Next generation sequencing for the diagnosis and diversity studies of viral pathogens in Swiss agriculture

• Research unit: COST
• Project number: C16.0082

Key words (English)

Next generation sequencing; small RNA biology; plant pathogens; emerging viral diseases; agriculture;Switzerland

Research programs (English)

COST-Action FA1407 - Application of next generation sequencing for the study and diagnosis of plant viral diseases in agriculture

Short description (English)

Owing to global trade and climate changes, newly emerging viral diseases threaten Swiss agriculture. Traditional methods of viral diagnostics such as PCR or ELISA fail to identify the disease agent if it is an unknown (or divergent) virus. Moreover, viral diseases are often associated with more than one virus or viruslike agent. Therefore, the development of unbiased, holistic methods of virus detection and virome reconstruction such as those based on next generation sequencing (NGS) is crucial for preventing spread of viral diseases. Fasteris (CH) and University of Basel (CH) have developed a pipeline for de novo reconstruction of consensus master genomes of DNA and RNA viruses, based on NGS and bioinformatics analysis of small RNAs. We will employ this pipeline to characterize the viromes of vegetatively-propagated crops (potato, tomato and grapevine) and fruit trees (cherry, plum and apple), which have been under investigation at Agroscope (CH). Furthermore, we will develop low-cost protocols and advanced bioinformatics tools for yearly certification process of seed potato tubers at Agroscope. More specifically, we will multiplex samples, physically enrich for viral sequences in NGS libraries and use bioinformatics filtering to facilitate virome reconstruction. We will cooperate with other members of the COST action to exchange NGS protocols and bioinformatics tools in order to achieve an ultimate goal of developing a universal pipeline for virome reconstruction.

Further information (English)

Full name of research-institution/enterprise: Agroscope Institut des sciences en production végétale IPV Groupe Virologie & Phytoplasmologie

Partners and International Organizations (English)

AT; BE, BA, BG, HR; CZ; DK, EE; FI; FR, DE, EL; HU; IL; IT, MNE; NL; NO; PL; PT; RO: RS; SK; SI; ES; SE; TR; UK; AM; AR; ZA; PE; MX

Abstract (English)

See short description

References in databases (English)

Swiss Database: COST-DB of the State Secretariat for Education and Research Hallwylstrasse 4 CH-3003 Berne, Switzerland Tel. [phone] Swiss Project-Number: C16.0082