“siRNA omics” for universal diagnostics and control of viral diseases and virus diversity studies

We use next generation sequencing technologies and bioinformatics to study the diversity and evolution of plant viruses in a changing environment as well as the interactions of plant viruses with the host plant antiviral defenses based on RNA silencing. Using “siRNA omics” approach based on deep sequencing of small RNAs and bioinformatics reconstruction of viral genomes and viral siRNA profiles, we are currently conducting a survey of viruses that infect various crops and wild plants in Switzerland. We are also sequencing of viral genomes and siRNA populations from virus-infected tropical and subtropical crops such as cassava, banana, and rice. Besides the basic science outcome in furthering our understanding of virus diversity and evolution, and mechanisms of induction and evasion of host defenses, this project has an important applied dimension for universal diagnostics of viral diseases and RNAi-based control of emerging viruses. Bioinformatics analysis of viral siRNAs is being used for designing RNAi transgenes and RNAi-based vaccines (RBV) to immunize crop plants against known and emerging viruses. One of the main principles of RBV action is to boost the plant silencing machinery in making massive amounts of siRNAs complementary to the regions of viral genomes that normally spawn little or no siRNAs. Such anti-viral siRNAs should prevent virus replication and systemic spread.

Selected publications:

Rajeswaran R, Seguin J, Chabannes M, Duroy PO, Laboureau N, Farinelli L, Iskra-Caruana ML, and  Pooggin MM. 2014. Evasion of siRNA-directed antiviral silencing in Musa acuminata persistently infected with six distinct banana streak pararetroviruses. J. Virol. published ahead of print 23 July

Seguin J, Otten P, Baerlocher L, Farinelli L, Pooggin MM. 2014. MISIS: A bioinformatics tool to view and analyze maps of small RNAs derived from viruses and genomic loci generating multiple small RNAs. J Virol Methods 195: 120-122.

Seguin J, Rajeswaran R, Malpica-López N, Martin RR, Kasschau K, Dolja VV, Otten P, Farinelli L, Pooggin MM. 2014. De Novo Reconstruction of Consensus Master Genomes of Plant RNA and DNA Viruses from siRNAs. PLoS One 9: e88513.