalez, Pedro Luis" uniqKey="Ramos Gonzalez P" first="Pedro Luis" last="Ramos-González">Pedro Luis Ramos-González</name><affiliation><nlm:aff id="af1-viruses-08-00153">Laboratório de Biotecnologia, Centro de Citricultura Sylvio Moreira, Instituto Agronômico de Campinas, Cordeirópolis, São Paulo 13490-970, Brazil;<email>plrg1970@gmail.com</email> (P.L.R.-G.);<email>millachabi@yahoo.com.br</email> (C.C.-J.);<email>mbreton@uol.com.br</email> (M.C.B.);<email>gaby.arena@gmail.com</email> (G.D.A.);<email>mandreian@yahoo.com</email> (M.A.N.);<email>marcos@centrodecitricultura.br</email> (M.A.M.)</nlm:aff></affiliation><affiliation><nlm:aff id="af2-viruses-08-00153">Departamento de Bioquímica Fitopatológica, Instituto Biológico, São Paulo 04014-002, Brazil;<email>onelio@protonmail.com</email></nlm:aff></affiliation></author><author><name sortKey="Chabi Jesus, Camila" sort="Chabi Jesus, Camila" uniqKey="Chabi Jesus C" first="Camila" last="Chabi-Jesus">Camila Chabi-Jesus</name><affiliation><nlm:aff id="af1-viruses-08-00153">Laboratório de Biotecnologia, Centro de Citricultura Sylvio Moreira, Instituto Agronômico de Campinas, Cordeirópolis, São Paulo 13490-970, Brazil;<email>plrg1970@gmail.com</email> (P.L.R.-G.);<email>millachabi@yahoo.com.br</email> (C.C.-J.);<email>mbreton@uol.com.br</email> (M.C.B.);<email>gaby.arena@gmail.com</email> (G.D.A.);<email>mandreian@yahoo.com</email> (M.A.N.);<email>marcos@centrodecitricultura.br</email> (M.A.M.)</nlm:aff></affiliation><affiliation><nlm:aff id="af2-viruses-08-00153">Departamento de Bioquímica Fitopatológica, Instituto Biológico, São Paulo 04014-002, Brazil;<email>onelio@protonmail.com</email></nlm:aff></affiliation><affiliation wicri:level="4"><nlm:aff id="af3-viruses-08-00153">Departamento de Microbiologia Agrícola, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, São Paulo 13418-900, Brazil</nlm:aff><country xml:lang="fr">Brésil</country><wicri:regionArea>Departamento de Microbiologia Agrícola, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, São Paulo 13418-900</wicri:regionArea><placeName><settlement type="city">São Paulo</settlement><region type="state">État de São Paulo</region></placeName><orgName type="university">Université de São Paulo</orgName><placeName><settlement type="city">São Paulo</settlement><region type="state">État de São Paulo</region></placeName></affiliation></author><author><name sortKey="Guerra Peraza, Orlene" sort="Guerra Peraza, Orlene" uniqKey="Guerra Peraza O" first="Orlene" last="Guerra-Peraza">Orlene Guerra-Peraza</name><affiliation><nlm:aff id="af2-viruses-08-00153">Departamento de Bioquímica Fitopatológica, Instituto Biológico, São Paulo 04014-002, Brazil;<email>onelio@protonmail.com</email></nlm:aff></affiliation></author><author><name sortKey="Breton, Michele Claire" sort="Breton, Michele Claire" uniqKey="Breton M" first="Michèle Claire" last="Breton">Michèle Claire Breton</name><affiliation><nlm:aff id="af1-viruses-08-00153">Laboratório de Biotecnologia, Centro de Citricultura Sylvio Moreira, Instituto Agronômico de Campinas, Cordeirópolis, São Paulo 13490-970, Brazil;<email>plrg1970@gmail.com</email> (P.L.R.-G.);<email>millachabi@yahoo.com.br</email> (C.C.-J.);<email>mbreton@uol.com.br</email> (M.C.B.);<email>gaby.arena@gmail.com</email> (G.D.A.);<email>mandreian@yahoo.com</email> (M.A.N.);<email>marcos@centrodecitricultura.br</email> (M.A.M.)</nlm:aff></affiliation></author><author><name sortKey="Arena, Gabriella Dias" sort="Arena, Gabriella Dias" uniqKey="Arena G" first="Gabriella Dias" last="Arena">Gabriella Dias Arena</name><affiliation><nlm:aff id="af1-viruses-08-00153">Laboratório de Biotecnologia, Centro de Citricultura Sylvio Moreira, Instituto Agronômico de Campinas, Cordeirópolis, São Paulo 13490-970, Brazil;<email>plrg1970@gmail.com</email> (P.L.R.