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.

对从植物中分离出的小RNA（sRNA）群体进行高通量深度测序技术和生物信息学分析，可以对给定样品进行通用病毒检测和完整的病毒体重建。在目前捷克共和国的病毒感染小麦样品的sRNA深度测序分析中，首先使用ELISA，RT对样品进行了大麦黄矮病毒（BYDVs），小麦条纹花叶病毒（WSMV）和小麦矮病毒（WDV）的测试-PCR和PCR。随后对这些样品进行sRNA测序后，对九个大田小麦样品产生了约6000万个单端50 bp读数，具有很高的置信度。总体而言，有16.5％的读取是病毒特异性的，有83.5％的读取是针对宿主的。发现的21-nt读数（〜7.7E + 06读数）比24-nt（〜6.20E + 06读数）或22-nt（〜4.30E + 06读数）更多。从头开始高质量重叠群的装配体表明，捷克共和国存在三种先前报道的病毒：BYDV（31.48％），WSMV（24.23％）和W​​DV（26.66％）。我们还发现存在谷类黄矮病毒（14.33％；两种CYDV-RPS和CYDV-RPV（黄病毒科/杆状病毒科）和小麦黄矮病毒（WYDV，3.30％；黄病毒科）；系统发育分析表明CYDV和WYDV分组此外，在黄色矮人病毒（BYDV，CYDV和WYDV）组中发现了几个重组断裂点，使用RNA深度测序，我们确认了三种已知病毒（BYDV，WSMV和WDV）的存在。捷克共和国小麦中CYDV和WYDV两种物种的第一个记录。