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 th...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 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 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.展开更多
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).
文摘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 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 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.
