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

中文翻译：

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用于检测和监测新发和复发植物病原体的宏基因组学方法

全球化对种子、水果和蔬菜的贸易和流动产生了巨大影响，跨境植物病原体引入造成的经济损失相应增加。目前的诊断技术提供了一种有用且精确的工具来制定有关特定生物体的监测方案，但这种方法具有严格的针对性，而元条形码和鸟枪式宏基因组学可用于同时检测所有已知的病原体和潜在的新病原体。本综述旨在介绍真菌和细菌植物病原体高通量测序（HTS）诊断的现状，讨论需要解决的挑战，并为开发检测有限数量的相关病原体的方法提供方向。类群（特定监测）或样本中存在的所有微生物（一般监测）。HTS 技术，特别是元条形码技术，可用于监测土传、种子传播和空气传播的病原体，以及识别新病原体和确定疫情爆发的起源。元条形码和鸟枪法宏基因组学仍然存在精度低的问题，但可以通过仔细选择引物和生物信息学算法来限制这个问题。生物信息学的进步将极大地加速宏基因组学的应用，以解决与植物材料和食品中植物病原体检测和监测相关的关键问题。