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) 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.
Laborat&#243;rio de Biotecnologia, Centro de Citricultura Sylvio Moreira, Instituto Agron&#244;mico de Campinas, Cordeir&#243;polis, S&#227;o Paulo 13490-970, Brazil. plrg1970@gmail.com.|Departamento de Bioqu&#237;mica Fitopatol&#243;gica, Instituto Biol&#243;gico, S&#227;o Paulo 04014-002, Brazil. plrg1970@gmail.com.
Pedro Luis
PL
Ramos-González
Laborat&#243;rio de Biotecnologia, Centro de Citricultura Sylvio Moreira, Instituto Agron&#244;mico de Campinas, Cordeir&#243;polis, S&#227;o Paulo 13490-970, Brazil. millachabi@yahoo.com.br.|Departamento de Bioqu&#237;mica Fitopatol&#243;gica, Instituto Biol&#243;gico, S&#227;o Paulo 04014-002, Brazil. millachabi@yahoo.com.br.|Departamento de Microbiologia Agr&#237;cola, Escola Superior de Agricultura Luiz de Queiroz, Universidade de S&#227;o Paulo, Piracicaba, S&#227;o Paulo 13418-900, Brazil. millachabi@yahoo.com.br.
Camila
C
Chabi-Jesus
Departamento de Bioqu&#237;mica Fitopatol&#243;gica, Instituto Biol&#243;gico, S&#227;o Paulo 04014-002, Brazil. onelio@protonmail.com.
Orlene
O
Guerra-Peraza
Laborat&#243;rio de Biotecnologia, Centro de Citricultura Sylvio Moreira, Instituto Agron&#244;mico de Campinas, Cordeir&#243;polis, S&#227;o Paulo 13490-970, Brazil. mbreton@uol.com.br.
Michèle Claire
MC
Breton
Laborat&#243;rio de Biotecnologia, Centro de Citricultura Sylvio Moreira, Instituto Agron&#244;mico de Campinas, Cordeir&#243;polis, S&#227;o Paulo 13490-970, Brazil. gaby.arena@gmail.com.|Instituto de Biologia, Universidade de Campinas, Campinas, S&#227;o Paulo 13083-970, Brazil. gaby.arena@gmail.com.
Gabriella Dias
GD
Arena
Laborat&#243;rio de Biotecnologia, Centro de Citricultura Sylvio Moreira, Instituto Agron&#244;mico de Campinas, Cordeir&#243;polis, S&#227;o Paulo 13490-970, Brazil. mandreian@yahoo.com.
Maria Andreia
MA
Nunes
Departamento de Fitopatologia e Nematologia, Escola Superior de Agricultura Luiz de Queiroz, Universidade de S&#227;o Paulo, Piracicaba, S&#227;o Paulo 13418-900, Brazil. ewkitaji@usp.br.
Elliot Watanabe
EW
Kitajima
Laborat&#243;rio de Biotecnologia, Centro de Citricultura Sylvio Moreira, Instituto Agron&#244;mico de Campinas, Cordeir&#243;polis, S&#227;o Paulo 13490-970, Brazil. marcos@centrodecitricultura.br.
Marcos Antonio
MA
Machado
Departamento de Bioqu&#237;mica Fitopatol&#243;gica, Instituto Biol&#243;gico, S&#227;o Paulo 04014-002, Brazil. juliana.astua@embrapa.br.|Embrapa Cassava and Fruits, Cruz das Almas, Bahia 44380-000, Brazil. juliana.astua@embrapa.br.
Juliana
J
Freitas-Astúa
D000818:Animals; D002957:Citrus / Q000821:virology*; D034822:Commelina / Q000821:virology; D018562:Disease Transmission, Infectious; D005814:Genes, Viral; D007303:Insect Vectors / Q000821:virology; D008925:Mites / Q000821:virology; D010802:Phylogeny; D010935:Plant Diseases / Q000821:virology*; D010942:Plant Viruses / Q000145:classification* / Q000235:genetics*; D012328:RNA Viruses / Q000145:classification* / Q000235:genetics*; D017385:Sequence Homology
Brevipalpus-transmitted viruses; cilevirus; citrus leprosis