<i>Theobroma cacao</i> 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. Des...
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| Format: | Article |
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2025-04-01
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| Series: | Viruses |
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| Online Access: | https://www.mdpi.com/1999-4915/17/5/624 |
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| author | Gabriel Victor Pina Rodrigues João Pedro Nunes Santos Lucas Yago Melo Ferreira Lucas Barbosa de Amorim Conceição Joel Augusto Moura Porto Eric Roberto Guimarães Rocha Aguiar |
| author_facet | Gabriel Victor Pina Rodrigues João Pedro Nunes Santos Lucas Yago Melo Ferreira Lucas Barbosa de Amorim Conceição Joel Augusto Moura Porto Eric Roberto Guimarães Rocha Aguiar |
| author_sort | Gabriel Victor Pina Rodrigues |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-8885c7d92a4b4fda8141a6d178920653 |
| institution | DOAJ |
| issn | 1999-4915 |
| language | English |
| publishDate | 2025-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj-art-8885c7d92a4b4fda8141a6d1789206532025-08-20T03:12:07ZengMDPI AGViruses1999-49152025-04-0117562410.3390/v17050624<i>Theobroma cacao</i> Virome: Exploring Public RNA-Seq Data for Viral Discovery and SurveillanceGabriel Victor Pina Rodrigues0João Pedro Nunes Santos1Lucas Yago Melo Ferreira2Lucas Barbosa de Amorim Conceição3Joel Augusto Moura Porto4Eric Roberto Guimarães Rocha Aguiar5Department of Biological Science, Center of Biotechnology and Genetics, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, BA, BrazilDepartment of Biological Science, Center of Biotechnology and Genetics, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, BA, BrazilDepartment of Biological Science, Center of Biotechnology and Genetics, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, BA, BrazilDepartment of Biological Science, Center of Biotechnology and Genetics, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, BA, BrazilDepartment of Biological Science, Center of Biotechnology and Genetics, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, BA, BrazilDepartment of Engineering and Computing, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, BA, BrazilCocoa (<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.https://www.mdpi.com/1999-4915/17/5/624cocoaBadnavirusmetatranscriptomemetaviromemycoviruses |
| spellingShingle | Gabriel Victor Pina Rodrigues João Pedro Nunes Santos Lucas Yago Melo Ferreira Lucas Barbosa de Amorim Conceição Joel Augusto Moura Porto Eric Roberto Guimarães Rocha Aguiar <i>Theobroma cacao</i> Virome: Exploring Public RNA-Seq Data for Viral Discovery and Surveillance Viruses cocoa Badnavirus metatranscriptome metavirome mycoviruses |
| title | <i>Theobroma cacao</i> Virome: Exploring Public RNA-Seq Data for Viral Discovery and Surveillance |
| title_full | <i>Theobroma cacao</i> Virome: Exploring Public RNA-Seq Data for Viral Discovery and Surveillance |
| title_fullStr | <i>Theobroma cacao</i> Virome: Exploring Public RNA-Seq Data for Viral Discovery and Surveillance |
| title_full_unstemmed | <i>Theobroma cacao</i> Virome: Exploring Public RNA-Seq Data for Viral Discovery and Surveillance |
| title_short | <i>Theobroma cacao</i> Virome: Exploring Public RNA-Seq Data for Viral Discovery and Surveillance |
| title_sort | i theobroma cacao i virome exploring public rna seq data for viral discovery and surveillance |
| topic | cocoa Badnavirus metatranscriptome metavirome mycoviruses |
| url | https://www.mdpi.com/1999-4915/17/5/624 |
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