A Complex of Badnavirus Species Infecting Cacao Reveals Mixed Infections, Extensive Genomic Variability, and Interspecific Recombination
Gutierrez, Osman A.
Brown, Judith K.
AffiliationUniv Arizona, Sch Plant Sci
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CitationRamos-Sobrinho, R.; Chingandu, N.; Gutierrez, O. A.; Marelli, J.-P.; Brown, J. K. A Complex of Badnavirus Species Infecting Cacao Reveals Mixed Infections, Extensive Genomic Variability, and Interspecific Recombination. Viruses 2020, 12, 443.
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AbstractThe incidence of cacao swollen shoot disease (CSSD) in cacao (Theobroma cacao L.) has increased in West Africa since similar to 2000. To investigate the genomic and species diversity of the CSSD-badnaviruses infecting cacao in Cote d'Ivoire and Ghana, symptomatic leaves were subjected to high-throughput sequencing. Among the 30 newly determined genomes, three badnaviruses were identified, Cacao swollen shoot Togo B virus (CSSTBV), Cacao swollen shoot CD virus, and Cacao swollen shoot CE virus (CSSCEV). The phylogenetic trees reconstructed for the reverse transcriptase (RT) and ribonuclease H (RNase H) sequences were incongruent with the complete viral genomes, which had the most robust statistical support. Recombination seems to be involved in the CSSD-badnavirus diversification. The genomic diversity varied among different CSSD-badnaviruses, with CSSTBV showing the lowest nucleotide diversity (pi = 0.06236), and CSSCEV exhibiting the greatest variability (pi = 0.21911). Evidence of strong purifying selection was found in the coding regions of the CSSTBV isolates.
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Except where otherwise noted, this item's license is described as Copyright © 2020 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/).
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