Location: National Germplasm Resources LaboratoryTitle: Next generation sequencing technology: a powerful tool for the genome characterization of sugarcane mosaic virus from Sorghum almum Author
Submitted to: Sugar Journal
Publication Type: Abstract Only
Publication Acceptance Date: 4/30/2016
Publication Date: 6/1/2016
Citation: Mollov, D.S., Grinstead, S.C., Tahir, M.N., Kaye, C., Wei, C., Rott, P. 2016. Next generation sequencing technology: a powerful tool for the genome characterization of sugarcane mosaic virus from Sorghum almum. Sugar Journal. P. 13. Interpretive Summary:
Technical Abstract: Next generation sequencing (NGS) technology was used to analyze the occurrence of viruses in Sorghum almum plants in Florida exhibiting mosaic symptoms. Total RNA was extracted from symptomatic leaves and used as a template for cDNA library preparation. The resulting library was sequenced on an Illumina NextSeq platform, and 27.9 million sequence reads were generated. Sequence reads assembled into 109,646 contigs and were analyzed using Qiagen's CLC Genomics Workbench software. BLASTs were run against the full NCBI database and a custom database of all viruses known to infect sugarcane. A single contig representing more than 99% of the Sugarcane mosaic virus (SCMV) genome length was identified and 4.25 million (15.2%) of the 27.9 million sequence reads mapped to this contig. This SCMV sequence encodes a single polyprotein of 3055 amino acids that shows a similar organization to those of other potyviruses. The nucleotide sequence of the coat protein (CP) from the S. almum isolate was 75 to 95% identical to the same sequence of sugarcane potyviruses from Florida, Louisiana, and other geographical locations. At the whole genome level, the nucleotide sequence identity ranged from 78 to 93%. Whole genome phylogenetic analysis, including SCMV, Sorghum mosaic virus and Maize dwarf mosaic virus clearly grouped the S. almum isolate within the SCMV group. This NGS approach allowed us to determine the entire genomic sequence of a SCMV isolate from S. almum, a recently discovered host of this virus in the U.S. Further studies are necessary to determine the relationship between genomic sequences of SCMV strains from S. almum and sequences of SCMV strains infecting sugarcane in order to better understand the role of S. almum in the epidemiology of sugarcane mosaic disease. Characterizing the genomic organization of SCMV strains is also very important for developing improved diagnostic methods for this virus, and will contribute to quarantine and disease management efforts.