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

Kód výsledku v 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>

Výsledek na webu

<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>

Jazyk výsledku

angličtina

Název v původním jazyce

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

Popis výsledku v původním jazyce

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.

Název v anglickém jazyce

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

Popis výsledku anglicky

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.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

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

Projekt

<a href="/cs/project/TF02000056" target="_blank" >TF02000056: NGS pro širokospektrální diagnostiku virových chorob rostlin a pro studium interakcí virus-hostitel</a><br>

Návaznosti

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

Rok uplatnění

2020

Kód důvěrnosti údajů

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

Název periodika

Journal of Integrative Agriculture

ISSN

2095-3119

e-ISSN

—

Svazek periodika

19

Číslo periodika v rámci svazku

7

Stát vydavatele periodika

GB - Spojené království Velké Británie a Severního Irska

Počet stran výsledku

9

Strana od-do

1825-1833

Kód UT WoS článku

000538956900014

EID výsledku v databázi Scopus

2-s2.0-85085609968