Location: National Germplasm Resources LaboratoryTitle: Nucleotide sequence and genome organization of a novel Panicovirus from Bermuda grass Author
|Tahir, Muhammad Nouman - US Department Of Agriculture (USDA)|
|Lockhart, Ben - University Of Minnesota|
Submitted to: Phytopathology
Publication Type: Abstract Only
Publication Acceptance Date: 3/16/2016
Publication Date: 12/1/2016
Citation: Tahir, M., Lockhart, B., Grinstead, S.C., Mollov, D.S. 2016. Nucleotide sequence and genome organization of a novel Panicovirus from Bermuda grass. Phytopathology. 106:S4.107.
Technical Abstract: Bermuda grass, (Cynodon dactylon) is widely used in tropical and subtropical areas for golf greens, athletic fields, and landscapes. Samples of Bermuda grass associated with decline symptoms were tested at the University of Minnesota plant virology lab. Spherical virus particles (28-30 nm) were observed by transmission electron microscopy. Total RNA was extracted and sent for high-throughput sequencing, or Next Generation Sequencing (NGS) on an Illumina platform. Contigs were assembled and analyzed using BLAST searches. A contig of about 4 kb contained four predicted ORFs in an arrangement typical of viruses in the family Tombusviridae. Subsequently overlapping primer pairs were designed from the consensus sequence for RT-PCR verification and sequence confirmation. All amplicons were cloned and the resulting sequences matched the original NGS conting. Amino acid sequence comparisons of the putative replicase (RdRp), movement and coat proteins (CP), showed sequence similarities in the range of 37-66% when compared to Thin paspalum asymptomatic virus, Cocksfoot mild mosaic virus, and Panicum mosaic virus. Phylogenetic analyses of the CP and RdRP of this newly identified virus place it in the genus Panicovirus. The sequence of this Bermuda grass virus is sufficiently different from other viruses to conclude it is a new member of the genus Panicuvirus, family Tombusviridae.