Characterization of small interfering RNAs derived from pepper mild mottle virus in infected pepper plants by high-throughput sequencing

Yubing Jiao; Xiuxiang Zhao; Kaiqiang Hao; Xinran Gao; Dan Xing; Zhiping Wang; Mengnan An; Zihao Xia; Yuanhua Wu

doi:10.1016/j.virusres.2021.198607

Characterization of small interfering RNAs derived from pepper mild mottle virus in infected pepper plants by high-throughput sequencing

Virus Res. 2022 Jan 2:307:198607. doi: 10.1016/j.virusres.2021.198607. Epub 2021 Oct 22.

Authors

Yubing Jiao¹, Xiuxiang Zhao², Kaiqiang Hao², Xinran Gao², Dan Xing³, Zhiping Wang², Mengnan An², Zihao Xia⁴, Yuanhua Wu⁵

Affiliations

¹ Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China; Key Laboratory of Tobacco Pest Monitoring Controlling & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
² Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China.
³ Institute of Pepper, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China.
⁴ Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China. Electronic address: zihao8337@syau.edu.cn.
⁵ Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China. Electronic address: wuyh09@syau.edu.cn.

PMID: 34688783
DOI: 10.1016/j.virusres.2021.198607

Abstract

Pepper mild mottle virus (PMMoV) infects pepper plants and induces severe yield losses in China. However, the molecular interaction between PMMoV and pepper plants is largely unknown. RNA silencing is a eukaryotically conserved mechanism against viruses mediated by virus-derived small interfering RNAs (vsiRNAs) in plants. In this study, the profiles of vsiRNAs from PMMoV in infected pepper plants were obtained by high-throughput sequencing. The results showed that vsiRNAs were predominantly 21 and 22 nucleotides (nts) in length, and had a U bias at the 5'-terminal. The single-nucleotide resolution maps revealed that vsiRNAs were heterogeneously distributed throughout PMMoV genomic RNAs and hotspots of sense and antisense strands were mainly located in the RdRp and CP coding regions. The host transcripts targeted by vsiRNAs were predicted and they are mainly involved in physiological pathways related to stress response, cell regulation, and metabolism process. In addition, PMMoV infection induced significant up-regulation of CaAGO1a/1b/2, CaDCL2 and CaRDR1 gene transcripts in pepper plants, which are important components involved in antiviral RNA silencing pathway. Taken together, our results suggest the possible roles of vsiRNAs in PMMoV-pepper interactions.

Keywords: High-throughput sequencing; Pepper mild mottle virus; RNA silencing; Virus-derived small interfering RNA.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

High-Throughput Nucleotide Sequencing
Plant Diseases*
RNA, Small Interfering / genetics
RNA, Small Interfering / metabolism
RNA, Viral* / genetics
RNA, Viral* / metabolism
Tobamovirus

Substances

RNA, Small Interfering
RNA, Viral

Supplementary concepts

Pepper mild mottle virus