-G.);<email>millachabi@yahoo.com.br</email> (C.C.-J.);<email>mbreton@uol.com.br</email> (M.C.B.);<email>gaby.arena@gmail.com</email> (G.D.A.);<email>mandreian@yahoo.com</email> (M.A.N.);<email>marcos@centrodecitricultura.br</email> (M.A.M.)</nlm:aff></affiliation><affiliation wicri:level="1"><nlm:aff id="af4-viruses-08-00153">Instituto de Biologia, Universidade de Campinas, Campinas, São Paulo 13083-970, Brazil</nlm:aff><country xml:lang="fr">Brésil</country><wicri:regionArea>Instituto de Biologia, Universidade de Campinas, Campinas, São Paulo 13083-970</wicri:regionArea><placeName><settlement type="city">São Paulo</settlement><region type="state">État de São Paulo</region></placeName></affiliation></author><author><name sortKey="Nunes, Maria Andreia" sort="Nunes, Maria Andreia" uniqKey="Nunes M" first="Maria Andreia" last="Nunes">Maria Andreia Nunes</name><affiliation><nlm:aff id="af1-viruses-08-00153">Laboratório de Biotecnologia, Centro de Citricultura Sylvio Moreira, Instituto Agronômico de Campinas, Cordeirópolis, São Paulo 13490-970, Brazil;<email>plrg1970@gmail.com</email> (P.L.R.-G.);<email>millachabi@yahoo.com.br</email> (C.C.-J.);<email>mbreton@uol.com.br</email> (M.C.B.);<email>gaby.arena@gmail.com</email> (G.D.A.);<email>mandreian@yahoo.com</email> (M.A.N.);<email>marcos@centrodecitricultura.br</email> (M.A.M.)</nlm:aff></affiliation></author><author><name sortKey="Kitajima, Elliot Watanabe" sort="Kitajima, Elliot Watanabe" uniqKey="Kitajima E" first="Elliot Watanabe" last="Kitajima">Elliot Watanabe Kitajima</name><affiliation><nlm:aff id="af5-viruses-08-00153">Departamento de Fitopatologia e Nematologia, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, São Paulo 13418-900, Brazil;<email>ewkitaji@usp.br</email></nlm:aff></affiliation></author><author><name sortKey="Machado, Marcos Antonio" sort="Machado, Marcos Antonio" uniqKey="Machado M" first="Marcos Antonio" last="Machado">Marcos Antonio Machado</name><affiliation><nlm:aff id="af1-viruses-08-00153">Laboratório de Biotecnologia, Centro de Citricultura Sylvio Moreira, Instituto Agronômico de Campinas, Cordeirópolis, São Paulo 13490-970, Brazil;<email>plrg1970@gmail.com</email> (P.L.R.-G.);<email>millachabi@yahoo.com.br</email> (C.C.-J.);<email>mbreton@uol.com.br</email> (M.C.B.);<email>gaby.arena@gmail.com</email> (G.D.A.);<email>mandreian@yahoo.com</email> (M.A.N.);<email>marcos@centrodecitricultura.br</email> (M.A.M.)</nlm:aff></affiliation></author><author><name sortKey="Freitas Astua, Juliana" sort="Freitas Astua, Juliana" uniqKey="Freitas Astua J" first="Juliana" last="Freitas-Astúa">Juliana Freitas-Astúa</name><affiliation><nlm:aff id="af2-viruses-08-00153">Departamento de Bioquímica Fitopatológica, Instituto Biológico, São Paulo 04014-002, Brazil;<email>onelio@protonmail.com</email></nlm:aff></affiliation><affiliation wicri:level="1"><nlm:aff id="af6-viruses-08-00153">Embrapa Cassava and Fruits, Cruz das Almas, Bahia 44380-000, Brazil</nlm:aff><country xml:lang="fr">Brésil</country><wicri:regionArea>Embrapa Cassava and Fruits, Cruz das Almas, Bahia 44380-000</wicri:regionArea><wicri:noRegion>Bahia 44380-000</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">27275832</idno><idno type="pmc">4926173</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4926173</idno><idno type="RBID">PMC:4926173</idno><idno type="doi">10.3390/v8060153</idno><date when="2016">2016</date><idno type="wicri:Area/Pmc/Corpus">000406</idno><idno type="wicri:Area/Pmc/Curation">000405</idno><idno type="wicri:Area/Pmc/Checkpoint">000070</idno><idno type="wicri:Area/Ncbi/Merge">002058</idno><idno type="wicri:Area/Ncbi/Curation">002058</idno><idno