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Diagnosis of viruses and virus-like pathogen by means of high-throughput sequencing (NGS)
Project
Project code: 2815ERA02K, JKI-EP-08-2288
Contract period: 01.07.2016
- 30.06.2018
Budget: 149,064 Euro
Purpose of research: Applied research
Aim of this project is the development and validation of a holistic concept for the detection and characterisation of plant viruses and virus-like organisms infecting legumes and vegetables using Next-Generation Sequencing (NGS) technologies. This includes sampling, sample preparation for NGS as well as development of a bioinformatic pipeline for data analysis. Package 1: Development and validation of a common pipeline from sample preparation to data analysis. Optimisation and validation of different nucleic acid extraction methods from different source material (dsRNA extraction, dsRNA enrichment using specific antibodies, siRNA extraction, rolling circle amplification of DNA). Comparison of in-house vs. commercial library preparation for NGS. NGS carried out by commercial suppliers. Adaptation of a bioinformatic pipeline to software package used at JKI (Galaxy). Package 2: Validation of protocols through laboratory comparison studies. Publication of results in scientific publications and deposit of sequences in reference databases. Package 3: Analysis of uncharacterised plant samples from JKI virus collection (Virothek) as well as samples derived from collaboration partners as well as samples from commercial production sites and trial stations. Keywords: EUPHRESCO II, potato, pea, virusus, bacteria, fungi, phytoplasma
Section overview
Subjects
- Crop Protection
Framework programme
Funding programme
Excutive institution
Institute for Epidemiology and Pathogen Diagnostics (JKI-EP)