Phylogenetic and Molecular Variability Studies Reveal a New Genetic Clade of Citrus leprosis virus C
by
Pedro Luis Ramos-González 1,2
, 
Camila Chabi-Jesus 1,2,3, Orlene Guerra-Peraza 2, Michèle Claire Breton 1, Gabriella Dias Arena 1,4, Maria Andreia Nunes 1, Elliot Watanabe Kitajima 5, Marcos Antonio Machado 1 and Juliana Freitas-Astúa 2,6,*
Pedro Luis Ramos-González 1,2, Camila Chabi-Jesus 1,2,3, Orlene Guerra-Peraza 2, Michèle Claire Breton 1, Gabriella Dias Arena 1,4, Maria Andreia Nunes 1, Elliot Watanabe Kitajima 5, Marcos Antonio Machado 1 and Juliana Freitas-Astúa 2,6,*
1
Laboratório de Biotecnologia, Centro de Citricultura Sylvio Moreira, Instituto Agronômico de Campinas, Cordeirópolis, São Paulo 13490-970, Brazil
2
Departamento de Bioquímica Fitopatológica, Instituto Biológico, São Paulo 04014-002, Brazil
3
Departamento de Microbiologia Agrícola, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, São Paulo 13418-900, Brazil
4
Instituto de Biologia, Universidade de Campinas, Campinas, São Paulo 13083-970, Brazil
5
Departamento de Fitopatologia e Nematologia, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, São Paulo 13418-900, Brazil
6
Embrapa Cassava and Fruits, Cruz das Almas, Bahia 44380-000, Brazil
*
Author to whom correspondence should be addressed.
Academic Editor: Thomas Hohn
Viruses 2016, 8(6), 153; https://doi.org/10.3390/v8060153
Received: 11 March 2016 / Revised: 10 May 2016 / Accepted: 24 May 2016 / Published: 6 June 2016
(This article belongs to the Section Viruses of Plants, Fungi and Protozoa)
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 πp29 and πMP were higher than those of πp15 and πRNA2–IR, whereas πMP 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.
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Keywords:
cilevirus; citrus leprosis; Brevipalpus-transmitted viruses
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited
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MDPI and ACS Style
Ramos-González, P.L.; Chabi-Jesus, C.; Guerra-Peraza, O.; Breton, M.C.; Arena, G.D.; Nunes, M.A.; Kitajima, E.W.; Machado, M.A.; Freitas-Astúa, J. Phylogenetic and Molecular Variability Studies Reveal a New Genetic Clade of Citrus leprosis virus C. Viruses 2016, 8, 153.
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