Next generation sequencing for studying viruses and RNA silencing-based antiviral defense in crop plants

• Research unit: COST
• Project number: C09.0176

Key words (English)

Next generation sequencing; Bioinformatics; Plant viruses; Genetics; Functional genomics; Crop plants; RNA silencing; siRNAs; RNA-based vaccine.

Research programs (English)

COST-Action FA0806 - Plant virus control employing RNA-based vaccines: A novel non-transgenic strategy

Short description (English)

See abstract

Partners and International Organizations (English)

AT, BE, BG, CH, CY, CZ, DE, DK, EE, ES, FI, FR, GR, HU, IL, IT, NL, NO, PL, PT, RO, SE, SI, SK, UK

Abstract (English)

Next generation sequencing methods such as the 454 and the Illumina ultra-high-throughput technologies have revolutionized the fields of genetics and functional genomics. These methods have enabled to sequence nearcomplete genomes of extinct species such as mammoth and Neanderthal man and provided a powerful alternative to microarray profiling of RNA transcriptomes and DNA methylomes in various organisms. Furthermore, deep-sequencing of small RNA populations from plants and animals has revealed a number of novel regulatory small RNAs including microRNAs and small interfering (si)RNAs and PIWI-associated RNAs. In this project we apply the Illumina technology for direct deep-sequencing of viral genomes and transcripts as well as virus-derived siRNAs from various infected crop plants. We develop bioinformatics tools for mining the deepsequencing data in order to de novo assemble complete genomic sequences of DNA and RNA viruses present in the infected plant tissues and to create genome-wide single-nucleotide resolution maps of virus-derived siRNAs. This information is being used for our COST Action devoted to design an RNA-based vaccine (RBV) to immunize crop plants against emerging viruses. One of the main principles of RBV action would be to boost the plant silencing machinery in making massive amounts of siRNAs complementary to the regions of viral genomes that normally give rise to little or no siRNAs. Such anti-viral siRNAs should prevent virus replication and systemic spread.

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: C09.0176