Agroforestry systems (AFS) for cocoa production combine traditional land-use practices with local biodiversity conservation, resulting in both ecological and agricultural benefits. The cacao-cabruca AFS model is widely implemented in regions of the Brazilian Atlantic Forest. Carpotroche brasiliensis (Raddi) A. Gray (Achariaceae) is a tree found in cabruca landscapes that is often used for reforestation and biotechnological applications. Despite its importance, we still lack information about viruses circulating in C. brasiliensis, particularly considering the possibility of spillover that could affect cocoa production. In our study, we analyzed the Carpotroche brasiliensis virome from Atlantic Forest and cacao-cabruca AFS regions using metatranscriptomics from several vegetative and reproductive organs. Our results revealed a diverse virome detecting near-complete or partial coding sequences of single- and double-stranded DNA and RNA viruses classified into at least six families (Botourmiaviridae, Bromoviridae, Caulimoviridae, Genomoviridae, Mitoviridae, and Rhabdoviridae) plus unclassified elements. We described with high confidence the near-complete and the partial genomes of two tentative novel viruses: Carpotroche-associated ilarvirus and Carpotroche-associated genomovirus, respectively. Interestingly, we also described sequences likely derived from a rhabdovirus, which could represent a novel member of the genus Gammanucleorhabdovirus. We observed higher viral diversity in cacao-cabruca AFS and reproductive organs of C. brasiliensis with preferential tropism to fruits, which could directly affect production. Altogether, our results provide data to better understand the virome in this unexplored agroecological interface, such as cacao-cabruca AFS and forest ecosystem, providing information on the aspects of virus–plant interactions.

Moniliasis caused by the fungus Moniliophthora roreri is one of the most destructive cacao diseases in tropical America. In 2021, the presence of the pathogen was confirmed in cacao plantations in Brazil. This is the first proteomic study of the M. roreri protein profile of ungerminated spores and mycelium compared by 2D SDS‐PAGE (Two‐dimensional gel electrophoresis) associated with mass spectrometry. A total of 446 spots were detected on ungerminated spores gels and 402 spots on M. roreri mycelial gels. A total of 29 proteins were identified from the ungerminated spores, 21 of them were exclusive, and 53 were identified in the mycelium, 16 of them were exclusive. Most of the identified proteins at both development stages were categorized as being involved in metabolic processes, reduction/oxidation processes, and protein synthesis and folding. The interaction networks observed expand the known interactions of these proteins, resulting in eight functional clusters for proteins identified in ungerminated spores and seven clusters for mycelial proteins. In addition, a biological model of ungerminated spores and mycelium with cell location of proteins was constructed. The results contribute to a better understanding of the metabolic mechanisms of M. roreri during dormancy and vegetative development, which can support future studies for strategies to control moniliasis.