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

Area of Science:

• Agricultural Science
• Virology
• Bioinformatics

Background:

• Cocoa (Theobroma cacao L.) is vital to the global chocolate industry and farmer livelihoods.
• Viral diseases, particularly Badnavirus infections, significantly threaten cocoa production, especially in Africa.
• The full spectrum of viruses (virome) affecting cocoa plants is not well understood, hindering disease management.

Purpose of the Study:

• To comprehensively assess the cocoa-associated virome using publicly available RNA-seq data.
• To identify novel viruses and characterize the diversity of known viruses within Theobroma cacao.
• To improve understanding of plant-virus interactions for sustainable cocoa production.

Main Methods:

• Analysis of 109 RNA-seq libraries from nine BioProjects covering diverse cocoa conditions and regions.
• Implementation of a bioinformatics pipeline including viral sequence enrichment and hybrid assembly.
• Sequence similarity searches against NCBI non-redundant databases for virus identification.

Main Results:

• Identification of ten putative novel viruses associated with the cocoa microbiome.
• Discovery of a novel Badnavirus species impacting Theobroma cacao.
• Characterization of the viral landscape within cocoa plants.

Conclusions:

• The study expands the catalog of viruses associated with cocoa plants.
• Findings enhance understanding of plant-virus-microbiome interactions in Theobroma cacao.
• Results contribute to developing improved disease surveillance and management strategies for sustainable cocoa farming.