type="wicri:Area/Ncbi/Checkpoint">002058</idno><idno type="wicri:Area/Main/Merge">000088</idno><idno type="wicri:Area/Main/Curation">000088</idno><idno type="wicri:Area/Main/Exploration">000088</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Phylogenetic and Molecular Variability Studies Reveal a New Genetic Clade of <italic>Citrus leprosis virus C</italic></title><author><name sortKey="Ramos Gonzalez, Pedro Luis" sort="Ramos Gonzalez, Pedro Luis" uniqKey="Ramos Gonzalez P" first="Pedro Luis" last="Ramos-González">Pedro Luis Ramos-González</name><affiliation><nlm:aff id="af1-viruses-08-00153">Laboratório de Biotecnologia, Centro de Citricultura Sylvio Moreira, Instituto Agronômico de Campinas, Cordeirópolis, São Paulo 13490-970, Brazil;<email>plrg1970@gmail.com</email> (P.L.R.-G.);<email>millachabi@yahoo.com.br</email> (C.C.-J.);<email>mbreton@uol.com.br</email> (M.C.B.);<email>gaby.arena@gmail.com</email> (G.D.A.);<email>mandreian@yahoo.com</email> (M.A.N.);<email>marcos@centrodecitricultura.br</email> (M.A.M.)</nlm:aff></affiliation><affiliation><nlm:aff id="af2-viruses-08-00153">Departamento de Bioquímica Fitopatológica, Instituto Biológico, São Paulo 04014-002, Brazil;<email>onelio@protonmail.com</email></nlm:aff></affiliation></author><author><name sortKey="Chabi Jesus, Camila" sort="Chabi Jesus, Camila" uniqKey="Chabi Jesus C" first="Camila" last="Chabi-Jesus">Camila Chabi-Jesus</name><affiliation><nlm:aff id="af1-viruses-08-00153">Laboratório de Biotecnologia, Centro de Citricultura Sylvio Moreira, Instituto Agronômico de Campinas, Cordeirópolis, São Paulo 13490-970, Brazil;<email>plrg1970@gmail.com</email> (P.L.R.-G.);<email>millachabi@yahoo.com.br</email> (C.C.-J.);<email>mbreton@uol.com.br</email> (M.C.B.);<email>gaby.arena@gmail.com</email> (G.D.A.);<email>mandreian@yahoo.com</email> (M.A.N.);<email>marcos@centrodecitricultura.br</email> (M.A.M.)</nlm:aff></affiliation><affiliation><nlm:aff id="af2-viruses-08-00153">Departamento de Bioquímica Fitopatológica, Instituto Biológico, São Paulo 04014-002, Brazil;<email>onelio@protonmail.com</email></nlm:aff></affiliation><affiliation wicri:level="4"><nlm:aff id="af3-viruses-08-00153">Departamento de Microbiologia Agrícola, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, São Paulo 13418-900, Brazil</nlm:aff><country xml:lang="fr">Brésil</country><wicri:regionArea>Departamento de Microbiologia Agrícola, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, São Paulo 13418-900</wicri:regionArea><placeName><settlement type="city">São Paulo</settlement><region type="state">État de São Paulo</region></placeName><orgName type="university">Université de São Paulo</orgName><placeName><settlement type="city">São Paulo</settlement><region type="state">État de São Paulo</region></placeName></affiliation></author><author><name sortKey="Guerra Peraza, Orlene" sort="Guerra Peraza, Orlene" uniqKey="Guerra Peraza O" first="Orlene" last="Guerra-Peraza">Orlene Guerra-Peraza</name><affiliation><nlm:aff id="af2-viruses-08-00153">Departamento de Bioquímica Fitopatológica, Instituto Biológico, São Paulo 04014-002, Brazil;<email>onelio@protonmail.com</email></nlm:aff></affiliation></author><author><name sortKey="Breton, Michele Claire" sort="Breton, Michele Claire" uniqKey="Breton M" first="Michèle Claire" last="Breton">Michèle Claire Breton</name><affiliation><nlm:aff id="af1-viruses-08-00153">Laboratório de Biotecnologia, Centro de Citricultura Sylvio Moreira, Instituto Agronômico de Campinas, Cordeirópolis, São Paulo 13490-970, Brazil;<email>plrg1970@gmail.com</email> (P.L.R.-G.);<email>millachabi@yahoo.com.br</email> (C.C.-J.);<email>mbreton@uol.com.br</email> (M.C.B.);<email>gaby.arena@gmail.com</email> (G.D.A.);<email>mandreian@yahoo.com</email> (M.A.N.);<email>marcos@centrodecitricultura.br</email> (M.A.M.)