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Identification and full genomic sequence of nerine yellow stripe virus

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Abstract

This study reports the first complete genome sequence of nerine yellow stripe virus (NeYSV, GenBank MT396083). The genome consists of 10,165 nucleotides, excluding the 3’-terminal poly(A) tail. A single open reading frame encodes a large polyprotein of 3294 amino acids with typical potyvirus features. The nuclear inclusion b and coat protein region shares 95% identity with a previously reported partial NeYSV sequence (NC_043153.1). Phylogenetic analysis of the polyprotein amino acid sequence showed that NeYSV clustered with hippeastrum mosaic virus (HiMV YP_006382256.1).

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Acknowledgements

Canterbury Christ Church University and the EUPHRESCO project VirusCurate funded this work.

Funding

Canterbury Christ Church University and the EUPHRESCO project VirusCurate funded this work.

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Authors and Affiliations

  1. Canterbury Christ Church University, North Holmes Road, Canterbury, Kent, CT1 1QU, UK

    Naomi Beddoe & Alec Forsyth

  2. Fera Science Limited, The National Agri-Food Innovation Campus, Sand Hutton, York, YO41 1LZ, UK

    Ian P. Adams & Sam McGreig

Authors
  1. Naomi Beddoe
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  2. Ian P. Adams
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  3. Sam McGreig
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  4. Alec Forsyth
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Corresponding author

Correspondence to Alec Forsyth.

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The authors declare that they have no conflict of interest.

Availability of data and material

GenBank accession no. MT396083.

Code availability (software application or custom code)

Sequence data were aligned and visualised using Sequencher (Gene Codes). MinION data were recalled using Guppy3.3 (Oxford Nanopore Technologies) quality checked using NanoPlot (https://github.com/wdecoster/NanoPlot), NanoQC (https://github.com/wdecoster/nanoQC) and Nanofilt (https://github.com/wdecoster/nanofilt) and analysed using the Pomoxis pipeline (https://github.com/nanoporetech/pomoxis). MiSeq data were trimmed using Sickle version 1.33 (https://github.com/najoshi/sickle) and assembled with Trinity version 2.8.4 (https://github.com/trinityrnaseq/trinityrnaseq). Phylogenetic analyses were performed using MEGAX (https://www.megasoftware.net). Recombination analyses were performed using RDP4.100 (http://web.cbio.uct.ac.za/~darren/rdp.html).

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Beddoe, N., Adams, I.P., McGreig, S. et al. Identification and full genomic sequence of nerine yellow stripe virus. Arch Virol 165, 2967–2971 (2020). https://doi.org/10.1007/s00705-020-04776-3

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  • DOI: https://doi.org/10.1007/s00705-020-04776-3

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