title: Identification and differential regulation of microRNAs in response to methyl jasmonate treatment in Lycoris aurea by deep sequencing.
abstract: 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.
  
  
  
  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.
  
  
  
  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.
authors.affiliation: Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China.
authors.forename: Sheng
authors.initials: S
authors.lastname: Xu
authors.affiliation: Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China.
authors.forename: Yumei
authors.initials: Y
authors.lastname: Jiang
authors.affiliation: National Center for Soybean Improvement/Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Ning
authors.initials: N
authors.lastname: Wang
authors.affiliation: Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China.
authors.forename: Bing
authors.initials: B
authors.lastname: Xia
authors.affiliation: Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China.
authors.forename: Yilong
authors.initials: Y
authors.lastname: Jiang
authors.affiliation: Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China.
authors.forename: Xiaodan
authors.initials: X
authors.lastname: Li
authors.affiliation: National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA.
authors.forename: Zhengzhi
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China.
authors.forename: Yikui
authors.initials: Y
authors.lastname: Li
authors.affiliation: Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China. jswangren@aliyun.com.
authors.forename: Ren
authors.initials: R
authors.lastname: Wang
mesh_terms: D000085:Acetates / Q000494:pharmacology*; D016000:Cluster Analysis; D019295:Computational Biology; D003517:Cyclopentanes / Q000494:pharmacology*; D019143:Evolution, Molecular; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000187:drug effects*; D059014:High-Throughput Nucleotide Sequencing; D031426:Lycoris / Q000187:drug effects* / Q000235:genetics*; D035683:MicroRNAs / Q000235:genetics*; D054883:Oxylipins / Q000494:pharmacology*; D010937:Plant Growth Regulators / Q000494:pharmacology*; D018749:RNA, Plant; D015203:Reproducibility of Results; D059467:Transcriptome
chemical_list: D000085:Acetates; D003517:Cyclopentanes; D035683:MicroRNAs; D054883:Oxylipins; D010937:Plant Growth Regulators; D018749:RNA, Plant; C072239:methyl jasmonate
keywords: Amaryllidaceae alkaloids; Deep sequencing; Degradome; Lycoris aurea; Methyl jasmonate; MicroRNA