Molecular characterization of two badnavirus genomes associated with Canna yellow mottle disease

- Wild canna lily species have been hybridized for floriculture production.
- Two badnavirus genomes of 6966 bp and 7385 bp in length were identified in cannas.
- PCR primers were developed for cloning and diagnostic detection of both virus species.
- These genomes are closely related to Canna yellow mottle virus from A. purpurata.

Members of the genus Badnavirus have a single non-covalently closed circular double-stranded DNA genome of 7.2-9.2 kb. The genome encodes three open reading frames (ORFs) on the positive DNA strand. Canna yellow mottle virus (CaYMV) is a badnavirus that has been described as the etiological cause of yellow mottle disease in canna, although only a 565 bp fragment of the genome has been previously reported from cannas. In this report, concentrated virions were recovered from infected canna plants and nucleic acids were extracted. Two full-length sequences represent two badnavirus genomes were recovered and were determined to be 6966 bp and 7385 bp in length. These DNAs represent a virus strain belonging to Canna yellow mottle virus and a novel species tentatively termed Canna yellow mottle associated virus. Phylogenetic analysis indicates that these two viruses are closely related to sugarcane bacilliform GD virus, pineapple bacilliform comosus virus, banana streak MY virus, and cycad leaf necrosis virus. We also showed naturally grown canna plants to be frequently co-infected by these two badnaviruses along with a potyvirus, Canna yellow streak virus.