High-throughput sequencing: Advantages beyond virus identification

Abstract

The application of high-throughput sequencing (HTS) in plant virology research had an immense influence on our perspective of disease etiology. The technology opened a new avenue of exploration that is unbiased and at an unparalleled level of sensitivity. Initially, HTS was used for virus discovery with the greatest success up until now being the discovery of Grapevine red blotch-associated virus (GRBaV) and Grapevine Pinot gris virus (GPGV). Most of the early studies constructed HTS libraries from either an enriched dsRNA extract or the small RNA fraction, but other nucleic acids have also been used. The expansion of virus databases and improved bioinformatic tools would suggest that HTS will be implemented as a sensitive virus detection tool more routinely. The discovery of the complex grapevine virome challenges the concept of what can be considered as a healthy vine although offering new opportunities to the implementation of certification schemes and exchanges of plant propagation materials. In this chapter the history of HTS in grapevine virus research is reviewed followed by the exploration of the different strategies used for the discovery of new viruses and new variants of known viruses. The concept of a "background" virome is introduced and explored within the context of its interaction with the host and the impact this might have on certification of healthy plant material. The chapter is concluded with some thoughts on the future of HTS in grapevine virus research.