A Complex of Badnavirus Species Infecting Cacao Reveals Mixed Infections, Extensive Genomic Variability, and Interspecific Recombination

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.

Construction of an Infectious Clone of the Badnavirus Cacao Swollen Shoot Ghana M Virus and Infectivity by Gene Gun- and Agrobacterium-Mediated Inoculation

“…Cacao "Amelonado" plants agroinoculated with a CSSTBV infectious clone exhibited red vein-banding symptoms 60 dpi (Jacquot et al, 1999). Because mixed infections of CSSD badnaviruses and potential coinfection by other plant viruses cannot be ruled out (Chingandu et al, 2019;Ramos-Sobrinho et al, 2020, badnaviral etiology underlying the previously reported foliar red veinbanding requires further investigation.…”

“…To date, at least seven badnavirus species, presumably endemic to West Africa, have been associated with cacao swollen shoot disease (CSSD) in the region (Muller et al, 2018;Ramos-Sobrinho et al, 2020. Several badnaviruses appear to have re-emerged following an era of reduced CSSD disease incidence and spread, while other species had not been characterized until recently.…”

“…A complex of at least seven badnaviruses (genus Badnavirus, family Caulimoviridae) have been associated with swollen shoot disease, cacao swollen shoot Togo A virus (CSSTAV), cacao swollen shoot Togo B virus (CSSTBV), cacao swollen shoot CD virus (CSSCDV), cacao swollen shoot CE virus (CSSCEV), cacao swollen shoot Ghana M virus (CSSGMV), cacao swollen shoot Ghana N virus (CSSGNV), and Cacao swollen shoot Ghana Q virus (CSSGQV) (Muller and Sackey, 2005;Oro et al, 2012;Chingandu et al, 2017aChingandu et al, ,b, 2019Muller et al, 2018;Ramos-Sobrinho et al, 2020). However, Koch's postulates have only been demonstrated for CSSTBV (Hagen et al, 1994).…”

“…The results of several delivery methods and infectivity for CSSTBV have been reported (Hagen et al, 1994;Jacquot et al, 1999;Friscina et al, 2017). However, Koch's postulates have not been fulfilled for CSSD badnaviruses in Nigeria, and no study has been carried out to compare the specific symptom phenotypes attributable to the plethora of divergent CSSD badnavirus species only recently discovered (Muller and Sackey, 2005;Muller et al, 2018;Ramos-Sobrinho et al, 2020).…”

Identification and distribution of novel badnaviral sequences integrated in the genome of cacao (Theobroma cacao)

“…One of the most obvious is whether the process of integration is completely random or whether there are specific sites into which such integration is most likely to occur. It is known that recombination can occur between badnavirus strains 30 , 31 , and it may be that the integration process itself occurs preferentially into recombinogenic sequences such as remnants of transposons found widely in plant genomes.…”