Complete genome sequences for three new discovered Cacao mild mosaic virus isolates from Theobroma cacao L. in Brazil and Puerto Rico and evidence for recombination

Authors: RAMOS-SOBRINHO, ROBERTO - UNIVERSITY OF ARIZONA; KEITH, CORY VON - UNIVERSITY OF ARIZONA; Puig, Alina; FERRO, MAYRA - UNIVERSITY OF ARIZONA; NAGATA, TATSUYA - UNIVERSITY OF ARIZONA; Gutierrez, Osman; MARELLI, JEAN-PHILIPPE - MARS, INC.; BROWN, JUDITH - UNIVERSITY OF ARIZONA

Submitted to: Archives of Virology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/17/2021
Publication Date: 4/26/2021
Citation: Ramos-Sobrinho, R., Keith, C., Puig, A.S., Ferro, M.M., Nagata, T., Gutierrez, O.A., Marelli, J., Brown, J.K. 2021. Complete genome sequences for three new discovered Cacao mild mosaic virus isolates from Theobroma cacao L. in Brazil and Puerto Rico and evidence for recombination. Archives of Virology. https://doi.org/10.1007/s00705-021-05063-5.
DOI: https://doi.org/10.1007/s00705-021-05063-5

Interpretive Summary: Cacao (Theobroma cacao L.) is a very significant crop grown in the tropical regions of the world. Diseases and pests severely affect cacao production and Badnavirus, which are transmitted by mealybugs, currently causes severe losses in West Africa. In the Americas, Badnaviruses affecting cacao growth were reported in Trinidad in the 1930s and it was called Cacao Trinidad virus (CTV) strains A and B. Later, this virus was classified as Cacao mild mosaic virus and Cacao yellow vein-clearing virus, respectively. Recently, Cacao mild mosaic virus was found in Puerto Rico and Brazil. However, it was necessary to determine if the two detected strains were identical. The main objective of this research was to sequence and characterize the Cacao mild mosaic virus genomes of the samples obtained in Brazil and Puerto Rico. Scientists the University of Arizona collaborated with MARS and USDA-ARS scientists to study genomic variability and genetic diversity of the Cacao mild mosaic virus samples collected at both places. Genome sequencing and phylogenetic analysis results indicated that the collected virus samples are in fact Cacao mild mosaic virus. However, the sample from Puerto Rico presented a recombination event which indicated that the samples from both locations are not identical. There results also indicated that Badnaviruses are widespread in the Americas cacao growing regions and that the use of quarantine facilities in combination with molecular diagnostic tools is a must during the transfer of cacao germplasm among countries.

Technical Abstract: To analyze the DNA virome associated with cacao (Theobroma cacao L.) trees showing virus-like symptoms in Brazil (BR) and Puerto Rico (PR) during 2018-2019, total DNA was isolated from symptomatic leaves and subjected to high-throughput Illumina sequencing. The assembled complete badnaviral genome sequences were verified by PCR amplification, cloning, and DNA sequencing. Based on pairwise distances and phylogenetic analysis, three badnaviral genomes were identified, and these viruses were found to be isolates of the previously described cacao mild mosaic virus (CaMMV). The three genomes were 7,520, 7,524, and 7,514 bp in size for the isolates CaMMV-BR321, CaMMV-BR322, and CaMMV-PR3, respectively. Each genome contained four predicted open reading frames: ORFs 1-3 and ORFY. The CaMMV-PR3 isolate was identified as a probable recombinant, with a CaMMV-BR-like virus as the major parent.