</nlm:aff></affiliation></author><author><name sortKey="Arena, Gabriella Dias" sort="Arena, Gabriella Dias" uniqKey="Arena G" first="Gabriella Dias" last="Arena">Gabriella Dias Arena</name><affiliation><nlm:aff id="af1-viruses-08-00153">Laboratório de Biotecnologia, Centro de Citricultura Sylvio Moreira, Instituto Agronômico de Campinas, Cordeirópolis, São Paulo 13490-970, Brazil;<email>plrg1970@gmail.com</email> (P.L.R.-G.);<email>millachabi@yahoo.com.br</email> (C.C.-J.);<email>mbreton@uol.com.br</email> (M.C.B.);<email>gaby.arena@gmail.com</email> (G.D.A.);<email>mandreian@yahoo.com</email> (M.A.N.);<email>marcos@centrodecitricultura.br</email> (M.A.M.)</nlm:aff></affiliation><affiliation wicri:level="1"><nlm:aff id="af4-viruses-08-00153">Instituto de Biologia, Universidade de Campinas, Campinas, São Paulo 13083-970, Brazil</nlm:aff><country xml:lang="fr">Brésil</country><wicri:regionArea>Instituto de Biologia, Universidade de Campinas, Campinas, São Paulo 13083-970</wicri:regionArea><placeName><settlement type="city">São Paulo</settlement><region type="state">État de São Paulo</region></placeName></affiliation></author><author><name sortKey="Nunes, Maria Andreia" sort="Nunes, Maria Andreia" uniqKey="Nunes M" first="Maria Andreia" last="Nunes">Maria Andreia Nunes</name><affiliation><nlm:aff id="af1-viruses-08-00153">Laboratório de Biotecnologia, Centro de Citricultura Sylvio Moreira, Instituto Agronômico de Campinas, Cordeirópolis, São Paulo 13490-970, Brazil;<email>plrg1970@gmail.com</email> (P.L.R.-G.);<email>millachabi@yahoo.com.br</email> (C.C.-J.);<email>mbreton@uol.com.br</email> (M.C.B.);<email>gaby.arena@gmail.com</email> (G.D.A.);<email>mandreian@yahoo.com</email> (M.A.N.);<email>marcos@centrodecitricultura.br</email> (M.A.M.)</nlm:aff></affiliation></author><author><name sortKey="Kitajima, Elliot Watanabe" sort="Kitajima, Elliot Watanabe" uniqKey="Kitajima E" first="Elliot Watanabe" last="Kitajima">Elliot Watanabe Kitajima</name><affiliation><nlm:aff id="af5-viruses-08-00153">Departamento de Fitopatologia e Nematologia, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, São Paulo 13418-900, Brazil;<email>ewkitaji@usp.br</email></nlm:aff></affiliation></author><author><name sortKey="Machado, Marcos Antonio" sort="Machado, Marcos Antonio" uniqKey="Machado M" first="Marcos Antonio" last="Machado">Marcos Antonio Machado</name><affiliation><nlm:aff id="af1-viruses-08-00153">Laboratório de Biotecnologia, Centro de Citricultura Sylvio Moreira, Instituto Agronômico de Campinas, Cordeirópolis, São Paulo 13490-970, Brazil;<email>plrg1970@gmail.com</email> (P.L.R.-G.);<email>millachabi@yahoo.com.br</email> (C.C.-J.);<email>mbreton@uol.com.br</email> (M.C.B.);<email>gaby.arena@gmail.com</email> (G.D.A.);<email>mandreian@yahoo.com</email> (M.A.N.);<email>marcos@centrodecitricultura.br</email> (M.A.M.)</nlm:aff></affiliation></author><author><name sortKey="Freitas Astua, Juliana" sort="Freitas Astua, Juliana" uniqKey="Freitas Astua J" first="Juliana" last="Freitas-Astúa">Juliana Freitas-Astúa</name><affiliation><nlm:aff id="af2-viruses-08-00153">Departamento de Bioquímica Fitopatológica, Instituto Biológico, São Paulo 04014-002, Brazil;<email>onelio@protonmail.com</email></nlm:aff></affiliation><affiliation wicri:level="1"><nlm:aff id="af6-viruses-08-00153">Embrapa Cassava and Fruits, Cruz das Almas, Bahia 44380-000, Brazil</nlm:aff><country xml:lang="fr">Brésil</country><wicri:regionArea>Embrapa Cassava and Fruits, Cruz das Almas, Bahia 44380-000</wicri:regionArea><wicri:noRegion>Bahia 44380-000</wicri:noRegion></affiliation></author></analytic><series><title level="j">Viruses</title><idno