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Volume 13
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Article

Integrating High throughput Sequencing into Survey Design Reveals Turnip Yellows Virus and Soybean Dwarf Virus in Pea (Pisum Sativum) in the United Kingdom

by
Aimee R. Fowkes
1,*,
Sam McGreig
1,
Hollie Pufal
2,
Shona Duffy
3,
Becky Howard
3,
Ian P. Adams
1,
Roy Macarthur
1,
Rebecca Weekes
1 and
Adrian Fox
1
1
Fera Science Ltd., Sand Hutton, York YO41 1LZ, UK
2
School of Natural and Environmental Sciences, University of Newcastle, Newcastle NE1 7RU, UK
3
Processors & Growers Research Organisation (PGRO), Peterborough PE8 6HJ, UK
*
Author to whom correspondence should be addressed.
Viruses 2021, 13(12), 2530; https://doi.org/10.3390/v13122530
Submission received: 18 November 2021 / Revised: 3 December 2021 / Accepted: 7 December 2021 / Published: 16 December 2021
(This article belongs to the Special Issue Plant Virus Surveillance and Metagenomics)
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Abstract

There is only limited knowledge of the presence and incidence of viruses in peas within the United Kingdom, therefore high-throughput sequencing (HTS) in combination with a bulk sampling strategy and targeted testing was used to determine the virome in cultivated pea crops. Bulks of 120 leaves collected from twenty fields from around the UK were initially tested by HTS, and presence and incidence of virus was then determined using specific real-time reverse-transcription PCR assays by testing smaller mixed-bulk size samples. This study presents the first finding of turnip yellows virus (TuYV) in peas in the UK and the first finding of soybean dwarf virus (SbDV) in the UK. While TuYV was not previously known to be present in UK peas, it was found in 13 of the 20 sites tested and was present at incidences up to 100%. Pea enation mosaic virus-1, pea enation mosaic virus-2, pea seed-borne mosaic virus, bean yellow mosaic virus, pea enation mosaic virus satellite RNA and turnip yellows virus associated RNA were also identified by HTS. Additionally, a subset of bulked samples were re-sequenced at greater depth to ascertain whether the relatively low depth of sequencing had missed any infections. In each case the same viruses were identified as had been identified using the lower sequencing depth. Sequencing of an isolate of pea seed-borne mosaic virus from 2007 also revealed the presence of TuYV and SbDV, showing that both viruses have been present in the UK for at least a decade, and represents the earliest whole genome of SbDV from Europe. This study demonstrates the potential of HTS to be used as a surveillance tool, or for crop-specific field survey, using a bulk sampling strategy combined with HTS and targeted diagnostics to indicate both presence and incidence of viruses in a crop.
Keywords: pea viruses; high throughput sequencing; surveillance pea viruses; high throughput sequencing; surveillance

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MDPI and ACS Style

Fowkes, A.R.; McGreig, S.; Pufal, H.; Duffy, S.; Howard, B.; Adams, I.P.; Macarthur, R.; Weekes, R.; Fox, A. Integrating High throughput Sequencing into Survey Design Reveals Turnip Yellows Virus and Soybean Dwarf Virus in Pea (Pisum Sativum) in the United Kingdom. Viruses 2021, 13, 2530. https://doi.org/10.3390/v13122530

AMA Style

Fowkes AR, McGreig S, Pufal H, Duffy S, Howard B, Adams IP, Macarthur R, Weekes R, Fox A. Integrating High throughput Sequencing into Survey Design Reveals Turnip Yellows Virus and Soybean Dwarf Virus in Pea (Pisum Sativum) in the United Kingdom. Viruses. 2021; 13(12):2530. https://doi.org/10.3390/v13122530

Chicago/Turabian Style

Fowkes, Aimee R., Sam McGreig, Hollie Pufal, Shona Duffy, Becky Howard, Ian P. Adams, Roy Macarthur, Rebecca Weekes, and Adrian Fox. 2021. "Integrating High throughput Sequencing into Survey Design Reveals Turnip Yellows Virus and Soybean Dwarf Virus in Pea (Pisum Sativum) in the United Kingdom" Viruses 13, no. 12: 2530. https://doi.org/10.3390/v13122530

APA Style

Fowkes, A. R., McGreig, S., Pufal, H., Duffy, S., Howard, B., Adams, I. P., Macarthur, R., Weekes, R., & Fox, A. (2021). Integrating High throughput Sequencing into Survey Design Reveals Turnip Yellows Virus and Soybean Dwarf Virus in Pea (Pisum Sativum) in the United Kingdom. Viruses, 13(12), 2530. https://doi.org/10.3390/v13122530

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