Viral metagenomic-based screening of sugarcane from Florida

A viral metagenomics study of the sugarcane virome in Florida was carried out in 2013/2014 to analyze occurrence of known and potentially new viruses. Two hundred and fourteen sugarcane leaf samples were collected from different commercial sugarcane (Saccharum interspecific hybrids) fields in Florida and from other Saccharum and related species taken from two local germplasm collections. Virion-associated nucleic acids (VANA) metagenomics was used for detection and identification of viruses present within the collected leaf samples. Sequence analyses revealed the presence of SCYLV isolates belonging to two different phylogenetic clades (I and II), including a new genotype of this virus, sugarcane mosaic virus, sugarcane mild mosaic virus, and sugarcane bacilliform virus. This viral metagenomics approach also resulted in the detection of a new sugarcane-infecting mastrevirus (recently described and named sugarcane striate virus), and two potential new viruses in the genera Chrysovirus and Umbravirus.