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通过深度测序鉴定黄花石蒜中响应茉莉酸甲酯处理的 microRNA 及其差异调控

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

作者信息

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

机构信息

Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China.

National Center for Soybean Improvement/Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Nanjing Agricultural University, Nanjing, 210095, China.

出版信息

BMC Genomics. 2016 Oct 10;17(1):789. doi: 10.1186/s12864-016-2645-y.

DOI:10.1186/s12864-016-2645-y
PMID:27724902
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC5057397/
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.

RESULTS

A 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.

CONCLUSIONS

A 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.

摘要

背景

忽地笑是一种具有药用价值的观赏植物，在中国广泛分布。先前的研究表明，茉莉酸甲酯（MJ）处理可增加石蒜属植物中加兰他敏（一种用于阿尔茨海默病对症治疗的全球药物）的含量。为了探究miRNA在茉莉酸信号通路调控中的可能作用，并揭示它们之间的潜在关联，我们利用新一代深度测序技术，研究了经MJ处理的忽地笑中小RNA（sRNA）及其靶标的表达谱。

结果

共鉴定出365个miRNA，包括342个已知miRNA（代表60个miRNA家族）和23个新miRNA。其中，143个已知miRNA和11个新miRNA在MJ处理下表达存在差异。对8个选定miRNA进行的定量实时PCR验证了这些位点在响应MJ处理时的表达模式。此外，降解组测序分析表明，49个miRNA分别验证了32个靶基因。基因功能和通路分析表明，这些靶标如生长素响应因子（ARF）、类鳞状启动子结合蛋白（SPL）、碱性螺旋-环-螺旋（bHLH）蛋白和泛素结合酶E2参与不同的植物过程，表明miRNA介导的调控可能在忽地笑对MJ处理的响应中发挥重要作用。此外，还分析了一些可能参与石蒜科生物碱生物合成的忽地笑miRNA及其靶基因。

结论

鉴定出了许多具有不同表达模式的miRNA，以及miRNA表达与靶标之间的复杂关系。本研究是基于转录组对石蒜属植物miRNA的首次分析，将有助于理解miRNA在调控MJ响应中的潜在作用。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9006/5057397/3fb23a486fa5/12864_2016_2645_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9006/5057397/60c820be2805/12864_2016_2645_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9006/5057397/971e01b9ee45/12864_2016_2645_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9006/5057397/c932d4be607b/12864_2016_2645_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9006/5057397/9f328dc73ed7/12864_2016_2645_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9006/5057397/84a551bc89ed/12864_2016_2645_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9006/5057397/5a097bbe66ce/12864_2016_2645_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9006/5057397/3fb23a486fa5/12864_2016_2645_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9006/5057397/60c820be2805/12864_2016_2645_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9006/5057397/971e01b9ee45/12864_2016_2645_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9006/5057397/c932d4be607b/12864_2016_2645_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9006/5057397/9f328dc73ed7/12864_2016_2645_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9006/5057397/84a551bc89ed/12864_2016_2645_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9006/5057397/5a097bbe66ce/12864_2016_2645_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9006/5057397/3fb23a486fa5/12864_2016_2645_Fig7_HTML.jpg

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