Virome identification in wheat in the Czech Republic using small RNA deep sequencing

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00027006%3A_____%2F20%3A10146900" target="_blank" >RIV/00027006:_____/20:10146900 - isvavai.cz</a>

Result on the web

<a href="https://reader.elsevier.com/reader/sd/pii/S2095311919628054?token=B5938742FC35E57DBB7CEEC23643F5423AFA5A582EDC9400D631AC5C299666DD9B9C101756DF3A1BB9D0510275B6B5A4" target="_blank" >https://reader.elsevier.com/reader/sd/pii/S2095311919628054?token=B5938742FC35E57DBB7CEEC23643F5423AFA5A582EDC9400D631AC5C299666DD9B9C101756DF3A1BB9D0510275B6B5A4</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1016/S2095-3119(19)62805-4" target="_blank" >10.1016/S2095-3119(19)62805-4</a>

Result language

angličtina

Original language name

Virome identification in wheat in the Czech Republic using small RNA deep sequencing

Original language description

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 similar to 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 (similar to 7.7E+06 reads) were found than 24-nt (similar to 6.20E+06 reads) or 22-nt (similar to 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.

Czech name

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Czech description

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Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

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OECD FORD branch

40106 - Agronomy, plant breeding and plant protection; (Agricultural biotechnology to be 4.4)

Project

<a href="/en/project/TF02000056" target="_blank" >TF02000056: Next generation sequencing (NGS) for the broad-spectrum diagnostics of plant viruses and for the study of virus-host interactions</a><br>

Continuities

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year

2020

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

Journal of Integrative Agriculture

ISSN

2095-3119

e-ISSN

—

Volume of the periodical

19

Issue of the periodical within the volume

7

Country of publishing house

GB - UNITED KINGDOM

Number of pages

9

Pages from-to

1825-1833

UT code for WoS article

000538956900014

EID of the result in the Scopus database

2-s2.0-85085609968