Plant Virology Protocols

Abstract

Viruses are obligate intracellular entities that infect all forms of life. In plants, invading viral nucleic acids trigger RNA silencing machinery and it results in the accumulation of viral short interfering RNAs (v-siRNAs). The study of v-siRNAs population in biological samples has become a major part of many research projects aiming to identify viruses infecting them, including unknown viruses, even at extremely low titer. Currently, siRNA populations are investigated by high-throughput sequencing approaches, which generate very large data sets. The major difficulty in these studies is to properly analyze such huge amount of data. In this regard, easy-to-use bioinformatics tools to groom and decipher siRNA libraries and to draw out v-siRNAs are needed. Here we describe a workflow, which permit users with little experience in bioinformatics to draw out v-siRNAs from raw data sequences obtained by Illumina technology. Such pipeline has been released in the context of Galaxy, an open source Web-based platform for bioinformatics analyses.