Next generation sequencing (NGS) as a multipurpose method for detection and differentiation of plant viruses

Abstract

This paper describes the application of next generation sequencing (NGS) in plant virus research. Although NGS has not been routinely used yet, it is increasingly adopted in diagnostics and genomics of phytopathogens. NGS technics enable the simultaneous detection of multiple viruses present in infected material. This makes it possible not only to determine which viruses are present in a single sample but also to determine their concentration and genetic diversity. The simultaneous identification of many viruses, the possibility of early detection of disease outbreaks as well as tracking and monitoring of epidemic development, make NGS a universal research tool that enables not only the detection but also the understanding of molecular mechanisms allowing viruses to adapt to environmental changes (host plant genotype, vector, presence of other pathogens).