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Phylogenetic and Molecular Variability Studies Reveal a New Genetic Clade of Citrus leprosis virus C
Citrus leprosis virus C (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 (p29, p15, MP and RNA2-intergenic region) distributed over its two RNAs. Nucleotide diversity (π)...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4926173/ https://www.ncbi.nlm.nih.gov/pubmed/27275832 http://dx.doi.org/10.3390/v8060153 |
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author | Ramos-González, Pedro Luis Chabi-Jesus, Camila Guerra-Peraza, Orlene Breton, Michèle Claire Arena, Gabriella Dias Nunes, Maria Andreia Kitajima, Elliot Watanabe Machado, Marcos Antonio Freitas-Astúa, Juliana |
author_facet | Ramos-González, Pedro Luis Chabi-Jesus, Camila Guerra-Peraza, Orlene Breton, Michèle Claire Arena, Gabriella Dias Nunes, Maria Andreia Kitajima, Elliot Watanabe Machado, Marcos Antonio Freitas-Astúa, Juliana |
author_sort | Ramos-González, Pedro Luis |
collection | PubMed |
description | Citrus leprosis virus C (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 (p29, p15, MP 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(p)(29) and π(MP) were higher than those of π(p)(15) and π(RNA2–IR,) whereas π(MP) 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 Cilevirus, 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 Commelina benghalensis and is efficiently transmitted by Brevipalpus yothersi 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. |
format | Online Article Text |
id | pubmed-4926173 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-49261732016-07-06 Phylogenetic and Molecular Variability Studies Reveal a New Genetic Clade of Citrus leprosis virus C Ramos-González, Pedro Luis Chabi-Jesus, Camila Guerra-Peraza, Orlene Breton, Michèle Claire Arena, Gabriella Dias Nunes, Maria Andreia Kitajima, Elliot Watanabe Machado, Marcos Antonio Freitas-Astúa, Juliana Viruses Article Citrus leprosis virus C (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 (p29, p15, MP 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(p)(29) and π(MP) were higher than those of π(p)(15) and π(RNA2–IR,) whereas π(MP) 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 Cilevirus, 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 Commelina benghalensis and is efficiently transmitted by Brevipalpus yothersi 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. MDPI 2016-06-06 /pmc/articles/PMC4926173/ /pubmed/27275832 http://dx.doi.org/10.3390/v8060153 Text en © 2016 by the authors; licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC-BY) license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Ramos-González, Pedro Luis Chabi-Jesus, Camila Guerra-Peraza, Orlene Breton, Michèle Claire Arena, Gabriella Dias Nunes, Maria Andreia Kitajima, Elliot Watanabe Machado, Marcos Antonio Freitas-Astúa, Juliana Phylogenetic and Molecular Variability Studies Reveal a New Genetic Clade of Citrus leprosis virus C |
title | Phylogenetic and Molecular Variability Studies Reveal a New Genetic Clade of Citrus leprosis virus C |
title_full | Phylogenetic and Molecular Variability Studies Reveal a New Genetic Clade of Citrus leprosis virus C |
title_fullStr | Phylogenetic and Molecular Variability Studies Reveal a New Genetic Clade of Citrus leprosis virus C |
title_full_unstemmed | Phylogenetic and Molecular Variability Studies Reveal a New Genetic Clade of Citrus leprosis virus C |
title_short | Phylogenetic and Molecular Variability Studies Reveal a New Genetic Clade of Citrus leprosis virus C |
title_sort | phylogenetic and molecular variability studies reveal a new genetic clade of citrus leprosis virus c |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4926173/ https://www.ncbi.nlm.nih.gov/pubmed/27275832 http://dx.doi.org/10.3390/v8060153 |
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