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Next generation sequencing for detection and discovery of plant viruses and viroids: Comparison of two approaches

Lookup NU author(s): Professor Neil Boonham



This work is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0).


© 2017 Pecman, Kutnjak, Gutiérrez-Aguirre, Adams, Fox, Boonham and Ravnikar. Next generation sequencing (NGS) technologies are becoming routinely employed in different fields of virus research. Different sequencing platforms and sample preparation approaches, in the laboratories worldwide, contributed to a revolution in detection and discovery of plant viruses and viroids. In this work, we are presenting the comparison of two RNA sequence inputs (small RNAs vs. ribosomal RNA depleted total RNA) for the detection of plant viruses by Illumina sequencing. This comparison includes several viruses, which differ in genome organization and viroids from both known families. The results demonstrate the ability for detection and identification of a wide array of known plant viruses/viroids in the tested samples by both approaches. In general, yield of viral sequences was dependent on viral genome organization and the amount of viral reads in the data. A putative novel Cytorhabdovirus, discovered in this study, was only detected by analysing the data generated from ribosomal RNA depleted total RNA and not from the small RNA dataset, due to the low number of short reads in the latter. On the other hand, for the viruses/viroids under study, the results showed higher yields of viral sequences in small RNA pool for viroids and viruses with no RNA replicative intermediates (single stranded DNA viruses).

Publication metadata

Author(s): Pecman A, Kutnjak D, Gutierrez-Aguirre I, Adams I, Fox A, Boonham N, Ravnikar M

Publication type: Article

Publication status: Published

Journal: Frontiers in Microbiology

Year: 2017

Volume: 8

Online publication date: 13/10/2017

Acceptance date: 28/09/2017

Date deposited: 20/11/2017

ISSN (electronic): 1664-302X

Publisher: Frontiers Media S.A.


DOI: 10.3389/fmicb.2017.01998


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