View graph of relations

This protocol details the wet lab preparation, extraction of fruit pollen samples, and analysis of the sequencing data following Illumina NextSeq small and total RNA sequencing. The protocol was developed for virus and viroid detection using NGS sequencing and was based on the results of a comparison between different extraction methods followed by yield, RNA purity, and integrity assessment. Moreover, the advantage of an additional ribosomal (r)RNA depletion step to the total RNA extraction protocol was evaluated. The smallRNA procedure is the preferred method of choice. If the total RNA protocol is chosen, the use of the mirVana kit followed by an rRNA depletion step is the best option. The library preparation and sequencing steps were outsourced. As a final step in the data analysis, the VirusDetect software was used to detect the viruses and viroids in the pollen samples.
Original languageEnglish
Title of host publicationViral Metagenomics : Methods and Protocols
Number of pages19
Volume1746
PublisherHumania Press
Publication date28-Feb-2018
Pages131-149
ISBN (Print)ISBN 978-1-4939-7682-9
ISBN (Electronic)ISBN 978-1-4939-7683-6
DOIs
Publication statusPublished - 28-Feb-2018

Bibliographical note

Cite this protocol as: De Jonghe K., Haegeman A., Foucart Y., Maes M. (2018) The Use of High-Throughput Sequencing for the Study and Diagnosis of Plant Viruses and Viroids in Pollen. In: Pantaleo V., Chiumenti M. (eds) Viral Metagenomics. Methods in Molecular Biology, vol 1746. Humana Press, New York, NY

ID: 6005663