type="eISSN">1999-4915</idno><imprint><date when="2016">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><italic>Citrus leprosis virus C</italic> (CiLV-C) causes a severe disease affecting citrus orchards in the Western hemisphere. This study reveals the molecular variability of the virus by analyzing four genomic regions (<italic>p29</italic>, <italic>p15</italic>, <italic>MP</italic> and RNA2-intergenic region) distributed over its two RNAs. Nucleotide diversity (π) values were relatively low but statistically different over the analyzed genes and subpopulations, indicating their distinct evolutionary history. Values of π<italic><sub>p</sub></italic><sub>29</sub> and π<italic><sub>MP</sub></italic> were higher than those of π<italic><sub>p</sub></italic><sub>15</sub> and π<sub>RNA2–IR,</sub> whereas π<italic><sub>MP</sub></italic> was increased due to novel discovered isolates phylogenetically clustered in a divergent clade that we called SJP. Isolate BR_SP_SJP_01 RNA1 and RNA2 sequences, clade SJP, showed an identity of 85.6% and 88.4%, respectively, with those corresponding to CiLV-C, the type member of the genus <italic>Cilevirus</italic>, and its RNA2 5′-proximal region was revealed as a minor donor in a putative inter-clade recombination event. In addition to citrus, BR_SP_SJP_01 naturally infects the weed <italic>Commelina benghalensis</italic> and is efficiently transmitted by <italic>Brevipalpus yothersi</italic> mites. Our data demonstrated that negative selection was the major force operating in the evaluated viral coding regions and defined amino acids putatively relevant for the biological function of cilevirus proteins. This work provides molecular tools and sets up a framework for further epidemiological studies.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Roy, A" uniqKey="Roy A">A. 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Freitas-Astúa</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Brésil</li></country><region><li>État de São Paulo</li></region><settlement><li>São Paulo</li></settlement><orgName><li>Université de São Paulo</li></orgName></list><tree><noCountry><name sortKey="Breton, Michele Claire" sort="Breton, Michele Claire" uniqKey="Breton M" first="Michèle Claire" last="Breton">Michèle Claire Breton</name><name sortKey="Guerra Peraza, Orlene" sort="Guerra Peraza, Orlene" uniqKey="Guerra Peraza O" first="Orlene" last="Guerra-Peraza">Orlene Guerra-Peraza</name><name sortKey="Kitajima, Elliot Watanabe" sort="Kitajima, Elliot Watanabe" uniqKey="Kitajima E" first="Elliot Watanabe" last="Kitajima">Elliot Watanabe Kitajima</name><name sortKey="Machado, Marcos Antonio" sort="Machado, Marcos Antonio" uniqKey="Machado M" first="Marcos Antonio" last="Machado">Marcos Antonio Machado</name><name sortKey="Nunes, Maria Andreia" sort="Nunes, Maria Andreia" uniqKey="Nunes M" first="Maria Andreia" last="Nunes">Maria Andreia Nunes</name><name sortKey="Ramos Gonzalez, Pedro Luis" sort="Ramos Gonzalez, Pedro Luis" uniqKey="Ramos Gonzalez P" first="Pedro Luis" last="Ramos-González">Pedro Luis Ramos-González</name></noCountry><country name="Brésil"><region name="État de São Paulo"><name sortKey="Chabi Jesus, Camila" sort="Chabi Jesus, Camila" uniqKey="Chabi Jesus C" first="Camila" last="Chabi-Jesus">Camila Chabi-Jesus</name></region><name sortKey="Arena, Gabriella Dias" sort="Arena, Gabriella Dias" uniqKey="Arena G" first="Gabriella Dias" last="Arena">Gabriella Dias Arena</name><name sortKey="Freitas Astua, Juliana" sort="Freitas Astua, Juliana" uniqKey="Freitas Astua J" first="Juliana" last="Freitas-Astúa">Juliana Freitas-Astúa</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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