Applications of Next Generation High Throughput Sequencing Technologies in Characterization, Discovery and Molecular Interaction of Plant Viruses

Abstract

Present era of molecular biology is witnessing revolutionary developments in sequencing technology. This advancement has considerably influenced plant virology in the field of diagnostics and host virus interaction. Next generation high-throughput sequencing technology has made it possible to directly detect, identify and discover novel viruses in several plants in an unbiased manner without antibodies or prior knowledge of the virus sequences. Entire viral genome could be sequenced from symptomatic or asymptomatic plants through next generation sequencing of total nucleic acids including small RNAs. It provides census of viral population in a particular ecosystem or cropping system. Viral genome variability, evolution within the host and virus defence mechanism in plants can also be easily understood by massive parallel sequencing. In this article, we provide an overview of the applications of next generation sequencing technology in characterization, discovery and molecular interaction of plant viruses.

Comparative analysis of virus-specific small RNA profiles of three biologically distinct strains of Potato virus Y in infected potato (Solanum tuberosum) cv. Russet Burbank

“…Deep sequencing technology has revolutionized the identification of new viruses and the study of vsiRNA profiles in virus-infected plants (Prabha et al, 2013;Wu et al, 2010). The observed differences among the three strains of PVY with respect to their vsiRNA profiles provide important clues to understanding the infection mechanism and pathogenicity of this important virus and viral strains of potato.…”

“…Recent high-throughput sequencing of vsiRNAs in different host-virus infection systems along with functional characterization have provided insights into the origin and composition of vsiRNAs and their potential for controlling gene expression (Prabha et al, 2013). Studies on various host-virus systems support the evidence that 21 nt class processed through the action of DCL4 is the most predominant amongst vsiRNAs with a few exceptions.…”

Analysis of intra-host genetic diversity of Prunus necrotic ringspot virus (PNRSV) using amplicon next generation sequencing

“…However, most applications of NGS, especially in plant virology, are designed for virus discovery and full genome sequencing, using de novo assembly and reference mapping tools to generate a virus consensus sequence output [13, 15, 16]. In addition, most sample preparation methods lead to high background levels of host sequences compared to virus sequences associated during NGS [17, 18].…”

Generic Amplicon Deep Sequencing to Determine Ilarvirus Species Diversity in Australian Prunus

“…However, most applications of NGS in plant virology are designed for virus discovery and full genome sequencing which frequently results only in consensus sequences of high occurring virus sequence variants and/or virus strains genomes (Adams et al, 2009; Radford et al, 2012; Prabha et al, 2013). In addition, most sample preparation methods lead to high background levels of host sequences compared to virus sequences associated during NGS (Marston et al, 2013; Hall et al, 2014).…”