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Genes 2017, 8(6), 163;

Using Small RNA-seq Data to Detect siRNA Duplexes Induced by Plant Viruses

College of Life Sciences, Nankai University, Tianjin 300071, China
State Key Laboratory of Veterinary Etiological Biology and Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou 730046, Gansu, China
U.S. Department of Agriculture-Agricultural Research Service, U.S. Vegetable Laboratory, Charleston, SC 29414, USA
School of Mathematical Sciences, Nankai University, Tianjin 300071, China
International Potato Center (CIP), Apartado 1558, Lima 12, Peru
Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
These authors contributed equally to this work.
Authors to whom correspondence should be addressed.
Academic Editor: Bin Yu
Received: 20 April 2017 / Revised: 26 May 2017 / Accepted: 12 June 2017 / Published: 16 June 2017
(This article belongs to the Section Plant Genetics and Genomics)
Full-Text   |   PDF [1398 KB, uploaded 16 June 2017]   |  


Small interfering RNA (siRNA) duplexes are short (usually 21 to 24 bp) double-stranded RNAs (dsRNAs) with several overhanging nucleotides at both 5′- and 3′-ends. It has been found that siRNA duplexes bind the RNA-induced silencing complex (RISC) and cleave the sense strands with endonucleases. In this study, for the first time, we detected siRNA duplexes induced by plant viruses on a large scale using next-generation sequencing (NGS) data. In addition, we used the detected 21 nucleotide (nt) siRNA duplexes with 2 nt overhangs to construct a dataset for future data mining. The analytical results of the features in the detected siRNA duplexes were consistent with those from previous studies. The investigation of siRNA duplexes is useful for a better understanding of the RNA interference (RNAi) mechanism. It can also help to improve the virus detection based on the small RNA sequencing (sRNA-seq) technologies and to rationally design siRNAs for RNAi experiments. View Full-Text
Keywords: siRNA duplex; RNAi; plant virus; small RNA-seq; virus detection siRNA duplex; RNAi; plant virus; small RNA-seq; virus detection

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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).

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Niu, X.; Sun, Y.; Chen, Z.; Li, R.; Padmanabhan, C.; Ruan, J.; Kreuze, J.F.; Ling, K.; Fei, Z.; Gao, S. Using Small RNA-seq Data to Detect siRNA Duplexes Induced by Plant Viruses. Genes 2017, 8, 163.

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