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Special Issue:
植物病理合辑Plant Protection—Plant Pathology
植物病毒合辑Plant Virus
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| Virome identification in wheat in the Czech Republic using small RNA deep sequencing |
Khushwant SINGH1, Jana JAROŠOVÁ1, Jan FOUSEK1, CHEN Huan2, Jiban Kumar KUNDU1 |
1 Plant Virus and Vector Interactions Group, Division of Crop Protection and Plant Health, Crop Research Institute, Prague 16106, Czech Republic
2 Zhejiang Tianke High-Technology Development Co., Ltd., Hangzhou 310012, P.R.China |
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Abstract High-throughput deep-sequencing technology and bioinformatics analysis of the small RNA (sRNA) population isolated from plants allows universal virus detection and complete virome reconstruction for a given sample. In the present sRNA deep-sequencing analysis of virus-infected wheat samples in the Czech Republic, samples were firstly tested for barley yellow dwarf viruses (BYDVs), wheat streak mosaic virus (WSMV) and wheat dwarf virus (WDV) using ELISA, RT-PCR and PCR. Subsequent sRNA sequencing of these samples yielded more than ~60 million single-end 50-bp reads with high confidence for nine field samples of wheat. Overall, 16.5% of reads were virus-specific and 83.5% were mapped to the host. More 21-nt reads (~7.7E+06 reads) were found than 24-nt (~6.20E+06 reads) or 22-nt (~4.30E+06 reads) reads. De novo assembly of the high-quality contigs revealed the presence of three earlier reported viruses in the Czech Republic: BYDVs (31.48%), WSMV (24.23%) and WDV (26.66%). We also showed the presence of cereal yellow dwarf virus (14.33%; two species CYDV-RPS and CYDV-RPV (family Luteoviridae/Polerovirus) and wheat yellow dwarf virus (WYDV, 3.30%; Luteoviridae). Phylogenetic analysis showed CYDV and WYDV grouped separately from BYDVs. Furthermore, several recombination breakpoints were found among the groups of yellow dwarf viruses (BYDVs, CYDV, and WYDV). Using RNA deep sequencing, we confirmed the presence of the three known viruses (BYDVs, WSMV, and WDV) and the first record of two species of CYDV and WYDV in wheat in the Czech Republic.
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Received: 30 May 2019
Accepted:
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| Fund: This work was supported by a grant from the Technology Agency of the Czech Republic (TF02000056). |
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Corresponding Authors:
Correspondence Jiban Kumar Kundu, E-mail: jiban@vurv.cz
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Cite this article:
Khushwant SINGH, Jana JAROŠOVÁ, Jan FOUSEK, CHEN Huan, Jiban Kumar KUNDU.
2020.
Virome identification in wheat in the Czech Republic using small RNA deep sequencing. Journal of Integrative Agriculture, 19(7): 1825-1833.
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