Dozens of economically significant viruses are known to cause damage to the yield and quality of individual agricultural crops. There is no test capable to identify all the pathogens in one reaction. The use of Next Generation Sequencing (NGS) has the potential to detect all viruses in a plant sample (e.g. 22 viruses in a cherry); not only known viruses but also new disease causing viruses, especially in case of multiple infections. It can be used not only in plant biology, where the current routine diagnosis of plant viruses, viroids and phytoplasma is based on ELISA (viruses) and polymerase chain reaction (viruses, viroids and phytoplasma), but also in agriculture. For example, for a specific area of genetic research aimed at the study of plant and animal genomes with the ultimate goal of generating agronomic enhancements, such as improving crop quality and yield, increasing plant resistance against pathogens, reducing herbicide use, improving plant breeding efficiency and increasing natural tolerance to abiotic stresses, such as drought or frost.
