DNA virome of Brazilian sugarcane germplasm via high-throughput sequencing reveals divergent badnavirus species

To analyze the circular DNA virome from badnavirus-infected sugarcane ( Saccharum spp.) accession materials, viral genomes were amplified via rolling circle amplification (RCA) using total DNA from PCR-positive samples as template. The RCA products were individually (n = 3) subjected to high-throughput sequencing. Complete genomes of the badnaviruses, sugarcane bacilliform GA virus (SCBGAV) and sugarcane bacilliform IM virus (SCBIMV), were assembled using Illumina short reads with a coverage depth of 487 to 3,331x. The SCBGAV-BR-RB10 isolate was further validated using MinION sequencing, which shared > 99.0% sequence identity with the Illumina-derived genome. The new SCBGAV isolates are putative recombinant sequences, with recombination breakpoints at the nucleotide positions 6940 and 7014, which are located in the viral intergenic region, and SCBIMV and banana streak MY virus were identified as putative minor and major parents, respectively. To our knowledge, these are the first complete badnavirus genome sequences characterized from sugarcane in Brazil.