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ARS Home » Southeast Area » Charleston, South Carolina » Vegetable Research » Research » Publications at this Location » Publication #342550

Research Project: Biological, Genetic and Genomic Based Disease Management for Vegetable Crops

Location: Vegetable Research

Title: Using small RNA deep sequencing data to detect siRNA duplexes induced by plant viruses

item LIU, CHANG - Nankai University
item SUN, YU - Nankai University
item Li, Rugang
item Padmanabhan, Chellappan
item RUAN, JISHOU - Nankai University
item KREUZE, JAN - International Potato Center
item Ling, Kai-Shu
item FEI, ZHANGJUN - Boyce Thompson Institute
item GAO, SHAN - Nankai University

Submitted to: Genes
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/12/2017
Publication Date: 6/16/2017
Citation: Liu, C., Sun, Y., Li, R., Padmanabhan, C., Ruan, J., Kreuze, J.F., Ling, K., Fei, Z., Gao, S. 2017. Using small RNA deep sequencing data to detect siRNA duplexes induced by plant viruses. Genes 2017, 8, 163; doi:10.3390/genes8060163.

Interpretive Summary: The strategy to allow for effective management of viral disease infections on crop plants is dependent on timely and accurate detection of the causal agent(s). Gene silencing is one of the major plant defense systems that operates against virus infection. Through this gene silencing process, numerous small interfering ribonucleic acids (siRNAs) of a viral origin are produced. The abundant siRNAs that accumulate in an infected plant during the gene silencing process can be captured through small ribonucleic acids sequencing (sRNA-seq), which has been recently used for virus detection. However, it is still unknown as to what are the structural features of these siRNA, which contain imperfect base-pairing of the two RNA strands. In this study, using sRNA-seq datasets from 14 complete virus genomes, ARS scientists along with international collaborators, for the first time, identified two nucleotides overhanging at the 3’ termini of these virus-derived siRNAs. The identification and analysis of siRNA structural features will provide useful information to help better understand the RNA interference mechanism in plants against virus infection, thus helping to facilitate breeding for viral disease resistance.

Technical Abstract: Small interfering RNA (siRNA) duplexes are produced in plants during virus infection, which are short (usually 21 to 24-base pair) double-stranded RNAs (dsRNAs) with several overhanging nucleotides on the 5' end and 3' end. The investigation of the siRNA duplexes is useful to better understand the RNA interference (RNAi) mechanism and rationally design siRNAs for RNAi experiments. It can also help improve the virus detection based on the small RNA sequencing (sRNA-seq) technologies. In this study, this is the first time to detect siRNA duplexes induced by plant viruses on a large scale using the next generation sequencing (NGS) data with 14 complete viral genomes as references. In addition, we used the detected 21-nt siRNA duplexes with 2-nt overhangs from seven nucleic acid sequences of four viruses to build a dataset for future data mining. The further analysis of the features in detected siRNA duplexes are consistent with the previous studies. But the results based on the NGS data could provide comprehensive information and insight for further studies.