Metagenomics Approaches for the Detection and Surveillance of Emerging and Recurrent Plant Pathogens

摘要: Globalization has a dramatic effect on the trade and movement of seeds, fruits vegetables, with corresponding increase in economic losses caused by introduction transboundary plant pathogens. Current diagnostic techniques provide useful precise tool to enact surveillance protocols regarding specific organisms, but this approach is strictly targeted, while metabarcoding shotgun metagenomics could be used simultaneously detect all known pathogens potentially new ones. This review aims present current status high-throughput sequencing (HTS) diagnostics fungal bacterial pathogens, discuss challenges that need addressed, direction for development methods detection restricted number related taxa (specific surveillance) or microorganisms sample (general surveillance). HTS techniques, particularly metabarcoding, soilborne, seedborne airborne as well identifying determining origin outbreaks. Metabarcoding still suffer from low precision, issue can limited carefully choosing primers bioinformatic algorithms. Advances bioinformatics will greatly accelerate use address critical aspects material foodstuffs.