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.
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Acknowledgements
This work was supported by a grant from Italian Ministry of Economy and Finance dedicated to CNR (C.I.S.I.A. Legge 191/2009) and by a DAA-CNR grant (award prize 2010 for advanced research in “Animal and Plant Genomics” to VP). COST FA0806 supported L.M. for attending a T.S. in Applied Bioinformatics in Plant Science.
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Miozzi, L., Pantaleo, V. (2015). Drawing siRNAs of Viral Origin Out from Plant siRNAs Libraries. In: Uyeda, I., Masuta, C. (eds) Plant Virology Protocols. Methods in Molecular Biology, vol 1236. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-1743-3_10
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DOI: https://doi.org/10.1007/978-1-4939-1743-3_10
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