Abstract
It has been known that many microRNAs (miRNAs) are involved in the regulation for the plant development and defense mechanism by regulating the expression of the target gene. Several previous studies has demonstrated functional roles of miRNAs in antiviral defense mechanisms. In this study, we employed high-throughput sequencing technology to identify rice miRNAs upon rice stripe virus (RSV) infection at three different time points. Six libraries from mock and RSV-infected samples were subjected for small RNA sequencing. Bioinformatic analyses revealed 374 known miRNAs and 19 novel miRNAs. Expression of most identified miRNAs was not dramatically changed at 3 days post infection (dpi) and 7 dpi by RSV infection. However, many numbers of miRNAs were up-regulated in mock and RSV-infected samples at 15 dpi by RSV infection. Moreover, expression profiles of identified miRNAs revealed that only few numbers of miRNAs were strongly regulated by RSV infection. In addition, 15 resistance genes were targets of six miRNAs suggesting that those identified miRNAs and 15 NBS-LRR resistance genes might be involved in RSV infection. Taken together, our results provide novel insight into the dynamic expression profiles of rice miRNAs upon RSV infection and clues for the understanding of the regulatory roles of miRNAs via time-course.
Highlights
Rice is one of economically important crops in the world and provides main food for more than half the world’s population
To identify known rice miRNAs, the mapped reads were used to align on known rice miRNA sequences by mirDeep2
We identified diverse known small RNA such as transfer RNA, ribosomal RNA, small nuclear RNA, small nucleolar RNAs, conserved miRNA, novel miRNA, and virus-derived small interfering RNAs
Summary
Rice is one of economically important crops in the world and provides main food for more than half the world’s population. Rice is a model research plant for monocotyledonous plants. The rice genome, which has relatively small genome of known cereal crops, has been sequenced. The size of rice genome is about 450 megabases containing more than 50,000 genes [1, 2].
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