Identification and differential regulation of microRNAs in response to methyl jasmonate treatment in Lycoris aurea by deep sequencing

Sheng Xu,Yumei Jiang,Yikui Li,Ren Wang,Xiaodan Li,Yilong Jiang,Zhengzhi Zhang,Ning Wang,Bing Xia

doi:10.1186/s12864-016-2645-y

Abstract

Background Lycoris aurea is a medicine-valuable and ornamental herb widely distributed in China. Former studied have showed that methyl jasmonate (MJ) treatment could increase the content of glanthamine-a worldwide medicine for symptomatic treatment of Alzheimer’s disease in genus Lycoris plants. To explore the possible role of miRNAs in the regulation of jasmonic acid signaling pathway and uncover their potential correlations, we investigated the expression profiles of small RNAs (sRNAs) and their targets in Lycoris aurea, with MJ treatment by using next-generation deep sequencing.ResultsA total of 365 miRNAs were identified, comprising 342 known miRNAs (representing 60 miRNA families) and 23 novel miRNAs. Among them, 143 known and 11 novel miRNAs were expressed differently under MJ treatment. Quantitative real-time PCR of eight selected miRNAs validated the expression pattern of these loci in response to MJ treatment. In addition, degradome sequencing analysis showed that 32 target genes were validated to be targeted by the 49 miRNAs, respectively. Gene function and pathway analyses showed that these targets such as auxin response factors (ARFs), squamosa promoter-binding like (SPL) proteins, basic helix-loop-helix (bHLH) proteins, and ubiquitin-conjugating enzyme E2 are involved in different plant processes, indicating miRNAs mediated regulation might play important roles in L. aurea response to MJ treatment. Furthermore, several L. aurea miRNAs associated with their target genes that might be involved in Amaryllidaceae alkloids biosynthehsis were also analyzed.ConclusionsA number of miRNAs with diverse expression patterns, and complex relationships between expression of miRNAs and targets were identified. This study represents the first transcriptome-based analysis of miRNAs in Lycoris and will contribute to understanding the potential roles of miRNAs involved in regulation of MJ response.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2645-y) contains supplementary material, which is available to authorized users.

Highlights

Lycoris aurea is a medicine-valuable and ornamental herb widely distributed in China
Our results indicate a complex and diverse small RNA population exists in L. aurea, thereby providing a meaningful database to microRNA study in Lycoris species
After removing poly (A) tails, short and low-quality tags, and adaptor contamination, 26,809,842 (CK) and 25,874,478 (MJ100) clean reads with a total of 2,412,885,780 and 2,328,703,020 nucleotides were obtained respectively, for the two pools

Summary

Introduction

Lycoris aurea is a medicine-valuable and ornamental herb widely distributed in China. Lycoris aurea (L’ Hér) Herb is a popular ornamental species of Amaryllidaceae plant widely distributed in China. It belongs to the genus Lycoris and the bulbs are very durable, tolerating the extremes of drought and waterlogging, as well as poor soil conditions. Amaryllidaceae alkaloids are regarded as derivatives of the common precursor 4′-O-methylnorbelladine via intramolecular oxidative phenol-coupling [11, 12]. There are three different groups of Amaryllidaceae alkaloids that are biosynthesized by three modes of intramolecular oxidative C–C phenol coupling (para-ortho’, para-para’ and ortho-para’). In some plants of Amaryllidaceae family, the improved production of Amaryllidaceae alkaloids was observed when treated with methyl jasmonate (MJ), or other elicitor like ethylene [13,14,15,16,17]

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