The impact of high throughput sequencing on plant health diagnostics

High throughput sequencing informed diagnostics
is revolutionising plant pathology. The application
of this technology is most advanced in plant virology,
where it is already becoming a front-line diagnostic
tool and it is envisaged that for other types of pathogen
and pests this will be the case in the near future. However,
there are implications to deploying this technology
due to a number of technical and scientific challenges.
Firstly, interpretation of data and the assessment of plant
health risk against a limited baseline of existing knowledge
of the presence of pathogens in a given geographic
region. Secondly, evidence of causality and the separation
of pathogenic from commensal organisms in the
sequence data, thirdly, the tension between the generation
of a rapid sequence result with the necessary but
laborious epidemiological characterisation in support of
plant health risk assessment. Finally, the validation and
accreditation of methods based on this rapidly evolving
technology. These in turn present challenges for plant
health policy and regulation. This review discusses the
development of this technology, its application in plant
health diagnostics, and explores the implications of
applying this technology in the plant health setting.