Integrative multi-omics approach identified emerging viral threat in Theobroma cacao plants

Theobroma cacao seeds are the source of chocolate and other valuable products. Pathogens can damage cocoa beans, reducing yield and quality. This study examined viruses linked to chlorosis and leaf deformation in cocoa plants in Bahia, Brazil, using an integrative approach.

Macroscopic and microscopic analysis of symptomatic T. cacao leaves revealed chlorosis and histological alterations consistent with viral infection, including cell and nuclear hypertrophy. Deep sequencing of small RNA (sRNA) from these tissues identified virus-derived sRNA (vsiRNAs) profile, which suggests that viral transcripts activate the antiviral RNA interference pathways. The vsiRNAs were used to assemble two viral sequences: one related to geminivirids and the other resembling a strain of the recently described Cacao swollen shoot Ghana S virus, a putative member of the family Caulimoviridae commonly found as an Endogenous Viral Element (EVE) in symptomless plants. The geminivirid was tentatively designated Citlodavirus theobromae, while the badnavirus isolate was named Brazilian cacao swollen shoot Ghana S virus Ilhéus. Mass spectrometry detected multiple viral peptides from coding genes from both viral genomes, supporting the potential occurrence of viral translation and replication. Notably, symptoms were observed only in association with the geminivirids. Although viral DNA from both viruses was present in symptomatic and asymptomatic leaves of the same plant, geminivirid RNA was exclusively detected in symptomatic tissues, suggesting a correlation between the citlodavirustranscript accumulation and symptom expression.

Our findings highlight the emergence of a new viral geminivirid threat that could affect cocoa production in South America.