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

作     者：Khushwant SINGH Jana JAROSOVA Jan FOUSEK CHEN Huan Jiban Kumar KUNDU Khushwant SINGH;Jana JARRO?OV;Jan FOUSEK;CHEEN Huan;Jiban Kumar KUNDU

作者机构：Plant Virus and Vector Interactions GroupDivision of Crop Protection and Plant HeatthCrop Research InstitutePrague 16106Czech Republic Zhejiang Tianke High-Technology Development Co.Ltd.Hangzhou 310012P.R.China 

出 版 物：《Journal of Integrative Agriculture》 (农业科学学报（英文版）)

年 卷 期：2020年第19卷第7期

页      面：1825-1833页

核心收录：

学科分类：09[农学] 0904[农学-植物保护] 090401[农学-植物病理学] 090402[农学-农业昆虫与害虫防治] 

基　　金：We thank Ms.Michaela Brozenska(Plant Virus and Vector Interactions Group Division of Crop Protection and Plant Health Crop Research Institute Czech Republic)for her excellent technical assistance.We also thank Dr.Beth E.Hazen(Willows End Scientific Editing and Writing Cortland NY USA)for editing the English of the manuscript.This work was supported by a grant from the Technology Agency of the Czech Republic(TF02000056) 

主　　题：NGS sRNA BYDVs CYDV WSMV WYDV WDV 

摘      要：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 *** 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 *** sRNA sequencing of these samples yielded more than^60 million single-end 50-bp reads with high confidence for nine field samples of ***,16.5%of reads were virus-specific and 83.5%were mapped to the *** 21-nt reads(-7.7E+06 reads)were found than 24-nt(~6.20E+06 reads)or 22-nt(-4.30E+06 reads)*** novo assembly of the high-quality contigs revealed the presence of three earlier repoted viruses in the Czech Republic:BYDVs(31.48%),WSMV(24.23%)and WDV(2666%).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 ***,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.