文献类型：期刊文献

英文题名：Identification of novel and conserved microRNAs in Panax notoginseng roots by high-throughput sequencing

作者：Wei, Rongchang[1,2,3] Qiu, Deyou[6] Wilson, Iain W.[7] Zhao, Huan[1,2] Lu, Shanfa[1,2] Miao, Jianhua[3] Feng, Shixin[3] Bai, Longhua[3] Wu, Qinghua[3] Tu, Dongping[1,2] Ma, Xiaojun[1,2] Tang, Qi[3,4,5]

第一作者：Wei, Rongchang

通信作者：Ma, XJ[1]

机构：[1]Chinese Acad Med Sci, Inst Med Plant Dev, Beijing 100193, Peoples R China;[2]Peking Union Med Coll, Beijing 100193, Peoples R China;[3]Guangxi Bot Garden Med Plants, Nanning 530023, Peoples R China;[4]Hunan Agr Univ, Hunan Prov Key Lab Crop Germplasm Innovat & Utili, Changsha 410128, Hunan, Peoples R China;[5]Hunan Agr Univ, Natl Chinese Med Herbs Hunan Technol Ctr, Changsha 410128, Hunan, Peoples R China;[6]Chinese Acad Forestry, Res Inst Forestry, Dept Mol Biol, Beijing 100091, Peoples R China;[7]CSIRO Agr, Canberra, ACT 2001, Australia

年份：2015

卷号：16

期号：1

外文期刊名：BMC GENOMICS

收录：;WOS:【SCI-EXPANDED(收录号:WOS:000363102300003)】；

基金：This research was supported by grants of the Guangxi Natural Science Foundation Program of China (No. 2013GXNSFAA019207 and 2014GXNSFAA118254), the Program of Guangxi Scientific Research and Technology Development (No. Guikezhong 1355001-1), Program for Innovative Research Team in IMPLAD (IT1306) and the Youth Foundation of Guangxi Botanical Garden of Medicinal Plants (No. Guiyaoji 201106).

语种：英文

外文关键词：Panax notoginseng; MicroRNA; High-throughput sequencing; qRT-PCR; Saponins

摘要：Background: MicroRNAs (miRNAs) are small, non-coding RNAs that are important regulators of gene expression, and play major roles in plant development and their response to the environment. Root extracts from Panax notoginseng contain triterpene saponins as their principal bioactive constituent, and demonstrate medicinal properties. To investigate the novel and conserved miRNAs in P. notoginseng, three small RNA libraries constructed from 1-, 2-, and 3-year-old roots in which root saponin levels vary underwent high-throughput sequencing. Methods: P. notoginseng roots, purified from 1-, 2-, and 3-year-old roots, were extracted for RNA, respectively. Three small libraries were constructed and subjected to next generation sequencing. Results: Sequencing of the three libraries generated 67,217,124 clean reads from P. notoginseng roots. A total of 316 conserved miRNAs (belonging to 67 miRNA families and one unclassified family) and 52 novel miRNAs were identified. MIR156 and MIR166 were the largest miRNA families, while miR156i and miR156g showed the highest abundance of miRNA species. Potential miRNA target genes were predicted and annotated using Cluster of Orthologous Groups, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes. Comparing these miRNAs between root samples revealed 33 that were differentially expressed between 2- and 1-year-old roots (8 increased, 25 decreased), 27 differentially expressed between 3- and 1-year-old roots (7 increased, 20 decreased), and 29 differentially expressed between 3- and 2-year-old roots (8 increased, 21 decreased). Two significantly differentially expressed miRNAs and four miRNAs predicted to target genes involved in the terpenoid backbone biosynthesis pathway were selected and validated by quantitative reverse transcription PCR. Furthermore, the expression patterns of these six miRNAs were analyzed in P. notoginseng roots, stems, and leaves at different developmental stages. Conclusions: This study identified a large number of P. notoginseng miRNAs and their target genes, functional annotations, and gene expression patterns. It provides the first known miRNA profiles of the P. notoginseng root development cycle.