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Viruses 2015, 7(7), 4152-4168; doi:10.3390/v7072814

Phylogenetic Studies of the Three RNA Silencing Suppressor Genes of South American CTV Isolates Reveal the Circulation of a Novel Genetic Lineage

1
Laboratorio de Virología Molecular, Centro Universitario Regional Noroeste (CENUR Noroeste), Universidad de la Republica (UdelaR), Rivera 1350, 50000 Salto, Uruguay
2
Programa Nacional de Investigación en Producción Citrícola, Instituto Nacional de Investigación Agropecuaria (INIA), Urguay
*
Author to whom correspondence should be addressed.
Academic Editor: Thomas Hohn
Received: 26 May 2015 / Revised: 4 July 2015 / Accepted: 17 July 2015 / Published: 22 July 2015
(This article belongs to the Section Viruses of Plants, Fungi and Protozoa)
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Abstract

Citrus Tristeza Virus (CTV) is the most economically important virus of citrus worldwide. Genetic diversity and population structure of CTV isolates from all citrus growing areas from Uruguay were analyzed by RT-PCR and cloning of the three RNA silencing suppressor genes (p25, p20 and p23). Bayesian phylogenetic analysis revealed the circulation of three known genotypes (VT, T3, T36) in the country, and the presence of a new genetic lineage composed by isolates from around the world, mainly from South America. Nucleotide and amino acid identity values for this new genetic lineage were both higher than 97% for the three analyzed regions. Due to incongruent phylogenetic relationships, recombination analysis was performed using Genetic Algorithms for Recombination Detection (GARD) and SimPlot software. Recombination events between previously described CTV isolates were detected. High intra-sample variation was found, confirming the co-existence of different genotypes into the same plant. This is the first report describing: (1) the genetic diversity of Uruguayan CTV isolates circulating in the country and (2) the circulation of a novel CTV genetic lineage, highly present in the South American region. This information may provide assistance to develop an effective cross-protection program. View Full-Text
Keywords: Citrus Tristeza Virus; RT-PCR; RNA Silencing Suppressor Genes; Phylogeny; Recombination; Novel Genetic Lineage; Uruguay Citrus Tristeza Virus; RT-PCR; RNA Silencing Suppressor Genes; Phylogeny; Recombination; Novel Genetic Lineage; Uruguay
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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. (CC BY 4.0).

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MDPI and ACS Style

Benítez-Galeano, M.J.; Rubio, L.; Bertalmío, A.; Maeso, D.; Rivas, F.; Colina, R. Phylogenetic Studies of the Three RNA Silencing Suppressor Genes of South American CTV Isolates Reveal the Circulation of a Novel Genetic Lineage. Viruses 2015, 7, 4152-4168.

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