Abstract
The incidence of cacao swollen shoot disease (CSSD) in cacao (Theobroma cacao L.) has increased in West Africa since ~2000. To investigate the genomic and species diversity of the CSSD-badnaviruses infecting cacao in Côte 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 (π = 0.06236), and CSSCEV exhibiting the greatest variability (π = 0.21911). Evidence of strong purifying selection was found in the coding regions of the CSSTBV isolates.
Highlights
The Amazon Basin in South America is the center of genetic diversity for cacao (Theobroma cacao L.), the source of the cocoa beans
Disease symptoms reminiscent of cacao swollen shoot disease (CSSD) in West Africa were observed in cacao in Sri Lanka in 1956–1957 [19]; only recently, the badnavirus Cacao bacilliform Sri Lanka virus (CBSLV) was identified in cacao trees showing symptoms similar to those described in the 1950s [15]
The assembly produced a number of partial badnavirus-like sequences; only sequences for which a complete genome was determined were used in the analyses reported here
Summary
The Amazon Basin in South America is the center of genetic diversity for cacao (Theobroma cacao L.), the source of the cocoa beans. Virus-like symptoms were first reported in cacao trees during 1936 in Ghana [6]. With the expansion of cacao production into other West African countries, outbreaks caused by cacao swollen shoot disease (CSSD) were reported throughout the entire region [8,9,10,11,12,13,14,15,16,17,18]. Disease symptoms reminiscent of CSSD in West Africa were observed in cacao in Sri Lanka in 1956–1957 [19]; only recently, the badnavirus Cacao bacilliform Sri Lanka virus (CBSLV) was identified in cacao trees showing symptoms similar to those described in the 1950s [15]. Foliar discoloration symptoms were prominent in diseased cacao plants from both Trinidad and West Africa, shoot swellings were not observed in Trinidad [20].
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