The impact of high throughput sequencing on plant health diagnostics

• Published in: European journal of plant pathology Vol. 152; no. 4; pp. 909 - 919
• Main Authors: Adams, Ian P., Fox, Adrian, Boonham, Neil, Massart, Sébastien, De Jonghe, Kris
• Format: Journal Article Web Resource
• Language: English
• Published: Dordrecht Springer Netherlands 01.12.2018; Springer Nature B.V
• Subjects: Accreditation; Agriculture; Biologie végétale (sciences végétales, sylviculture, mycologie...); Biomedical and Life Sciences; Data processing; Diagnostic software; Diagnostic systems; Diagnostics; Ecology; Epidemiology; Health policy; Health risk assessment; Health risks; High throughput sequencing; Life Sciences; Next-generation sequencing; NGS; Pathogens; Pests; Phytobiology (plant sciences, forestry, mycology...); Plant Pathology; Plant Sciences; Risk assessment; Sciences du vivant; SI: Plant Pathology for Innovative Agroecology; Validation; Validation; Accreditation; NGS; High throughput sequencing; Diagnostics
• ISSN: 0929-1873; 1573-8469; 1573-8469
• DOI: 10.1007/s10658-018-1570-0

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.