Genome-wide identification of microRNAs and phased siRNAs in soybean roots under long-term salt stress
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Genes & Genomics https://doi.org/10.1007/s13258-020-00990-0
RESEARCH ARTICLE
Genome‑wide identification of microRNAs and phased siRNAs in soybean roots under long‑term salt stress Qian Wang1 · Yingxia Yang1 · Guoqing Lu1 · Xianjun Sun2 · Youren Feng3 · Shuangyong Yan4 · Huiyuan Zhang2 · Qiyan Jiang2 · Hui Zhang2 · Zheng Hu2 · Rui Chen1 Received: 4 July 2020 / Accepted: 19 August 2020 © The Genetics Society of Korea 2020
Abstract Background Salinity stress, as the key limiting factor for agricultural productivity, can activate a series of molecular responses and alter gene expression in plants. Endogenous regulatory small RNAs, such as microRNAs (miRNAs) and phased siRNAs (phasiRNAs), play crucial roles during stress adaptation and prevent the injury from environmental circumstances. Objective To identify long-term salt stress responsive miRNAs and phasiRNAs as well as their associated genes and pathways in soybean roots. Methods Small RNA and degradome sequencing strategies were applied to genome widely investigate miRNAs and phasiRNAs in soybean roots under control and long-term salt stress conditions. Results In this study, stringent bioinformatic analysis led to the identification of 253 conserved and 38 novel miRNA candidates. Results of expression profiling, target and endogenous target mimics predictions provided valuable clues to their functional roles. Furthermore, 156 genes were identified to be capable of generating 21 nt and 24 nt phasiRNAs, in which 37 candidates were confirmed by degradome data for miRNA-directed cleavage. Approximately 90% of these phasiRNA loci were protein coding genes. And GO enrichment analysis pointed to “signal transduction” and “ADP binding” entries and reflected the functional roles of identified phasiRNA genes. Conclusion Taken together, our findings extended the knowledge of salt responsive miRNAs and phasiRNAs in soybean roots, and provided valuable information for a better understanding of the regulatory events caused by small RNAs underlying plant adaptations to long-term salt stress. Keywords Long-term salt stress · Soybean roots · MicroRNA · Phased siRNA · Endogenous target mimicry
Introduction Endogenous regulatory RNAs play diverse roles during plant development and response to biotic and abiotic stresses. Except for three types of house-keeping RNAs: messenger RNA (mRNA), ribosomal RNA (rRNA) and Qian Wang, Yingxia Yang, Guoqing Lu have equal contributors. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s13258-020-00990-0) contains supplementary material, which is available to authorized users. * Zheng Hu [email protected] * Rui Chen [email protected] Extended author information available on the last page of the article
transfer RNA (tRNA), diverse non-coding RNAs (ncRNAs) have emerged as master regulators and aroused broad attentions in the last decade (Cech and Steitz 2014). According to their molecular size, ncRNAs can be classified into two broad categories: small RNAs and long noncoding RNAs (lncRN
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