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

Xiaoran Niu^{1

2}, Yu Sun³, Ze Chen⁴, Rugang Li⁵, Chellappan Padmanabhan⁶, Jishou Ruan⁷, Jan F Kreuze⁸, KaiShu Ling⁹, ZhangJun Fei¹⁰, Shan Gao¹¹

Affiliations

¹ College of Life Sciences, Nankai University, Tianjin 300071, China. niuxiaoran@mail.nankai.edu.cn.
² 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. niuxiaoran@mail.nankai.edu.cn.
³ College of Life Sciences, Nankai University, Tianjin 300071, China. sun_yu@mail.nankai.edu.cn.
⁴ 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. chenze@caas.cn.
⁵ U.S. Department of Agriculture-Agricultural Research Service, U.S. Vegetable Laboratory, Charleston, SC 29414, USA. rugangli@yahoo.com.
⁶ U.S. Department of Agriculture-Agricultural Research Service, U.S. Vegetable Laboratory, Charleston, SC 29414, USA. Chellappan.padmanabhan@ars.usda.gov.
⁷ School of Mathematical Sciences, Nankai University, Tianjin 300071, China. jsruan@nankai.edu.cn.
⁸ International Potato Center (CIP), Apartado 1558, Lima 12, Peru. j.kreuze@cgiar.org.
⁹ U.S. Department of Agriculture-Agricultural Research Service, U.S. Vegetable Laboratory, Charleston, SC 29414, USA. Kai.ling@ars.usda.gov.
¹⁰ Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA. zf25@cornell.edu.
¹¹ College of Life Sciences, Nankai University, Tianjin 300071, China. gao_shan@mail.nankai.edu.cn.

PMID: 28621718
PMCID: PMC5485527
DOI: 10.3390/genes8060163

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

Xiaoran Niu et al. Genes (Basel). 2017.

. 2017 Jun 16;8(6):163.

doi: 10.3390/genes8060163.

Authors

Xiaoran Niu^{1

2}, Yu Sun³, Ze Chen⁴, Rugang Li⁵, Chellappan Padmanabhan⁶, Jishou Ruan⁷, Jan F Kreuze⁸, KaiShu Ling⁹, ZhangJun Fei¹⁰, Shan Gao¹¹

Affiliations

¹ College of Life Sciences, Nankai University, Tianjin 300071, China. niuxiaoran@mail.nankai.edu.cn.
² 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. niuxiaoran@mail.nankai.edu.cn.
³ College of Life Sciences, Nankai University, Tianjin 300071, China. sun_yu@mail.nankai.edu.cn.
⁴ 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. chenze@caas.cn.
⁵ U.S. Department of Agriculture-Agricultural Research Service, U.S. Vegetable Laboratory, Charleston, SC 29414, USA. rugangli@yahoo.com.
⁶ U.S. Department of Agriculture-Agricultural Research Service, U.S. Vegetable Laboratory, Charleston, SC 29414, USA. Chellappan.padmanabhan@ars.usda.gov.
⁷ School of Mathematical Sciences, Nankai University, Tianjin 300071, China. jsruan@nankai.edu.cn.
⁸ International Potato Center (CIP), Apartado 1558, Lima 12, Peru. j.kreuze@cgiar.org.
⁹ U.S. Department of Agriculture-Agricultural Research Service, U.S. Vegetable Laboratory, Charleston, SC 29414, USA. Kai.ling@ars.usda.gov.
¹⁰ Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA. zf25@cornell.edu.
¹¹ College of Life Sciences, Nankai University, Tianjin 300071, China. gao_shan@mail.nankai.edu.cn.

PMID: 28621718
PMCID: PMC5485527
DOI: 10.3390/genes8060163

Abstract

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.

Keywords: RNAi; plant virus; siRNA duplex; small RNA-seq; virus detection.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

**Figure 1**
Read-count distribution of small interfering RNA (siRNA) duplexes. (A) The read count of siRNA duplexes varies with the duplex length and the overhang length, using KP772568 as an example. (B) The median of read counts varies with the internal GC content using 21 nt siRNA duplexes with 2 nt overhangs from seven viral sequences.

**Figure 2**
Distribution of viral reads along the reference genomes. The genome coverages of seven viral sequences calculated using aligned 21 nt siRNA duplexes with 2 nt overhangs are close to the genome coverages calculated using all aligned reads, using KP772568 as an example. The results of all 14 sequences can be seen in Supplementary File 1.

**Figure 3**
Positive and negative-strands of siRNA duplexes. (A) This pattern shows symmetric read-count distribution of positive and negative strands in 21 nt siRNA duplexes with 2 nt overhangs, using KP223323 as an example. (B) This pattern shows read-count distribution biased to positive strands in 21 nt siRNA duplexes with 2 nt overhangs, using KP772568 as an example. The results of all seven sequences can be seen in Supplementary File 3.

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

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

Authors

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Conflict of interest statement

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