Abstract
Nanopore sequencing has proven to be a useful tool for the generic detection of plant viruses, especially in laboratories working with small number of samples. In this chapter, we describe the steps prior to library preparation as well as the library preparation itself, which we found provides comparable results to Illumina sequencing.
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References
Branton D, Deamer D (2018) Nanopore sequencing. Nanopore Seq 1:1–16. https://doi.org/10.1142/10995
Quick J, Loman NJ, Duraffour S et al (2016) Ebola surveillance. Nature. https://doi.org/10.1038/nature16996
Meredith LW, Hamilton WL, Warne B et al (2020) Rapid implementation of SARS-CoV-2 sequencing to investigate cases of health-care associated COVID-19: a prospective genomic surveillance study. Lancet Infect Dis 20:1263–1272. https://doi.org/10.1016/S1473-3099(20)30562-4
Tan S, Dvorak CMT, Murtaugh MP (2019) Rapid, unbiased PRRSV strain detection using MinION direct RNA sequencing and bioinformatics tools. Viruses 11. https://doi.org/10.3390/v11121132
Filloux D, Fernandez E, Loire E et al (2018) Nanopore-based detection and characterization of yam viruses. Sci Rep 8:17879. https://doi.org/10.1038/s41598-018-36042-7
Pecman A, Adams I, Gutiérrez-Aguirre I et al (2022) Systematic comparison of nanopore and illumina sequencing for the detection of plant viruses and viroids using total RNA sequencing approach. Front Microbiol 13:1–14. https://doi.org/10.3389/fmicb.2022.883921
Oxford Nanopore Technologies (2022) Polyadenylation of non-poly(A) transcripts using E. coli poly(A) polymerase, v3, April 2022. https://nanoporetech.com/. Accessed 31 Jan 2023
Oxford Nanopore Technologies (2022) MinION Mk1B IT requirements. https://nanoporetech.com/products/minion. Accessed 14 Feb 2023
Oxford Nanopore Technologies PCR-cDNA sequencing – barcoding (SQK-PCB109). https://nanoporetech.com/. Accessed 1 Mar 2023
Massart S, Adams I, Rwahnih MA et al (2022) Guidelines for the reliable use of high throughput sequencing technologies to detect plant pathogens and pests. Peer Commun J 10.24072/pcjournal.181
Kesanakurti P, Belton M, Saeed H et al (2016) Screening for plant viruses by next generation sequencing using a modified double strand RNA extraction protocol with an internal amplification control. J Virol Methods 236:35–40. https://doi.org/10.1016/j.jviromet.2016.07.001
Oxford Nanopore Technologies (2022) Input DNA/RNA QC. https://nanoporetech.com/. Accessed 31 Jan 2023
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Pecman, A., Mehle, N., Kutnjak, D. (2024). Detection of Plant Viruses Using Nanopore Sequencing Based Metagenomic Approach. In: Pantaleo, V., Miozzi, L. (eds) Viral Metagenomics. Methods in Molecular Biology, vol 2732. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3515-5_17
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DOI: https://doi.org/10.1007/978-1-0716-3515-5_17
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