High-throughput sequencing technologies for plant pest diagnosis: challenges and opportunities

A. Olmos (1) , N. Boonham (2) , Thierry T. Candresse (3) , P. Gentit (4) , B. Giovani (5) , D. Kutnjak (6) , L. Liefting (7) , H.J. Maree (8) , A. Minafra (9) , A. Moreira (10) , M.K. Nakhla (11) , F. Petter (5) , M. Ravnikar (6) , B. Rodoni (12) , J.W. Roenhorst (13) , M. Rott (14) , A.B. Ruiz-García (14) , J. Santala (15) , G. Stancanelli (16) , R. van Der Vlugt (17) , C. Varveri (18) , M. Westenberg (13) , T. Wetzel (19) , H. Ziebell (20) , S. Massart (21)

1 IVIA - Instituto Valenciano de Investigaciones Agrarias - Institut Valencià d'Investigacions Agraries - Valencian Institute for agricultural Research
2 Newcastle University [Newcastle]
3 BFP - Biologie du fruit et pathologie
4 LSV - Laboratoire de la santé des végétaux
5 EPPO - European and Mediterranean Plant Protection Organization - Organisation Européenne et Méditerranéenne pour la Protection des Plantes
6 NIB - National Institute of Biology [Ljubljana]
7 Ministry for Primary Industries
8 Stellenbosch University
9 IPSP - CNR Istituto per la Protezione Sostenibile delle Piante [Torino, Italia]
10 International Plant Protection Convention
11 USDA-ARS : Agricultural Research Service
12 AgriBio
13 NPPO - National Plant Protection Organization
14 CFIA - Canadian Food Inspection Agency
15 Finnish Food Safety Authority Evira
16 EFSA - European Food Safety Authority
17 WUR - Wageningen University and Research Centre
18 BPI - Benaki Phytopathological Institute
19 DLR - Dienstleistungszentren Landlicher Raum Rheinland-Pfalz
20 Institute for Epidemiology and Pathogen Diagnostics
21 Université de Liège

High-throughput sequencing (HTS) technologies have revolutionized plant pest research and are now raising interest for plant pest diagnostics, with plant virus diagnostics at the forefront of development. However, the application of HTS in plant pest diagnostics raises important challenges that plant health regulators will have to address. Adapted infrastructures, technical guidelines and training are pivotal for further use and adoption of the HTS technologies in the phytosanitary framework.

Domaines: Phytopathologie et phytopharmacie

A. Olmos, N. Boonham, Thierry T. Candresse, P. Gentit, B. Giovani, et al.. High-throughput sequencing technologies for plant pest diagnosis: challenges and opportunities. Bulletin OEPP, 2018, 48 (2), pp.219-224. ⟨10.1111/epp.12472⟩. ⟨hal-02620627⟩