Theobroma cacao Virome: Exploring Public RNA-Seq Data for Viral Discovery and Surveillance

Cocoa (<i>Theobroma cacao</i> L.) is a major agricultural commodity, essential for the global chocolate industry and the livelihoods of millions of farmers. However, viral diseases pose a significant threat to cocoa production, with Badnavirus species causing severe losses in Africa. Despite its economic importance, the overall virome of <i>T. cacao</i> remains poorly characterized, limiting our understanding of viral diversity and potential disease interactions. This study aims to assess the cocoa-associated virome by analyzing 109 publicly available RNA-seq libraries from nine BioProjects, covering diverse conditions and geographic regions. We implemented a comprehensive bioinformatics pipeline integrating multiple viral sequence enrichment steps, a hybrid assembly strategy using different assemblers, and sequence similarity searches against NCBI non-redundant databases. Our approach identified ten putative novel viruses associated with the cocoa microbiome and a novel Badnavirus species. These findings provide new insights into the viral landscape of <i>T. cacao</i>, characterizing the diversity of cacao-associated viruses and their potential ecological roles. Expanding the catalog of viruses associated with cocoa plants not only enhances our understanding of plant-virus-microbiome interactions but also contributes to the development of more effective disease surveillance and management strategies, ultimately supporting sustainable cocoa production.